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	255923	255924	+	IGR	INS	-	TC	TC			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:255923_255924insTC								OR4F5 (185915 upstream) : LOC100132287 (66113 downstream)																																			---	---	---	---
LOC643837	643837	broad.mit.edu	37	1	788351	788351	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:788351delT	uc009vjn.1	+						LOC643837_uc001abp.1_Intron|LOC643837_uc001abq.1_Intron|LOC643837_uc009vjo.1_Intron|LOC643837_uc001abr.1_Intron					Homo sapiens cDNA: FLJ23220 fis, clone ADSU01957.												0																		---	---	---	---
PLEKHN1	84069	broad.mit.edu	37	1	907632	907632	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:907632delC	uc001ace.2	+						PLEKHN1_uc001acd.2_Intron|PLEKHN1_uc001acf.2_Intron	NM_032129	NP_115505			pleckstrin homology domain containing, family N												0	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;4.31e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.93e-23)|Colorectal(212;0.000159)|COAD - Colon adenocarcinoma(227;0.000193)|BRCA - Breast invasive adenocarcinoma(365;0.00095)|Kidney(185;0.0023)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0342)|Lung(427;0.199)														---	---	---	---
KIAA1751	85452	broad.mit.edu	37	1	1894972	1894973	+	Intron	INS	-	A	A	rs145936947	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1894972_1894973insA	uc001aim.1	-						KIAA1751_uc009vkz.1_Intron	NM_001080484	NP_001073953			hypothetical protein LOC85452											pancreas(1)	1	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;6.04e-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)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)		Epithelial(90;8.79e-39)|OV - Ovarian serous cystadenocarcinoma(86;9.61e-25)|GBM - Glioblastoma multiforme(42;1.2e-07)|Colorectal(212;4.84e-05)|COAD - Colon adenocarcinoma(227;0.000214)|Kidney(185;0.00254)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.037)|Lung(427;0.205)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	1942710	1942711	+	IGR	INS	-	TT	TT	rs111618224		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1942710_1942711insTT								KIAA1751 (7434 upstream) : GABRD (8057 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	2367482	2367493	+	IGR	DEL	TTCCTCTCTCCT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2367482_2367493delTTCCTCTCTCCT								PEX10 (23472 upstream) : PLCH2 (40261 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	2629838	2629838	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2629838delC								MMEL1 (65357 upstream) : ACTRT2 (308208 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	2736276	2736277	+	IGR	DEL	CA	-	-	rs34620269		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2736276_2736277delCA								MMEL1 (171795 upstream) : ACTRT2 (201769 downstream)																																			---	---	---	---
PRDM16	63976	broad.mit.edu	37	1	3165066	3165066	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3165066delA	uc001akf.2	+						PRDM16_uc001akc.2_Intron|PRDM16_uc001akd.2_Intron|PRDM16_uc001ake.2_Intron|PRDM16_uc009vlh.2_Intron	NM_022114	NP_071397			PR domain containing 16 isoform 1						brown fat cell differentiation|negative regulation of granulocyte differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|regulation of cellular respiration|transcription, DNA-dependent	transcriptional repressor complex	protein binding|sequence-specific DNA binding|transcription coactivator activity|zinc ion binding			lung(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7	all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111)	all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134)		Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137)				T	EVI1	MDS|AML								---	---	---	---
Unknown	0	broad.mit.edu	37	1	4198331	4198331	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:4198331delC								LOC100133612 (364454 upstream) : LOC284661 (273780 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	4928586	4928586	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:4928586delT								AJAP1 (84736 upstream) : NPHP4 (994284 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	5539178	5539180	+	IGR	DEL	TGC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5539178_5539180delTGC								AJAP1 (695328 upstream) : NPHP4 (383690 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	5797098	5797101	+	IGR	DEL	GATG	-	-	rs112300365		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5797098_5797101delGATG								AJAP1 (953248 upstream) : NPHP4 (125769 downstream)																																			---	---	---	---
CHD5	26038	broad.mit.edu	37	1	6197142	6197144	+	Intron	DEL	GGA	-	-	rs71568642		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6197142_6197144delGGA	uc001amb.1	-						CHD5_uc001ama.1_Intron|CHD5_uc001amc.1_Intron|CHD5_uc009vlx.1_5'Flank	NM_015557	NP_056372			chromodomain helicase DNA binding protein 5						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)														---	---	---	---
DNAJC11	55735	broad.mit.edu	37	1	6697869	6697869	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6697869delA	uc001aof.2	-						DNAJC11_uc010nzt.1_Intron|DNAJC11_uc001aog.2_Intron|DNAJC11_uc010nzu.1_Intron	NM_018198	NP_060668			DnaJ (Hsp40) homolog, subfamily C, member 11						protein folding		heat shock protein binding|unfolded protein binding			ovary(1)|skin(1)	2	Ovarian(185;0.0265)|all_lung(157;0.154)	all_cancers(23;1.97e-27)|all_epithelial(116;1.76e-17)|all_lung(118;2.27e-05)|Lung NSC(185;9.97e-05)|Renal(390;0.00188)|Breast(487;0.00289)|Colorectal(325;0.00342)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.156)		Colorectal(212;2.34e-07)|COAD - Colon adenocarcinoma(227;2.05e-05)|Kidney(185;7.67e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000639)|KIRC - Kidney renal clear cell carcinoma(229;0.00128)|STAD - Stomach adenocarcinoma(132;0.00179)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
DNAJC11	55735	broad.mit.edu	37	1	6703939	6703939	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6703939delT	uc001aof.2	-						DNAJC11_uc010nzt.1_Intron|DNAJC11_uc001aog.2_Intron|DNAJC11_uc010nzu.1_Intron	NM_018198	NP_060668			DnaJ (Hsp40) homolog, subfamily C, member 11						protein folding		heat shock protein binding|unfolded protein binding			ovary(1)|skin(1)	2	Ovarian(185;0.0265)|all_lung(157;0.154)	all_cancers(23;1.97e-27)|all_epithelial(116;1.76e-17)|all_lung(118;2.27e-05)|Lung NSC(185;9.97e-05)|Renal(390;0.00188)|Breast(487;0.00289)|Colorectal(325;0.00342)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.156)		Colorectal(212;2.34e-07)|COAD - Colon adenocarcinoma(227;2.05e-05)|Kidney(185;7.67e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000639)|KIRC - Kidney renal clear cell carcinoma(229;0.00128)|STAD - Stomach adenocarcinoma(132;0.00179)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
CAMTA1	23261	broad.mit.edu	37	1	6958959	6958960	+	Intron	INS	-	T	T	rs148785498	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6958959_6958960insT	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	7403822	7403822	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7403822delT	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	7540316	7540317	+	Intron	INS	-	GTGTGA	GTGTGA	rs139720755	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7540316_7540317insGTGTGA	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)														---	---	---	---
UTS2	10911	broad.mit.edu	37	1	7931636	7931636	+	Intron	DEL	T	-	-	rs36029078		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7931636delT	uc001aoq.2	-							NM_006786	NP_006777			urotensin 2 isoform b preproprotein						muscle contraction|regulation of blood pressure|synaptic transmission	extracellular space	hormone activity				0	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;1.38e-20)|all_lung(118;1.29e-06)|Lung NSC(185;7.5e-06)|Renal(390;0.000147)|Breast(348;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.26e-71)|GBM - Glioblastoma multiforme(8;5.15e-36)|Colorectal(212;1.27e-07)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000386)|KIRC - Kidney renal clear cell carcinoma(229;0.000894)|STAD - Stomach adenocarcinoma(132;0.000951)|READ - Rectum adenocarcinoma(331;0.0642)														---	---	---	---
UTS2	10911	broad.mit.edu	37	1	7948439	7948439	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7948439delC	uc001aoq.2	-							NM_006786	NP_006777			urotensin 2 isoform b preproprotein						muscle contraction|regulation of blood pressure|synaptic transmission	extracellular space	hormone activity				0	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;1.38e-20)|all_lung(118;1.29e-06)|Lung NSC(185;7.5e-06)|Renal(390;0.000147)|Breast(348;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.26e-71)|GBM - Glioblastoma multiforme(8;5.15e-36)|Colorectal(212;1.27e-07)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000386)|KIRC - Kidney renal clear cell carcinoma(229;0.000894)|STAD - Stomach adenocarcinoma(132;0.000951)|READ - Rectum adenocarcinoma(331;0.0642)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	8151608	8151608	+	IGR	DEL	T	-	-	rs80082338		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8151608delT								ERRFI1 (65215 upstream) : SLC45A1 (232782 downstream)																																			---	---	---	---
RERE	473	broad.mit.edu	37	1	8497495	8497495	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8497495delT	uc001ape.2	-						RERE_uc001apf.2_Intron|RERE_uc010nzx.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)														---	---	---	---
RERE	473	broad.mit.edu	37	1	8601148	8601148	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8601148delT	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)														---	---	---	---
RERE	473	broad.mit.edu	37	1	8616316	8616317	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8616316_8616317delAA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	8913656	8913658	+	IGR	DEL	AAA	-	-	rs12752838		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8913656_8913658delAAA								RERE (35957 upstream) : ENO1 (7405 downstream)																																			---	---	---	---
SLC2A5	6518	broad.mit.edu	37	1	9136855	9136856	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9136855_9136856delTT	uc010oab.1	-							NM_003039	NP_003030			solute carrier family 2 (facilitated						carbohydrate metabolic process	integral to membrane|plasma membrane	fructose transmembrane transporter activity|glucose transmembrane transporter activity			pancreas(2)|ovary(1)	3	Ovarian(185;0.112)|all_lung(157;0.185)	all_epithelial(116;1.34e-15)|all_lung(118;9.46e-05)|Lung NSC(185;0.000172)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.00715)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;7.78e-07)|COAD - Colon adenocarcinoma(227;8.83e-05)|Kidney(185;0.000286)|KIRC - Kidney renal clear cell carcinoma(229;0.00103)|STAD - Stomach adenocarcinoma(132;0.0019)|BRCA - Breast invasive adenocarcinoma(304;0.00199)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	9204644	9204644	+	IGR	DEL	A	-	-	rs35629217		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9204644delA								GPR157 (15288 upstream) : MIR34A (7083 downstream)																																			---	---	---	---
KIF1B	23095	broad.mit.edu	37	1	10274034	10274034	+	Intron	DEL	A	-	-	rs112027662		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10274034delA	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)														---	---	---	---
PEX14	5195	broad.mit.edu	37	1	10658936	10658937	+	Intron	INS	-	T	T	rs139615321	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10658936_10658937insT	uc001arn.2	+						PEX14_uc009vmu.1_Intron|PEX14_uc009vmv.2_Intron|PEX14_uc010oam.1_Intron|PEX14_uc010oan.1_Intron|PEX14_uc009vmw.2_Intron	NM_004565	NP_004556			peroxisomal biogenesis factor 14						negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription, DNA-dependent|protein homooligomerization|protein import into peroxisome matrix|transmembrane transport	integral to membrane|nucleus|peroxisomal membrane|protein complex	protein N-terminus binding|transcription corepressor activity			breast(1)	1	Ovarian(185;0.203)	all_lung(284;6.02e-06)|Lung NSC(185;9.62e-06)|Renal(390;0.000147)|Breast(348;0.000932)|Colorectal(325;0.00215)|Hepatocellular(190;0.00913)|Ovarian(437;0.023)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0292)|Colorectal(212;9.13e-08)|COAD - Colon adenocarcinoma(227;2.07e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000482)|Kidney(185;0.00174)|KIRC - Kidney renal clear cell carcinoma(229;0.00457)|STAD - Stomach adenocarcinoma(132;0.0249)|READ - Rectum adenocarcinoma(331;0.0419)														---	---	---	---
C1orf127	148345	broad.mit.edu	37	1	11007833	11007833	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11007833delC	uc010oao.1	-	8	1917	c.1912delG	c.(1912-1914)GCCfs	p.A638fs	C1orf127_uc001arr.1_Frame_Shift_Del_p.A620fs|C1orf127_uc001ars.1_Frame_Shift_Del_p.A612fs	NM_173507	NP_775778	B7ZLG7	B7ZLG7_HUMAN	hypothetical protein LOC148345	638										ovary(1)	1	Ovarian(185;0.249)	Lung NSC(185;0.000226)|all_lung(284;0.000302)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.0139)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0731)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.71e-07)|COAD - Colon adenocarcinoma(227;7.79e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000305)|Kidney(185;0.000785)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|READ - Rectum adenocarcinoma(331;0.0509)														---	---	---	---
MTOR	2475	broad.mit.edu	37	1	11187619	11187619	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11187619delT	uc001asd.2	-						MTOR_uc001asc.2_Intron	NM_004958	NP_004949			FK506 binding protein 12-rapamycin associated						cell growth|cellular response to hypoxia|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|phosphatidylinositol-mediated signaling|protein autophosphorylation|protein catabolic process|response to amino acid stimulus|response to nutrient|T cell costimulation|TOR signaling cascade	endoplasmic reticulum membrane|Golgi membrane|lysosome|mitochondrial outer membrane|phosphatidylinositol 3-kinase complex|PML body|TORC1 complex|TORC2 complex	ATP binding|phosphoprotein binding|protein serine/threonine kinase activity			central_nervous_system(7)|lung(6)|ovary(6)|skin(3)|kidney(3)|large_intestine(2)|breast(2)	29																		---	---	---	---
UBIAD1	29914	broad.mit.edu	37	1	11338925	11338925	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11338925delT	uc001asg.2	+							NM_013319	NP_037451			UbiA prenyltransferase domain containing 1						menaquinone biosynthetic process	endoplasmic reticulum membrane|integral to membrane|mitochondrion|nucleus	prenyltransferase activity				0	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.000818)|all_lung(284;0.00105)|Colorectal(325;0.0062)|Breast(348;0.012)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;1.52e-06)|COAD - Colon adenocarcinoma(227;0.000254)|BRCA - Breast invasive adenocarcinoma(304;0.000299)|Kidney(185;0.000754)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00727)|READ - Rectum adenocarcinoma(331;0.0487)														---	---	---	---
CLCN6	1185	broad.mit.edu	37	1	11871266	11871267	+	Intron	DEL	AA	-	-	rs55738737	byFrequency;by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11871266_11871267delAA	uc001ate.3	+						CLCN6_uc009vne.1_Intron|CLCN6_uc009vnf.1_Intron|CLCN6_uc009vng.1_Intron|CLCN6_uc009vnh.1_Intron|CLCN6_uc010oat.1_Intron|CLCN6_uc010oau.1_Intron	NM_001286	NP_001277			chloride channel 6 isoform ClC-6a						cell volume homeostasis|signal transduction	endosome membrane|integral to membrane	antiporter activity|ATP binding|voltage-gated chloride channel activity				0	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.13e-06)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.000816)|KIRC - Kidney renal clear cell carcinoma(229;0.00268)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	12111959	12111959	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12111959delA								MIIP (19853 upstream) : TNFRSF8 (11475 downstream)																																			---	---	---	---
VPS13D	55187	broad.mit.edu	37	1	12404471	12404471	+	Intron	DEL	A	-	-	rs78303918	byFrequency;by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12404471delA	uc001atv.2	+						VPS13D_uc001atw.2_Intron|VPS13D_uc001atx.2_Intron	NM_015378	NP_056193			vacuolar protein sorting 13D isoform 1						protein localization					ovary(4)|pancreas(1)	5	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)														---	---	---	---
DHRS3	9249	broad.mit.edu	37	1	12643521	12643522	+	Intron	INS	-	ATCC	ATCC	rs145059013	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12643521_12643522insATCC	uc001auc.2	-						DHRS3_uc001aub.2_Intron|DHRS3_uc009vnm.2_Intron|DHRS3_uc001aud.3_Intron|DHRS3_uc001aue.1_Intron	NM_004753	NP_004744			dehydrogenase/reductase (SDR family) member 3						retinol metabolic process|visual perception	integral to membrane	electron carrier activity|NADP-retinol dehydrogenase activity|nucleotide binding			skin(1)	1	Ovarian(185;0.249)	Lung NSC(185;4.11e-05)|all_lung(284;4.58e-05)|Renal(390;0.000147)|Colorectal(325;0.000585)|Breast(348;0.000596)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|Colorectal(212;9.25e-07)|COAD - Colon adenocarcinoma(227;0.000326)|BRCA - Breast invasive adenocarcinoma(304;0.000344)|Kidney(185;0.00235)|KIRC - Kidney renal clear cell carcinoma(229;0.00656)|STAD - Stomach adenocarcinoma(313;0.00798)|READ - Rectum adenocarcinoma(331;0.0419)	Vitamin A(DB00162)													---	---	---	---
PRAMEF11	440560	broad.mit.edu	37	1	12891957	12891958	+	5'Flank	INS	-	C	C	rs33994876		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12891957_12891958insC	uc001auk.2	-							NM_001146344	NP_001139816			PRAME family member 11												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	13851827	13851828	+	IGR	DEL	AC	-	-	rs147486335		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:13851827_13851828delAC								PRAMEF17 (132763 upstream) : PDPN (58424 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	14165081	14165082	+	IGR	INS	-	CCTTTTTCC	CCTTTTTCC	rs141200821	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:14165081_14165082insCCTTTTTCC								PRDM2 (13509 upstream) : KAZ (760131 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	14223953	14223953	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:14223953delC								PRDM2 (72381 upstream) : KAZ (701260 downstream)																																			---	---	---	---
KAZ	23254	broad.mit.edu	37	1	15200967	15200970	+	Intron	DEL	TGGA	-	-	rs143917589		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15200967_15200970delTGGA	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	15391242	15391242	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15391242delG	uc001avm.3	+						KAZ_uc009vog.1_Intron|KAZ_uc010obj.1_Intron|KAZ_uc001avo.2_Intron|KAZ_uc001avp.2_Intron|KAZ_uc001avq.2_Intron|KAZ_uc001avr.2_Intron	NM_201628	NP_963922			kazrin isoform E						keratinization	cornified envelope|cytoplasm|desmosome|nucleus					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	15732436	15732449	+	IGR	DEL	CCAGTGCCCAGTGC	-	-	rs111617487		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15732436_15732449delCCAGTGCCCAGTGC								FHAD1 (5660 upstream) : EFHD2 (3942 downstream)																																			---	---	---	---
DNAJC16	23341	broad.mit.edu	37	1	15859200	15859200	+	Intron	DEL	G	-	-	rs71002908		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15859200delG	uc001aws.2	+						DNAJC16_uc001awr.1_Intron|DNAJC16_uc001awt.2_Intron	NM_015291	NP_056106			DnaJ (Hsp40) homolog, subfamily C, member 16						cell redox homeostasis|protein folding	integral to membrane	heat shock protein binding|unfolded protein binding			urinary_tract(1)|lung(1)|kidney(1)	3		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00173)|all_lung(284;0.00459)|Lung NSC(340;0.00499)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.18e-07)|COAD - Colon adenocarcinoma(227;4.5e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00774)|READ - Rectum adenocarcinoma(331;0.0657)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	15927144	15927145	+	IGR	INS	-	T	T	rs112818749		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15927144_15927145insT								DNAJC16 (8272 upstream) : DDI2 (16925 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	16007463	16007463	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16007463delT								RSC1A1 (19247 upstream) : PLEKHM2 (3364 downstream)																																			---	---	---	---
ARHGEF19	128272	broad.mit.edu	37	1	16533831	16533834	+	Intron	DEL	ATTC	-	-	rs113001974		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16533831_16533834delATTC	uc001ayc.1	-						ARHGEF19_uc009voo.1_5'Flank|ARHGEF19_uc001ayb.1_5'Flank	NM_153213	NP_694945			Rho guanine nucleotide exchange factor (GEF) 19						regulation of actin cytoskeleton organization	intracellular	GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			skin(2)|ovary(1)	3		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|Colorectal(212;3.48e-07)|COAD - Colon adenocarcinoma(227;2.19e-05)|BRCA - Breast invasive adenocarcinoma(304;9.46e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.0117)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
FBXO42	54455	broad.mit.edu	37	1	16597440	16597440	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16597440delA	uc001ayg.2	-						FBXO42_uc001ayf.2_Intron	NM_018994	NP_061867			F-box protein 42											upper_aerodigestive_tract(1)|skin(1)	2		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00475)|all_lung(284;0.00671)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0193)|Colorectal(212;3.16e-07)|COAD - Colon adenocarcinoma(227;1.46e-05)|BRCA - Breast invasive adenocarcinoma(304;4.37e-05)|Kidney(64;0.000246)|KIRC - Kidney renal clear cell carcinoma(64;0.00336)|STAD - Stomach adenocarcinoma(313;0.0139)|READ - Rectum adenocarcinoma(331;0.0693)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	16857848	16857848	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16857848delT								CROCCL2 (38652 upstream) : NBPF1 (32564 downstream)																																			---	---	---	---
ESPNP	284729	broad.mit.edu	37	1	17038327	17038327	+	Intron	DEL	A	-	-	rs59855586		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17038327delA	uc001azn.1	-						ESPNP_uc010ocj.1_5'Flank	NR_026567				RecName: Full=Espin; AltName: Full=Ectoplasmic specialization protein; AltName: Full=Autosomal recessive deafness type 36 protein;												0																		---	---	---	---
MST1P9	11223	broad.mit.edu	37	1	17082264	17082264	+	3'UTR	DEL	G	-	-	rs56384488		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17082264delG	uc010ock.1	-	15					CROCC_uc009voy.1_Intron|MST1P9_uc001azp.3_3'UTR	NR_002729				SubName: Full=Hepatocyte growth factor-like protein homolog;												0																		---	---	---	---
CROCC	9696	broad.mit.edu	37	1	17242679	17242679	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17242679delA	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)														---	---	---	---
PADI1	29943	broad.mit.edu	37	1	17567546	17567546	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17567546delT	uc001bah.1	+						PADI1_uc010oco.1_Intron|PADI1_uc010ocp.1_Intron|PADI1_uc010ocq.1_Intron|PADI1_uc009vpb.1_Intron	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)													---	---	---	---
PADI4	23569	broad.mit.edu	37	1	17680744	17680744	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17680744delA	uc001baj.2	+							NM_012387	NP_036519			peptidyl arginine deiminase, type IV						chromatin modification|peptidyl-citrulline biosynthetic process from peptidyl-arginine|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	calcium ion binding|protein-arginine deiminase activity			ovary(1)|skin(1)	2		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000338)|Lung NSC(340;0.00042)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00537)|BRCA - Breast invasive adenocarcinoma(304;8.54e-06)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(64;0.000223)|KIRC - Kidney renal clear cell carcinoma(64;0.00313)|STAD - Stomach adenocarcinoma(196;0.00707)|READ - Rectum adenocarcinoma(331;0.0689)|Lung(427;0.199)	L-Citrulline(DB00155)													---	---	---	---
RCC2	55920	broad.mit.edu	37	1	17748540	17748540	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17748540delA	uc001bal.2	-						RCC2_uc001bam.2_Intron	NM_001136204	NP_001129676			regulator of chromosome condensation 2						cell division|mitotic prometaphase	chromosome, centromeric region|cytosol|microtubule|nucleolus|spindle					0		Colorectal(325;0.000147)|Breast(348;0.00122)|Renal(390;0.00145)|all_lung(284;0.0054)|Lung NSC(340;0.00566)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00492)|BRCA - Breast invasive adenocarcinoma(304;7.69e-06)|COAD - Colon adenocarcinoma(227;1.19e-05)|Kidney(64;0.000189)|KIRC - Kidney renal clear cell carcinoma(64;0.00273)|STAD - Stomach adenocarcinoma(196;0.0135)|READ - Rectum adenocarcinoma(331;0.0656)|Lung(427;0.19)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	18214813	18214813	+	IGR	DEL	G	-	-	rs34867682		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:18214813delG								ACTL8 (61257 upstream) : IGSF21 (219427 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	18717330	18717331	+	IGR	DEL	GG	-	-	rs112150540		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:18717330_18717331delGG								IGSF21 (12354 upstream) : KLHDC7A (90093 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	19138809	19138809	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19138809delC								PAX7 (63450 upstream) : TAS1R2 (27284 downstream)																																			---	---	---	---
VWA5B1	127731	broad.mit.edu	37	1	20615991	20615991	+	5'Flank	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20615991delG	uc009vps.2	+						VWA5B1_uc001bdd.2_5'Flank|VWA5B1_uc010odc.1_5'Flank	NM_001039500	NP_001034589			von Willebrand factor A domain containing 5B1							extracellular region					0																		---	---	---	---
MUL1	79594	broad.mit.edu	37	1	20826076	20826076	+	3'UTR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20826076delA	uc001bdi.3	-	4						NM_024544	NP_078820			mitochondrial ubiquitin ligase activator of NFKB						activation of caspase activity|activation of JUN kinase activity|induction of apoptosis|mitochondrial fission|mitochondrion localization|negative regulation of cell growth|positive regulation of I-kappaB kinase/NF-kappaB cascade	integral to mitochondrial outer membrane|nucleus|peroxisome	identical protein binding|signal transducer activity|ubiquitin-protein ligase activity|zinc ion binding				0		Colorectal(325;0.000147)|Renal(390;0.000469)|Lung NSC(340;0.00412)|all_lung(284;0.00419)|Breast(348;0.00748)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|COAD - Colon adenocarcinoma(152;1.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000137)|Kidney(64;0.00017)|GBM - Glioblastoma multiforme(114;0.00124)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.198)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	20896570	20896570	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20896570delT								FAM43B (15058 upstream) : CDA (18874 downstream)																																			---	---	---	---
EIF4G3	8672	broad.mit.edu	37	1	21307743	21307747	+	Intron	DEL	ATTTT	-	-	rs74258939		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21307743_21307747delATTTT	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)														---	---	---	---
EIF4G3	8672	broad.mit.edu	37	1	21475324	21475324	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21475324delA	uc001bef.2	-						EIF4G3_uc001bed.2_Intron|EIF4G3_uc001bee.2_Intron|EIF4G3_uc001beh.2_Intron	NM_003760	NP_003751			eukaryotic translation initiation factor 4						interspecies interaction between organisms|regulation of translational initiation|RNA metabolic process	eukaryotic translation initiation factor 4F complex	protein binding|RNA cap binding|translation initiation factor activity			skin(1)	1		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)														---	---	---	---
ECE1	1889	broad.mit.edu	37	1	21560487	21560488	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21560487_21560488insT	uc001bek.2	-						ECE1_uc001bem.2_Intron|ECE1_uc001bej.2_Intron|ECE1_uc001bei.2_Intron|ECE1_uc010odl.1_Intron|ECE1_uc009vqa.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)														---	---	---	---
ECE1	1889	broad.mit.edu	37	1	21590156	21590157	+	Intron	DEL	TT	-	-	rs35054949		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21590156_21590157delTT	uc001bek.2	-						ECE1_uc001bem.2_Intron|ECE1_uc001bej.2_Intron|ECE1_uc001bei.2_Intron|ECE1_uc010odl.1_Intron|ECE1_uc009vqa.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	21827604	21827604	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21827604delA								NBPF3 (16212 upstream) : ALPL (8254 downstream)																																			---	---	---	---
CDC42	998	broad.mit.edu	37	1	22376219	22376221	+	5'Flank	DEL	TTT	-	-	rs71660803		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22376219_22376221delTTT	uc001bfq.2	+						CDC42_uc009vqg.1_5'Flank|CDC42_uc001bfp.2_5'Flank|CDC42_uc001bfr.2_5'Flank|CDC42_uc010odr.1_5'Flank|CDC42_uc010ods.1_5'Flank|CDC42_uc009vqh.2_5'Flank	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	22686988	22686991	+	IGR	DEL	GAAA	-	-	rs72298765		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22686988_22686991delGAAA								WNT4 (216603 upstream) : ZBTB40 (91353 downstream)																																			---	---	---	---
EPHA8	2046	broad.mit.edu	37	1	22902610	22902610	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22902610delT	uc001bfx.1	+						EPHA8_uc001bfw.2_Intron	NM_020526	NP_065387			ephrin receptor EphA8 isoform 1 precursor							integral to plasma membrane	ATP binding|ephrin receptor activity			central_nervous_system(5)|breast(3)|lung(2)|large_intestine(1)|stomach(1)|skin(1)	13		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.29e-27)|Colorectal(126;1.61e-07)|COAD - Colon adenocarcinoma(152;1.14e-05)|GBM - Glioblastoma multiforme(114;1.74e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000554)|KIRC - Kidney renal clear cell carcinoma(1967;0.00272)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)														---	---	---	---
EPHA8	2046	broad.mit.edu	37	1	22913274	22913274	+	Intron	DEL	G	-	-	rs66713995		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22913274delG	uc001bfx.1	+						EPHA8_uc001bfw.2_Intron	NM_020526	NP_065387			ephrin receptor EphA8 isoform 1 precursor							integral to plasma membrane	ATP binding|ephrin receptor activity			central_nervous_system(5)|breast(3)|lung(2)|large_intestine(1)|stomach(1)|skin(1)	13		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.29e-27)|Colorectal(126;1.61e-07)|COAD - Colon adenocarcinoma(152;1.14e-05)|GBM - Glioblastoma multiforme(114;1.74e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000554)|KIRC - Kidney renal clear cell carcinoma(1967;0.00272)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)														---	---	---	---
EPHB2	2048	broad.mit.edu	37	1	23172214	23172215	+	Intron	DEL	CC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23172214_23172215delCC	uc009vqj.1	+						EPHB2_uc001bge.2_Intron|EPHB2_uc001bgf.2_Intron|EPHB2_uc010odu.1_Intron	NM_017449	NP_059145			ephrin receptor EphB2 isoform 1 precursor						axon guidance	integral to plasma membrane	ATP binding|transmembrane-ephrin receptor activity			ovary(3)|lung(1)|pancreas(1)	5		Colorectal(325;3.46e-05)|Lung NSC(340;3.7e-05)|all_lung(284;5.45e-05)|Renal(390;0.000228)|Breast(348;0.0027)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0258)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0348)|OV - Ovarian serous cystadenocarcinoma(117;3.67e-26)|Colorectal(126;3.23e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|GBM - Glioblastoma multiforme(114;2.93e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000606)|KIRC - Kidney renal clear cell carcinoma(1967;0.00371)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.126)|Lung(427;0.153)										Hereditary_Prostate_Cancer				---	---	---	---
LUZP1	7798	broad.mit.edu	37	1	23464135	23464135	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23464135delA	uc001bgk.2	-						LUZP1_uc010odv.1_Intron|LUZP1_uc001bgl.2_Intron|LUZP1_uc001bgm.1_Intron	NM_033631	NP_361013			leucine zipper protein 1							nucleus					0		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Ovarian(437;0.00373)|Breast(348;0.00815)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;4.88e-27)|Colorectal(126;8.36e-08)|COAD - Colon adenocarcinoma(152;4.31e-06)|GBM - Glioblastoma multiforme(114;8.64e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00112)|KIRC - Kidney renal clear cell carcinoma(1967;0.00176)|STAD - Stomach adenocarcinoma(196;0.0146)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.0967)|LUSC - Lung squamous cell carcinoma(448;0.199)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	23875442	23875442	+	IGR	DEL	G	-	-	rs35128676		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23875442delG								E2F2 (17729 upstream) : ID3 (8968 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	23968877	23968877	+	IGR	DEL	A	-	-	rs35190480		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23968877delA								MDS2 (1821 upstream) : RPL11 (49417 downstream)																																			---	---	---	---
CLIC4	25932	broad.mit.edu	37	1	25156946	25156947	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25156946_25156947delTT	uc001bjo.2	+						CLIC4_uc001bjn.2_Intron|CLIC4_uc001bjp.1_Intron	NM_013943	NP_039234			chloride intracellular channel 4						cellular response to calcium ion|establishment or maintenance of apical/basal cell polarity|keratinocyte differentiation|negative regulation of cell migration|regulation of cytoskeleton organization	actin cytoskeleton|apical part of cell|cell surface|cell-cell junction|centrosome|chloride channel complex|cytoplasmic vesicle membrane|cytosol|microvillus|midbody|mitochondrion|nuclear matrix|perinuclear region of cytoplasm|soluble fraction	voltage-gated chloride channel activity				0		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000778)|all_lung(284;0.00106)|Ovarian(437;0.00764)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0479)|OV - Ovarian serous cystadenocarcinoma(117;1.06e-24)|Colorectal(126;1.03e-07)|COAD - Colon adenocarcinoma(152;4.93e-06)|STAD - Stomach adenocarcinoma(196;0.000418)|GBM - Glioblastoma multiforme(114;0.000451)|BRCA - Breast invasive adenocarcinoma(304;0.00215)|KIRC - Kidney renal clear cell carcinoma(1967;0.00216)|READ - Rectum adenocarcinoma(331;0.0693)|Lung(427;0.0853)|LUSC - Lung squamous cell carcinoma(448;0.18)														---	---	---	---
MAN1C1	57134	broad.mit.edu	37	1	26082955	26082956	+	Intron	INS	-	A	A	rs145048522	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26082955_26082956insA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	26478495	26478495	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26478495delT								PDIK1L (26471 upstream) : GRRP1 (7016 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	26832586	26832586	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26832586delT								HMGN2 (29455 upstream) : RPS6KA1 (23663 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	27490282	27490285	+	IGR	DEL	TGTG	-	-	rs112271839		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27490282_27490285delTGTG								SLC9A1 (8831 upstream) : WDTC1 (70722 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	27528684	27528684	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27528684delA								SLC9A1 (47233 upstream) : WDTC1 (32323 downstream)																																			---	---	---	---
WDTC1	23038	broad.mit.edu	37	1	27587433	27587433	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27587433delT	uc009vst.2	+						WDTC1_uc001bno.2_Intron|WDTC1_uc001bnp.1_5'Flank	NM_015023	NP_055838			WD and tetratricopeptide repeats 1								protein binding			ovary(1)|central_nervous_system(1)	2		all_cancers(24;3.12e-19)|all_epithelial(13;4.18e-18)|Colorectal(325;0.000147)|all_lung(284;0.000366)|Lung NSC(340;0.000548)|Renal(390;0.00211)|Breast(348;0.00257)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0443)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-27)|Colorectal(126;8.83e-09)|COAD - Colon adenocarcinoma(152;1.02e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000544)|KIRC - Kidney renal clear cell carcinoma(1967;0.00201)|STAD - Stomach adenocarcinoma(196;0.00321)|READ - Rectum adenocarcinoma(331;0.0476)														---	---	---	---
FAM76A	199870	broad.mit.edu	37	1	28085983	28085983	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28085983delT	uc001boq.2	+						FAM76A_uc009vtb.2_Intron|FAM76A_uc001bor.2_Intron|FAM76A_uc001bos.2_Intron|FAM76A_uc001bot.2_Intron|FAM76A_uc010ofm.1_Intron	NM_152660	NP_689873			hypothetical protein LOC199870 isoform 3												0		Colorectal(325;0.000147)|all_lung(284;0.00181)|Lung NSC(340;0.00278)|Renal(390;0.00357)|Breast(348;0.0115)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0545)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0429)|OV - Ovarian serous cystadenocarcinoma(117;3.52e-24)|Colorectal(126;3.23e-08)|COAD - Colon adenocarcinoma(152;1.75e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00253)|KIRC - Kidney renal clear cell carcinoma(1967;0.00292)|STAD - Stomach adenocarcinoma(196;0.00308)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	28426415	28426415	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28426415delA								LOC653566 (3346 upstream) : PTAFR (49449 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	28462058	28462058	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28462058delA								LOC653566 (38989 upstream) : PTAFR (13806 downstream)																																			---	---	---	---
ATPIF1	93974	broad.mit.edu	37	1	28564029	28564029	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28564029delT	uc001bpq.2	+						ATPIF1_uc001bpp.2_Intron|ATPIF1_uc001bpr.2_3'UTR	NM_016311	NP_057395			ATPase inhibitory factor 1 isoform 1 precursor						angiogenesis|generation of precursor metabolites and energy|negative regulation of endothelial cell proliferation|negative regulation of hydrolase activity|negative regulation of nucleotide metabolic process|protein homotetramerization	cell surface|mitochondrion	angiostatin binding|ATPase binding|ATPase inhibitor activity|calmodulin binding|protein homodimerization activity				0		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;4.76e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)		OV - Ovarian serous cystadenocarcinoma(117;2.36e-22)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00269)|BRCA - Breast invasive adenocarcinoma(304;0.00574)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
PHACTR4	65979	broad.mit.edu	37	1	28756540	28756541	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28756540_28756541delTT	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)														---	---	---	---
TAF12	6883	broad.mit.edu	37	1	28951893	28951893	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28951893delT	uc009vti.2	-						TAF12_uc001bqx.2_Intron|TAF12_uc001bqy.2_Intron	NM_005644	NP_005635			TAF12 RNA polymerase II, TATA box binding						histone H3 acetylation|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	PCAF complex|STAGA complex|transcription factor TFIID complex|transcription factor TFTC complex	DNA binding|protein binding|transcription coactivator activity			ovary(1)	1		Colorectal(325;3.46e-05)|Lung NSC(340;0.000451)|all_lung(284;0.00063)|Renal(390;0.00121)|Breast(348;0.00502)|all_neural(195;0.0227)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)		Colorectal(126;3.21e-08)|COAD - Colon adenocarcinoma(152;1.74e-06)|STAD - Stomach adenocarcinoma(196;0.00303)|KIRC - Kidney renal clear cell carcinoma(1967;0.0109)|BRCA - Breast invasive adenocarcinoma(304;0.0228)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
TAF12	6883	broad.mit.edu	37	1	28952499	28952499	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28952499delT	uc009vti.2	-						TAF12_uc001bqx.2_Intron|TAF12_uc001bqy.2_Intron	NM_005644	NP_005635			TAF12 RNA polymerase II, TATA box binding						histone H3 acetylation|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	PCAF complex|STAGA complex|transcription factor TFIID complex|transcription factor TFTC complex	DNA binding|protein binding|transcription coactivator activity			ovary(1)	1		Colorectal(325;3.46e-05)|Lung NSC(340;0.000451)|all_lung(284;0.00063)|Renal(390;0.00121)|Breast(348;0.00502)|all_neural(195;0.0227)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)		Colorectal(126;3.21e-08)|COAD - Colon adenocarcinoma(152;1.74e-06)|STAD - Stomach adenocarcinoma(196;0.00303)|KIRC - Kidney renal clear cell carcinoma(1967;0.0109)|BRCA - Breast invasive adenocarcinoma(304;0.0228)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
EPB41	2035	broad.mit.edu	37	1	29248120	29248121	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29248120_29248121insT	uc001brl.1	+						EPB41_uc001brg.1_Intron|EPB41_uc001brh.1_Intron|EPB41_uc001bri.1_Intron|EPB41_uc001brj.1_Intron|EPB41_uc009vtk.1_Intron|EPB41_uc001brk.2_Intron	NM_004437	NP_976217			erythrocyte membrane protein band 4.1						blood circulation|cortical actin cytoskeleton organization|positive regulation of protein binding	extrinsic to membrane|Golgi apparatus|nucleus|plasma membrane|protein complex|spectrin|spectrin-associated cytoskeleton	1-phosphatidylinositol binding|actin binding|spectrin binding|structural constituent of cytoskeleton			ovary(1)	1		Colorectal(325;3.46e-05)|Prostate(1639;0.000244)|Lung NSC(340;0.00328)|all_lung(284;0.00412)|Breast(348;0.00765)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)		Colorectal(126;3.12e-07)|COAD - Colon adenocarcinoma(152;1.21e-05)|STAD - Stomach adenocarcinoma(196;0.00395)|KIRC - Kidney renal clear cell carcinoma(1967;0.0249)|BRCA - Breast invasive adenocarcinoma(304;0.0289)|READ - Rectum adenocarcinoma(331;0.0757)														---	---	---	---
EPB41	2035	broad.mit.edu	37	1	29377195	29377195	+	Intron	DEL	T	-	-	rs113149173		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29377195delT	uc001brm.1	+						EPB41_uc001brg.1_Intron|EPB41_uc001brh.1_Intron|EPB41_uc001bri.1_Intron|EPB41_uc001brj.1_Intron|EPB41_uc009vtk.1_Intron|EPB41_uc001brk.2_Intron|EPB41_uc001brl.1_Intron|EPB41_uc009vtl.1_Intron|EPB41_uc009vtm.1_Intron	NM_203342	NP_976217			erythrocyte membrane protein band 4.1						blood circulation|cortical actin cytoskeleton organization|positive regulation of protein binding	extrinsic to membrane|Golgi apparatus|nucleus|plasma membrane|protein complex|spectrin|spectrin-associated cytoskeleton	1-phosphatidylinositol binding|actin binding|spectrin binding|structural constituent of cytoskeleton			ovary(1)	1		Colorectal(325;3.46e-05)|Prostate(1639;0.000244)|Lung NSC(340;0.00328)|all_lung(284;0.00412)|Breast(348;0.00765)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)		Colorectal(126;3.12e-07)|COAD - Colon adenocarcinoma(152;1.21e-05)|STAD - Stomach adenocarcinoma(196;0.00395)|KIRC - Kidney renal clear cell carcinoma(1967;0.0249)|BRCA - Breast invasive adenocarcinoma(304;0.0289)|READ - Rectum adenocarcinoma(331;0.0757)														---	---	---	---
PTPRU	10076	broad.mit.edu	37	1	29566212	29566212	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29566212delC	uc001bru.2	+						PTPRU_uc001brv.2_Intron|PTPRU_uc001brw.2_Intron|PTPRU_uc009vtq.2_Intron|PTPRU_uc009vtr.2_Intron	NM_005704	NP_005695			protein tyrosine phosphatase, receptor type, U						canonical Wnt receptor signaling pathway|cell differentiation|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of transcription, DNA-dependent|protein localization at cell surface|transmembrane receptor protein tyrosine phosphatase signaling pathway	cell-cell junction|integral to plasma membrane	beta-catenin binding|transmembrane receptor protein tyrosine phosphatase activity			large_intestine(3)|ovary(1)|kidney(1)|central_nervous_system(1)|skin(1)	7		Colorectal(325;0.000399)|Lung NSC(340;0.00953)|all_lung(284;0.0112)|Breast(348;0.0126)|all_neural(195;0.0199)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;6.99e-07)|COAD - Colon adenocarcinoma(152;3.18e-05)|STAD - Stomach adenocarcinoma(196;0.0234)|READ - Rectum adenocarcinoma(331;0.0686)|BRCA - Breast invasive adenocarcinoma(304;0.0871)														---	---	---	---
ZCCHC17	51538	broad.mit.edu	37	1	31786719	31786719	+	Intron	DEL	T	-	-	rs80321152		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31786719delT	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)														---	---	---	---
COL16A1	1307	broad.mit.edu	37	1	32131296	32131296	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32131296delG	uc001btk.1	-						COL16A1_uc001bti.1_Intron|COL16A1_uc001btj.1_Intron	NM_001856	NP_001847			alpha 1 type XVI collagen precursor						cell adhesion|female pregnancy|integrin-mediated signaling pathway	collagen type XVI	integrin binding|structural molecule activity			ovary(8)	8		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0423)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.059)														---	---	---	---
TMEM39B	55116	broad.mit.edu	37	1	32557038	32557038	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32557038delC	uc010ogv.1	+						TMEM39B_uc010ogt.1_Intron|TMEM39B_uc010ogu.1_Intron|TMEM39B_uc001bue.3_Intron|TMEM39B_uc001buf.3_Intron|TMEM39B_uc010ogw.1_Intron	NM_018056	NP_060526			transmembrane protein 39B							integral to membrane					0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.174)																---	---	---	---
KPNA6	23633	broad.mit.edu	37	1	32634966	32634967	+	Intron	DEL	AA	-	-	rs75451136		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32634966_32634967delAA	uc001bug.2	+						KPNA6_uc001buh.2_Intron|KPNA6_uc010ogx.1_Intron|KPNA6_uc010ogy.1_Intron|KPNA6_uc009vtz.2_Intron	NM_012316	NP_036448			karyopherin alpha 6						NLS-bearing substrate import into nucleus	cytoplasm|nuclear pore	protein binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.174)																---	---	---	---
BSDC1	55108	broad.mit.edu	37	1	32834302	32834302	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32834302delT	uc001bvh.3	-						BSDC1_uc010ohg.1_Intron|BSDC1_uc010ohh.1_Intron|BSDC1_uc010ohi.1_Intron|BSDC1_uc001bvg.3_Intron|BSDC1_uc001bvj.2_Intron|BSDC1_uc001bvi.2_Intron	NM_018045	NP_060515			BSD domain containing 1 isoform b								protein binding			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	32920571	32920571	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32920571delC								BSDC1 (60509 upstream) : ZBTB8A (10087 downstream)																																			---	---	---	---
ZBTB8A	653121	broad.mit.edu	37	1	32981431	32981431	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32981431delA	uc001bvk.2	+							NM_001145720				zinc finger and BTB domain containing 8B						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	33526046	33526046	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33526046delA								AK2 (23554 upstream) : ADC (20668 downstream)																																			---	---	---	---
PHC2	1912	broad.mit.edu	37	1	33799659	33799660	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33799659_33799660delAA	uc001bxg.1	-						PHC2_uc001bxh.1_Intron|PHC2_uc009vuh.1_Intron|PHC2_uc001bxe.1_Intron|PHC2_uc001bxf.1_Intron	NM_198040	NP_932157			polyhomeotic-like 2 isoform a						multicellular organismal development	PcG protein complex	DNA binding|identical protein binding|zinc ion binding			ovary(1)	1		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	33923515	33923515	+	IGR	DEL	T	-	-	rs72019022		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33923515delT								PHC2 (26900 upstream) : ZSCAN20 (14717 downstream)																																			---	---	---	---
CSMD2	114784	broad.mit.edu	37	1	34172508	34172509	+	Intron	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34172508_34172509delTG	uc001bxn.1	-						CSMD2_uc001bxm.1_Intron|CSMD2_uc001bxo.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)																---	---	---	---
CSMD2	114784	broad.mit.edu	37	1	34580299	34580299	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34580299delA	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	35517133	35517133	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35517133delA								ZMYM6 (19564 upstream) : ZMYM1 (27839 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	35616610	35616611	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35616610_35616611delTT								ZMYM1 (35156 upstream) : SFPQ (25371 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	36872260	36872261	+	IGR	INS	-	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36872260_36872261insC								LSM10 (8767 upstream) : OSCP1 (11247 downstream)																																			---	---	---	---
OSCP1	127700	broad.mit.edu	37	1	36907828	36907831	+	Intron	DEL	AAAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36907828_36907831delAAAA	uc001cap.2	-						OSCP1_uc001caq.2_Intron|OSCP1_uc001car.2_Intron	NM_145047	NP_659484			oxidored-nitro domain-containing protein isoform						transport	basal plasma membrane				ovary(2)|central_nervous_system(1)|pancreas(1)	4																		---	---	---	---
GRIK3	2899	broad.mit.edu	37	1	37420538	37420539	+	Intron	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37420538_37420539delAC	uc001caz.2	-						GRIK3_uc001cba.1_Intron	NM_000831	NP_000822			glutamate receptor, ionotropic, kainate 3						negative regulation of synaptic transmission, glutamatergic|regulation of membrane potential|synaptic transmission	cell junction|dendrite cytoplasm|integral to plasma membrane|perikaryon|postsynaptic membrane|terminal button	adenylate cyclase inhibiting metabotropic glutamate receptor activity|extracellular-glutamate-gated ion channel activity|G-protein-coupled receptor binding|kainate selective glutamate receptor activity			ovary(3)|skin(2)|large_intestine(1)|breast(1)	7		Myeloproliferative disorder(586;0.0258)|all_neural(195;0.169)			L-Glutamic Acid(DB00142)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	37637713	37637713	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37637713delT								GRIK3 (137869 upstream) : ZC3H12A (302406 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	37734274	37734274	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37734274delA								GRIK3 (234430 upstream) : ZC3H12A (205845 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	38067546	38067547	+	IGR	INS	-	T	T	rs112716464		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38067546_38067547insT								GNL2 (5960 upstream) : RSPO1 (9404 downstream)																																			---	---	---	---
CDCA8	55143	broad.mit.edu	37	1	38170966	38170966	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	38798111	38798111	+	IGR	DEL	T	-	-	rs2637847	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38798111delT								POU3F1 (285661 upstream) : RRAGC (506904 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	39116455	39116456	+	IGR	INS	-	T	T	rs141067972	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39116455_39116456insT								POU3F1 (604005 upstream) : RRAGC (188559 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	39164284	39164284	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39164284delC								POU3F1 (651834 upstream) : RRAGC (140731 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	39228367	39228367	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39228367delA								POU3F1 (715917 upstream) : RRAGC (76648 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	39430319	39430322	+	IGR	DEL	TTTT	-	-	rs10715711		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39430319_39430322delTTTT								RHBDL2 (22863 upstream) : AKIRIN1 (26594 downstream)																																			---	---	---	---
NT5C1A	84618	broad.mit.edu	37	1	40136541	40136542	+	Intron	INS	-	C	C	rs139040048	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40136541_40136542insC	uc001cdq.1	-							NM_032526	NP_115915			5'-nucleotidase, cytosolic IA						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)															---	---	---	---
ZNF684	127396	broad.mit.edu	37	1	40998318	40998318	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40998318delA	uc001cft.1	+							NM_152373	NP_689586			zinc finger protein 684						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;5.42e-18)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	41065185	41065187	+	IGR	DEL	TTT	-	-	rs151235010		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41065185_41065187delTTT								ZNF684 (51346 upstream) : RIMS3 (21165 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	41332438	41332438	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41332438delA								CITED4 (4420 upstream) : CTPS (112569 downstream)																																			---	---	---	---
SCMH1	22955	broad.mit.edu	37	1	41658168	41658169	+	Intron	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41658168_41658169delAC	uc001cgs.2	-						SCMH1_uc001cgr.2_Intron|SCMH1_uc001cgt.2_Intron|SCMH1_uc001cgq.2_Intron	NM_012236	NP_036368			sex comb on midleg 1 isoform 2						anatomical structure morphogenesis|gene silencing|multicellular organismal development|negative regulation of transcription, DNA-dependent		DNA binding|sequence-specific DNA binding transcription factor activity				0	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)|Breast(333;0.162)	Myeloproliferative disorder(586;0.0393)																---	---	---	---
HIVEP3	59269	broad.mit.edu	37	1	42216375	42216376	+	Intron	DEL	TT	-	-	rs72283438		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42216375_42216376delTT	uc001cgz.3	-						HIVEP3_uc001cha.3_Intron	NM_024503	NP_078779			human immunodeficiency virus type I enhancer						positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	zinc ion binding			ovary(4)|large_intestine(1)|central_nervous_system(1)	6	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)																---	---	---	---
HIVEP3	59269	broad.mit.edu	37	1	42438718	42438719	+	Intron	DEL	CA	-	-	rs71853116		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42438718_42438719delCA	uc001chb.1	-											Homo sapiens kappa B and V(D)J recombination signal sequences binding protein (KRC) mRNA, complete cds.						positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	zinc ion binding			ovary(4)|large_intestine(1)|central_nervous_system(1)	6	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)																---	---	---	---
CCDC30	728621	broad.mit.edu	37	1	42982339	42982339	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42982339delT	uc001chn.2	+						CCDC30_uc001chm.2_Intron|CCDC30_uc010oju.1_Intron	NM_001080850	NP_001074319			coiled-coil domain containing 30												0																		---	---	---	---
CCDC30	728621	broad.mit.edu	37	1	43011397	43011398	+	Intron	DEL	CG	-	-	rs112575083		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43011397_43011398delCG	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	43142432	43142432	+	5'Flank	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43142432delT	uc001chr.2	+											Homo sapiens full length insert cDNA clone YZ92E04.																														---	---	---	---
C1orf50	79078	broad.mit.edu	37	1	43235514	43235514	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43235514delA	uc001cia.3	+						LEPRE1_uc001chv.2_5'Flank|LEPRE1_uc001chw.2_5'Flank|LEPRE1_uc001chx.3_5'Flank|LEPRE1_uc001chy.3_5'Flank|LEPRE1_uc001chz.2_5'Flank	NM_024097	NP_077002			hypothetical protein LOC79078											ovary(1)	1	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	43337111	43337111	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43337111delA	uc001cij.1	+											Homo sapiens cDNA clone IMAGE:5170739.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	44095532	44095533	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44095532_44095533delAA								PTPRF (6190 upstream) : KDM4A (20264 downstream)																																			---	---	---	---
ST3GAL3	6487	broad.mit.edu	37	1	44192963	44192964	+	Intron	DEL	TT	-	-	rs79414880		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44192963_44192964delTT	uc001ckc.2	+						ST3GAL3_uc009vwu.1_Intron|ST3GAL3_uc010okj.1_Intron|ST3GAL3_uc001cjz.2_Intron|ST3GAL3_uc001cka.2_Intron|ST3GAL3_uc001ckb.2_Intron|ST3GAL3_uc001ckd.2_Intron|ST3GAL3_uc001cke.2_Intron|ST3GAL3_uc001ckf.2_Intron|ST3GAL3_uc001ckg.2_Intron|ST3GAL3_uc001ckh.2_Intron|ST3GAL3_uc001cki.2_Intron	NM_006279	NP_006270			sialyltransferase 6 isoform j						protein glycosylation	extracellular region|Golgi cisterna membrane|integral to Golgi membrane	N-acetyllactosaminide alpha-2,3-sialyltransferase activity			ovary(3)	3	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0518)																---	---	---	---
ST3GAL3	6487	broad.mit.edu	37	1	44299105	44299105	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44299105delA	uc001ckc.2	+						ST3GAL3_uc009vwu.1_Intron|ST3GAL3_uc010okj.1_Intron|ST3GAL3_uc001cjz.2_Intron|ST3GAL3_uc001cka.2_Intron|ST3GAL3_uc001ckb.2_Intron|ST3GAL3_uc001ckd.2_Intron|ST3GAL3_uc001cke.2_Intron|ST3GAL3_uc001ckf.2_Intron|ST3GAL3_uc001ckg.2_Intron|ST3GAL3_uc001ckh.2_Intron|ST3GAL3_uc001cki.2_Intron|ST3GAL3_uc009vwv.2_Intron|ST3GAL3_uc001ckj.2_Intron|ST3GAL3_uc009vww.2_Intron|ST3GAL3_uc001ckk.2_Intron|ST3GAL3_uc009vwy.2_Intron|ST3GAL3_uc009vwx.2_Intron|ST3GAL3_uc001ckm.2_Intron|ST3GAL3_uc001ckl.2_Intron|ST3GAL3_uc009vwz.2_Intron|ST3GAL3_uc001ckn.2_Intron|ST3GAL3_uc001ckp.2_Intron|ST3GAL3_uc001cko.2_Intron|ST3GAL3_uc009vxa.2_Intron|ST3GAL3_uc001ckq.2_Intron|ST3GAL3_uc001ckr.2_Intron|ST3GAL3_uc009vxb.2_Intron	NM_006279	NP_006270			sialyltransferase 6 isoform j						protein glycosylation	extracellular region|Golgi cisterna membrane|integral to Golgi membrane	N-acetyllactosaminide alpha-2,3-sialyltransferase activity			ovary(3)	3	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0518)																---	---	---	---
KLF17	128209	broad.mit.edu	37	1	44530959	44530960	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44530959_44530960delAA	uc009vxf.1	+							NM_173484	NP_775755			zinc finger protein 393						regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|zinc ion binding			ovary(1)|skin(1)	2	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
KLF17	128209	broad.mit.edu	37	1	44589588	44589588	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44589588delT	uc001clp.2	+						KLF17_uc009vxf.1_Intron	NM_173484	NP_775755			zinc finger protein 393						regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|zinc ion binding			ovary(1)|skin(1)	2	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	44670518	44670518	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44670518delT								KLF17 (69711 upstream) : DMAP1 (8607 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	44672874	44672875	+	IGR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44672874_44672875insA								KLF17 (72067 upstream) : DMAP1 (6250 downstream)																																			---	---	---	---
C1orf228	339541	broad.mit.edu	37	1	45155594	45155594	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45155594delA	uc001cmf.2	+							NM_001145636	NP_001139108			hypothetical protein LOC339541								binding				0																		---	---	---	---
TESK2	10420	broad.mit.edu	37	1	45861282	45861285	+	Intron	DEL	TTTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45861282_45861285delTTTT	uc001cns.1	-						TESK2_uc009vxr.1_Intron|TESK2_uc010olo.1_Intron|TESK2_uc009vxs.1_Intron	NM_007170	NP_009101			testis-specific protein kinase 2						actin cytoskeleton organization|focal adhesion assembly|spermatogenesis	nucleus	ATP binding|metal ion binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(2)|breast(2)|pancreas(1)	5	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
TESK2	10420	broad.mit.edu	37	1	45868917	45868918	+	Intron	INS	-	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45868917_45868918insG	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)																	---	---	---	---
IPP	3652	broad.mit.edu	37	1	46206445	46206445	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46206445delA	uc001cou.2	-						IPP_uc001cos.3_Intron	NM_005897	NP_005888			intracisternal A particle-promoted polypeptide							actin cytoskeleton|cytoplasm	actin binding			ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
MAST2	23139	broad.mit.edu	37	1	46371448	46371448	+	Intron	DEL	A	-	-	rs79857460		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46371448delA	uc001cov.2	+						MAST2_uc001cow.2_Intron|MAST2_uc001cox.1_Intron|MAST2_uc001coy.1_Intron	NM_015112	NP_055927			microtubule associated serine/threonine kinase						regulation of interleukin-12 biosynthetic process|spermatid differentiation	cytoplasm|cytoskeleton|plasma membrane	ATP binding|magnesium ion binding|phosphatase binding|protein serine/threonine kinase activity			ovary(5)|lung(3)|stomach(2)|breast(1)	11	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.184)																	---	---	---	---
MAST2	23139	broad.mit.edu	37	1	46469150	46469151	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46469150_46469151delTT	uc001cov.2	+						MAST2_uc001cow.2_Intron|MAST2_uc001cox.1_Intron|MAST2_uc001coy.1_Intron|MAST2_uc001coz.1_Intron|MAST2_uc009vya.2_Intron|MAST2_uc001cpa.2_5'Flank	NM_015112	NP_055927			microtubule associated serine/threonine kinase						regulation of interleukin-12 biosynthetic process|spermatid differentiation	cytoplasm|cytoskeleton|plasma membrane	ATP binding|magnesium ion binding|phosphatase binding|protein serine/threonine kinase activity			ovary(5)|lung(3)|stomach(2)|breast(1)	11	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.184)																	---	---	---	---
PIK3R3	8503	broad.mit.edu	37	1	46613584	46613584	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46613584delA	uc010olw.1	-							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)																	---	---	---	---
AGBL4	84871	broad.mit.edu	37	1	49284995	49284995	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:49284995delA	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	49531734	49531734	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:49531734delA	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	49608012	49608012	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:49608012delA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	51544958	51544960	+	IGR	DEL	ACA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51544958_51544960delACA								CDKN2C (104651 upstream) : C1orf185 (22946 downstream)																																			---	---	---	---
RNF11	26994	broad.mit.edu	37	1	51708312	51708313	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51708312_51708313insT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	51740420	51740420	+	IGR	DEL	A	-	-	rs34783054		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51740420delA								RNF11 (1303 upstream) : TTC39A (12511 downstream)																																			---	---	---	---
EPS15	2060	broad.mit.edu	37	1	51904542	51904542	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51904542delT	uc001csq.1	-						EPS15_uc009vyz.1_Intron	NM_001981	NP_001972			epidermal growth factor receptor pathway						cell proliferation|clathrin coat assembly|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway|protein transport	cytosol|early endosome membrane	calcium ion binding|SH3 domain binding			lung(1)|kidney(1)	2								T	MLL	ALL								---	---	---	---
RAB3B	5865	broad.mit.edu	37	1	52406298	52406299	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52406298_52406299delAA	uc001cth.2	-							NM_002867	NP_002858			RAB3B, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding|GTPase activity			ovary(1)	1																		---	---	---	---
ZFYVE9	9372	broad.mit.edu	37	1	52761012	52761015	+	Intron	DEL	GTTT	-	-	rs144066928		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52761012_52761015delGTTT	uc001cto.2	+						ZFYVE9_uc001ctp.2_Intron	NM_004799	NP_004790			zinc finger, FYVE domain containing 9 isoform 3						endocytosis|SMAD protein complex assembly|SMAD protein import into nucleus|transforming growth factor beta receptor signaling pathway	early endosome membrane	metal ion binding|protein binding|receptor activity|serine-type peptidase activity			ovary(2)|lung(2)|central_nervous_system(2)|skin(2)	8																		---	---	---	---
ZFYVE9	9372	broad.mit.edu	37	1	52761197	52761197	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52761197delT	uc001cto.2	+						ZFYVE9_uc001ctp.2_Intron	NM_004799	NP_004790			zinc finger, FYVE domain containing 9 isoform 3						endocytosis|SMAD protein complex assembly|SMAD protein import into nucleus|transforming growth factor beta receptor signaling pathway	early endosome membrane	metal ion binding|protein binding|receptor activity|serine-type peptidase activity			ovary(2)|lung(2)|central_nervous_system(2)|skin(2)	8																		---	---	---	---
ECHDC2	55268	broad.mit.edu	37	1	53373495	53373496	+	Intron	INS	-	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53373495_53373496insG	uc001cup.3	-						ECHDC2_uc001cun.2_Intron|ECHDC2_uc001cuo.3_Intron|ECHDC2_uc010onk.1_Intron|ECHDC2_uc010onl.1_Intron|ECHDC2_uc010onm.1_Intron|ECHDC2_uc010onn.1_Intron	NM_018281	NP_060751			enoyl Coenzyme A hydratase domain containing 2						fatty acid metabolic process	mitochondrion	lyase activity			central_nervous_system(1)	1																		---	---	---	---
PODN	127435	broad.mit.edu	37	1	53538171	53538171	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53538171delG	uc001cuv.2	+						PODN_uc001cuw.2_Intron|PODN_uc010onr.1_Intron|PODN_uc010ons.1_Intron	NM_153703	NP_714914			podocan						negative regulation of cell migration|negative regulation of cell proliferation	cytoplasm|extracellular space|proteinaceous extracellular matrix	collagen binding			ovary(1)|pancreas(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	53630415	53630415	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53630415delT								SLC1A7 (22126 upstream) : CPT2 (31686 downstream)																																			---	---	---	---
LRP8	7804	broad.mit.edu	37	1	53775878	53775883	+	Intron	DEL	GGGGCA	-	-	rs66792259		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53775878_53775883delGGGGCA	uc001cvi.1	-						LRP8_uc001cvh.1_Intron|LRP8_uc001cvk.1_Intron|LRP8_uc001cvj.1_Intron|LRP8_uc001cvl.1_Intron	NM_004631	NP_004622			low density lipoprotein receptor-related protein						cytokine-mediated signaling pathway|endocytosis|lipid metabolic process|platelet activation|proteolysis	caveola	calcium ion binding|very-low-density lipoprotein particle receptor activity				0																		---	---	---	---
LRP8	7804	broad.mit.edu	37	1	53783913	53783916	+	Intron	DEL	TTTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53783913_53783916delTTTT	uc001cvi.1	-						LRP8_uc001cvh.1_Intron|LRP8_uc001cvk.1_Intron|LRP8_uc001cvj.1_Intron|LRP8_uc001cvl.1_Intron	NM_004631	NP_004622			low density lipoprotein receptor-related protein						cytokine-mediated signaling pathway|endocytosis|lipid metabolic process|platelet activation|proteolysis	caveola	calcium ion binding|very-low-density lipoprotein particle receptor activity				0																		---	---	---	---
GLIS1	148979	broad.mit.edu	37	1	54120792	54120792	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54120792delT	uc001cvr.1	-							NM_147193	NP_671726			GLIS family zinc finger 1						negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	DNA binding|zinc ion binding			skin(1)	1																		---	---	---	---
TMEM48	55706	broad.mit.edu	37	1	54273150	54273150	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54273150delA	uc001cvs.2	-						TMEM48_uc010onu.1_Intron|TMEM48_uc001cvt.2_Intron|TMEM48_uc009vzk.2_Intron|TMEM48_uc010onv.1_Intron	NM_018087	NP_060557			transmembrane protein 48						mRNA transport|nuclear pore complex assembly|nuclear pore distribution|protein transport|transmembrane transport	nuclear membrane|nuclear pore	protein binding|structural constituent of nuclear pore			ovary(1)|pancreas(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	54631778	54631779	+	IGR	DEL	AA	-	-	rs149904121		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54631778_54631779delAA								CDCP2 (12335 upstream) : CYB5RL (6250 downstream)																																			---	---	---	---
ACOT11	26027	broad.mit.edu	37	1	55006112	55006112	+	5'Flank	DEL	A	-	-	rs148064910		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55006112delA	uc001cxj.1	+											RecName: Full=Acyl-coenzyme A thioesterase 11;          Short=Acyl-CoA thioesterase 11;          EC=3.1.2.-; AltName: Full=Acyl-CoA thioester hydrolase 11; AltName: Full=Brown fat-inducible thioesterase;          Short=BFIT; AltName: Full=Adipose-associated thioesterase;						fatty acid metabolic process|intracellular signal transduction|response to cold		acyl-CoA thioesterase activity|carboxylesterase activity			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	56410540	56410540	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:56410540delA								USP24 (729778 upstream) : PPAP2B (549893 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	56582932	56582933	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:56582932_56582933delAA								USP24 (902170 upstream) : PPAP2B (377500 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	56818066	56818066	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:56818066delT								None (None upstream) : PPAP2B (142367 downstream)																																			---	---	---	---
PRKAA2	5563	broad.mit.edu	37	1	57158313	57158313	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57158313delT	uc001cyk.3	+							NM_006252	NP_006243			AMP-activated protein kinase alpha 2 catalytic						carnitine shuttle|cell cycle arrest|cholesterol biosynthetic process|energy reserve metabolic process|fatty acid biosynthetic process|insulin receptor signaling pathway|regulation of fatty acid biosynthetic process|regulation of fatty acid oxidation	cytosol|nucleoplasm	ATP binding|metal ion binding			breast(4)|ovary(1)|stomach(1)	6																		---	---	---	---
DAB1	1600	broad.mit.edu	37	1	58246386	58246386	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:58246386delT	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	58659528	58659528	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:58659528delA	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	58894904	58894904	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:58894904delA	uc001cyt.1	-							NM_021080	NP_066566			disabled homolog 1						cell differentiation|nervous system development					skin(2)|ovary(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	59270925	59270928	+	Intron	DEL	ACAA	-	-	rs71860440		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59270925_59270928delACAA	uc001czf.2	+						uc010oop.1_Intron					Homo sapiens cDNA FLJ30588 fis, clone BRAWH2008128.																														---	---	---	---
CYP2J2	1573	broad.mit.edu	37	1	60375861	60375861	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:60375861delA	uc001czq.2	-							NM_000775	NP_000766			cytochrome P450, family 2, subfamily J,						epoxygenase P450 pathway|linoleic acid metabolic process|regulation of heart contraction|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	arachidonic acid 11,12-epoxygenase activity|arachidonic acid 14,15-epoxygenase activity|aromatase activity|electron carrier activity|heme binding|linoleic acid epoxygenase activity			ovary(1)	1	all_cancers(7;0.000396)																	---	---	---	---
C1orf87	127795	broad.mit.edu	37	1	60520735	60520735	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:60520735delA	uc001czs.1	-							NM_152377	NP_689590			hypothetical protein LOC127795								calcium ion binding			ovary(1)|breast(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	60937680	60937683	+	IGR	DEL	ACAG	-	-	rs4453073	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:60937680_60937683delACAG								C1orf87 (398254 upstream) : NFIA (605263 downstream)																																			---	---	---	---
TM2D1	83941	broad.mit.edu	37	1	62189461	62189461	+	Intron	DEL	A	-	-	rs147863719		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62189461delA	uc001czz.1	-							NM_032027	NP_114416			beta-amyloid binding protein precursor						apoptosis					ovary(1)	1																		---	---	---	---
INADL	10207	broad.mit.edu	37	1	62265624	62265625	+	Intron	DEL	TA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62265624_62265625delTA	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	62267609	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62267609delT	uc001dab.2	+						INADL_uc009waf.1_Intron|INADL_uc001daa.2_Intron|INADL_uc001dad.3_Intron	NM_176877	NP_795352			InaD-like						intracellular signal transduction|tight junction assembly	apical plasma membrane|perinuclear region of cytoplasm|tight junction	protein binding			ovary(3)|skin(1)	4																		---	---	---	---
INADL	10207	broad.mit.edu	37	1	62399613	62399613	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62399613delT	uc001dab.2	+						INADL_uc009waf.1_Intron|INADL_uc001daa.2_Intron|INADL_uc001dad.3_Intron|INADL_uc001dac.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																		---	---	---	---
DOCK7	85440	broad.mit.edu	37	1	62978586	62978586	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62978586delA	uc001daq.2	-						DOCK7_uc001dan.2_Intron|DOCK7_uc001dao.2_Intron|DOCK7_uc001dap.2_Intron|DOCK7_uc001dam.2_Intron|DOCK7_uc010oov.1_Intron	NM_033407	NP_212132			dedicator of cytokinesis 7						activation of Rac GTPase activity|axonogenesis|establishment of neuroblast polarity|microtubule cytoskeleton organization|positive regulation of peptidyl-serine phosphorylation	axon|basal part of cell|growth cone	GTP binding|guanyl-nucleotide exchange factor activity|Rac GTPase binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	63595309	63595310	+	IGR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:63595309_63595310insA								ATG4C (265260 upstream) : FOXD3 (193420 downstream)																																			---	---	---	---
JAK1	3716	broad.mit.edu	37	1	65310329	65310330	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65310329_65310330delAA	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	65314878	65314878	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65314878delT	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								---	---	---	---
AK3L1	205	broad.mit.edu	37	1	65635569	65635570	+	Intron	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65635569_65635570delTG	uc001dby.2	+						AK3L1_uc009wan.2_Intron|AK3L1_uc001dbz.2_Intron|AK3L1_uc001dca.2_Intron	NM_203464	NP_982289			adenylate kinase 3-like 1 isoform 7							mitochondrial matrix	adenylate kinase activity|ATP binding|GTP binding				0																		---	---	---	---
DNAJC6	9829	broad.mit.edu	37	1	65834391	65834391	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65834391delT	uc001dcd.1	+						DNAJC6_uc001dcc.1_Intron|DNAJC6_uc010opc.1_Intron|DNAJC6_uc001dce.1_Intron	NM_014787	NP_055602			DnaJ (Hsp40) homolog, subfamily C, member 6						cellular membrane organization|post-Golgi vesicle-mediated transport	cytosol	heat shock protein binding|protein tyrosine phosphatase activity|SH3 domain binding			large_intestine(1)|lung(1)|ovary(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	66118330	66118332	+	IGR	DEL	CCT	-	-	rs142071086		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:66118330_66118332delCCT								LEPR (15510 upstream) : PDE4B (139861 downstream)																																			---	---	---	---
PDE4B	5142	broad.mit.edu	37	1	66490375	66490375	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:66490375delT	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)													---	---	---	---
SGIP1	84251	broad.mit.edu	37	1	67206944	67206944	+	Intron	DEL	T	-	-	rs76751942		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67206944delT	uc001dcr.2	+						SGIP1_uc010opd.1_Intron|SGIP1_uc001dcs.2_Intron|SGIP1_uc001dct.2_Intron|SGIP1_uc009wat.2_Intron|SGIP1_uc001dcu.2_Intron	NM_032291	NP_115667			SH3-domain GRB2-like (endophilin) interacting						positive regulation of energy homeostasis|positive regulation of feeding behavior|positive regulation of receptor-mediated endocytosis|response to dietary excess	AP-2 adaptor complex	microtubule binding|phospholipid binding|SH3 domain binding			ovary(3)	3																		---	---	---	---
C1orf141	400757	broad.mit.edu	37	1	67594694	67594694	+	5'Flank	DEL	T	-	-	rs78968634		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67594694delT	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	67655618	67655618	+	Intron	DEL	A	-	-	rs80252747		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67655618delA	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	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	67871676	67871676	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67871676delT								IL12RB2 (9094 upstream) : SERBP1 (1819 downstream)																																			---	---	---	---
WLS	79971	broad.mit.edu	37	1	68679373	68679374	+	Intron	DEL	AA	-	-	rs75666120		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:68679373_68679374delAA	uc001def.1	-						WLS_uc001dee.2_Intron|WLS_uc001deg.1_Intron|WLS_uc001deh.1_Intron	NM_024911	NP_079187			G protein-coupled receptor 177 isoform 1						multicellular organismal development|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|Wnt receptor signaling pathway	cytoplasmic vesicle membrane|Golgi membrane|integral to membrane	signal transducer activity				0																		---	---	---	---
DEPDC1	55635	broad.mit.edu	37	1	68964511	68964512	+	5'Flank	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:68964511_68964512delTG	uc001dem.3	-						DEPDC1_uc001del.3_5'Flank|uc001den.2_Intron	NM_001114120	NP_001107592			DEP domain containing 1 isoform a						intracellular signal transduction|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	transcriptional repressor complex	GTPase activator activity|protein binding				0				OV - Ovarian serous cystadenocarcinoma(397;7.21e-36)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	69118194	69118194	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:69118194delA								DEPDC1 (155395 upstream) : LRRC7 (914674 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	69828058	69828059	+	IGR	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:69828058_69828059delAC								DEPDC1 (865259 upstream) : LRRC7 (204809 downstream)																																			---	---	---	---
LRRC7	57554	broad.mit.edu	37	1	70031679	70031679	+	5'Flank	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70031679delA	uc001deo.1	+											SubName: Full=Leucine rich repeat containing 7; SubName: Full=cDNA FLJ54846, highly similar to Leucine-rich repeat-containing protein 7;							centrosome|focal adhesion|nucleolus	protein binding			ovary(9)|breast(2)|central_nervous_system(2)|liver(1)	14																		---	---	---	---
LRRC7	57554	broad.mit.edu	37	1	70482950	70482951	+	Intron	DEL	AA	-	-	rs80143790		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70482950_70482951delAA	uc001dep.2	+						LRRC7_uc009wbg.2_Intron	NM_020794	NP_065845			leucine rich repeat containing 7							centrosome|focal adhesion|nucleolus	protein binding			ovary(9)|breast(2)|central_nervous_system(2)|liver(1)	14																		---	---	---	---
ANKRD13C	81573	broad.mit.edu	37	1	70730792	70730792	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70730792delA	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	70971563	70971563	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70971563delA								CTH (66311 upstream) : PTGER3 (346473 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	71528265	71528266	+	Intron	INS	-	CACACA	CACACA	rs35523285	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:71528265_71528266insCACACA	uc001dfr.2	+											Homo sapiens cDNA clone IMAGE:5271818.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	71626921	71626921	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:71626921delA	uc001dfu.1	+											Homo sapiens cDNA clone IMAGE:6592429, partial cds.																														---	---	---	---
NEGR1	257194	broad.mit.edu	37	1	72533401	72533402	+	Intron	DEL	AA	-	-	rs112631946		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:72533401_72533402delAA	uc001dfw.2	-						NEGR1_uc001dfv.2_Intron|NEGR1_uc010oqs.1_Intron	NM_173808	NP_776169			neuronal growth regulator 1 precursor						cell adhesion	anchored to membrane|plasma membrane				ovary(1)	1		all_cancers(4;1.26e-06)|Renal(4;1.32e-08)|all_epithelial(4;5.39e-07)|Hepatocellular(141;0.117)		KIRC - Kidney renal clear cell carcinoma(4;0.00529)|Kidney(4;0.00609)|all cancers(265;0.022)|GBM - Glioblastoma multiforme(62;0.0382)|Epithelial(280;0.242)														---	---	---	---
NEGR1	257194	broad.mit.edu	37	1	72534948	72534951	+	Intron	DEL	AAAC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:72534948_72534951delAAAC	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	73472567	73472567	+	IGR	DEL	A	-	-	rs66531723		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:73472567delA								NEGR1 (724162 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	73489349	73489350	+	IGR	INS	-	GT	GT	rs149412631	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:73489349_73489350insGT								NEGR1 (740944 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	73856129	73856130	+	IGR	INS	-	T	T	rs74765472		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:73856129_73856130insT								None (None upstream) : LRRIQ3 (635574 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	74349284	74349284	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:74349284delA								None (None upstream) : LRRIQ3 (142420 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	76457321	76457321	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:76457321delT								ASB17 (59205 upstream) : ST6GALNAC3 (83068 downstream)																																	OREG0013566	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
MGC27382	149047	broad.mit.edu	37	1	78752618	78752618	+	Intron	DEL	C	-	-	rs57600470		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78752618delC	uc001dil.1	+						MGC27382_uc009wcc.2_Intron					Homo sapiens cDNA FLJ34438 fis, clone HLUNG2001144.												0																		---	---	---	---
PTGFR	5737	broad.mit.edu	37	1	78980732	78980732	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78980732delT	uc001din.2	+						PTGFR_uc001dim.2_Intron	NM_000959	NP_000950			prostaglandin F receptor isoform a precursor						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)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	79068848	79068848	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:79068848delT								PTGFR (62463 upstream) : IFI44L (17240 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	79485346	79485347	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:79485346_79485347delTT								ELTD1 (12851 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	80768464	80768465	+	IGR	INS	-	A	A	rs113925057		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:80768464_80768465insA								None (None upstream) : None (None downstream)																																			---	---	---	---
LPHN2	23266	broad.mit.edu	37	1	82282649	82282650	+	Intron	DEL	TT	-	-	rs71779644		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:82282649_82282650delTT	uc001dit.3	+						LPHN2_uc001dis.2_Intron|LPHN2_uc001diu.2_Intron|LPHN2_uc001div.2_Intron|LPHN2_uc009wcd.2_Intron	NM_012302	NP_036434			latrophilin 2 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|latrotoxin receptor activity|sugar binding			ovary(3)|lung(3)|breast(2)|central_nervous_system(1)	9				all cancers(265;0.00142)|Epithelial(280;0.00829)|OV - Ovarian serous cystadenocarcinoma(397;0.077)|STAD - Stomach adenocarcinoma(256;0.248)														---	---	---	---
LPHN2	23266	broad.mit.edu	37	1	82453521	82453521	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:82453521delT	uc001dit.3	+						LPHN2_uc001dis.2_Intron|LPHN2_uc001diu.2_Intron|LPHN2_uc001div.2_Intron|LPHN2_uc009wcd.2_Intron|LPHN2_uc001diw.2_Intron	NM_012302	NP_036434			latrophilin 2 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|latrotoxin receptor activity|sugar binding			ovary(3)|lung(3)|breast(2)|central_nervous_system(1)	9				all cancers(265;0.00142)|Epithelial(280;0.00829)|OV - Ovarian serous cystadenocarcinoma(397;0.077)|STAD - Stomach adenocarcinoma(256;0.248)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	82863567	82863570	+	IGR	DEL	TTTT	-	-	rs6683802		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:82863567_82863570delTTTT								LPHN2 (405461 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	84259638	84259638	+	Intron	DEL	A	-	-	rs111685871		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:84259638delA	uc001diz.3	-											Homo sapiens cDNA clone IMAGE:4815396.																														---	---	---	---
PRKACB	5567	broad.mit.edu	37	1	84684911	84684911	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:84684911delT	uc001djj.2	+						PRKACB_uc001djl.2_Intron|PRKACB_uc010ort.1_Intron|PRKACB_uc001djn.2_Intron|PRKACB_uc010oru.1_Intron|PRKACB_uc001djp.2_Intron|PRKACB_uc001djq.2_Intron|PRKACB_uc010orv.1_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	84745037	84745037	+	IGR	DEL	T	-	-	rs71706750		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:84745037delT								PRKACB (40858 upstream) : SAMD13 (19012 downstream)																																			---	---	---	---
CTBS	1486	broad.mit.edu	37	1	85020568	85020568	+	3'UTR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85020568delT	uc001dka.2	-	7					SPATA1_uc001djz.1_Intron|CTBS_uc001dkc.2_3'UTR|CTBS_uc001dkd.2_3'UTR|CTBS_uc001dkb.2_3'UTR	NM_004388	NP_004379			chitobiase, di-N-acetyl- precursor							lysosome	cation binding				0				all cancers(265;0.00727)|Epithelial(280;0.0192)|OV - Ovarian serous cystadenocarcinoma(397;0.166)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	85043689	85043689	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85043689delT								CTBS (3526 upstream) : C1orf180 (50224 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	85264403	85264403	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85264403delA								SSX2IP (107963 upstream) : LPAR3 (14683 downstream)																																			---	---	---	---
CYR61	3491	broad.mit.edu	37	1	86047289	86047289	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86047289delA	uc001dle.2	+						CYR61_uc001dlg.2_5'Flank|CYR61_uc009wcp.1_5'Flank	NM_001554	NP_001545			cysteine-rich, angiogenic inducer, 61 precursor						cell proliferation|chemotaxis|positive regulation of BMP signaling pathway|positive regulation of cell migration|positive regulation of osteoblast differentiation|positive regulation of osteoblast proliferation|positive regulation of protein kinase activity|positive regulation of protein phosphorylation|positive regulation of transcription from RNA polymerase II promoter|regulation of cell growth|regulation of ERK1 and ERK2 cascade|wound healing, spreading of cells	extracellular region	heparin binding|insulin-like growth factor binding			central_nervous_system(1)	1				all cancers(265;0.0216)|Epithelial(280;0.0441)												OREG0013583	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	87688167	87688169	+	IGR	DEL	TTG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:87688167_87688169delTTG								LOC339524 (53283 upstream) : LMO4 (105982 downstream)																																			---	---	---	---
LMO4	8543	broad.mit.edu	37	1	87806074	87806074	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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	88230192	88230193	+	IGR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:88230192_88230193insA								LMO4 (415589 upstream) : PKN2 (919729 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	88469477	88469477	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:88469477delA								LMO4 (654874 upstream) : PKN2 (680445 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	88555313	88555313	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:88555313delG								LMO4 (740710 upstream) : PKN2 (594609 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	88644933	88644933	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:88644933delA								LMO4 (830330 upstream) : PKN2 (504989 downstream)																																			---	---	---	---
PKN2	5586	broad.mit.edu	37	1	89174611	89174611	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89174611delT	uc001dmn.2	+						PKN2_uc001dmm.1_Intron|PKN2_uc010osp.1_Intron|PKN2_uc010osq.1_Intron|PKN2_uc009wcv.2_Intron	NM_006256	NP_006247			protein kinase N2						signal transduction	cytoplasm	ATP binding|histone deacetylase binding|protein kinase C activity			large_intestine(1)|lung(1)|skin(1)	3		Lung NSC(277;0.123)		all cancers(265;0.0136)|Epithelial(280;0.0301)														---	---	---	---
GBP7	388646	broad.mit.edu	37	1	89632845	89632845	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89632845delG	uc001dna.2	-							NM_207398	NP_997281			guanylate binding protein 4-like							integral to membrane	GTP binding|GTPase activity			ovary(1)|skin(1)	2		Lung NSC(277;0.0908)		all cancers(265;0.00835)|Epithelial(280;0.0322)														---	---	---	---
GBP7	388646	broad.mit.edu	37	1	89638740	89638740	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89638740delT	uc001dna.2	-							NM_207398	NP_997281			guanylate binding protein 4-like							integral to membrane	GTP binding|GTPase activity			ovary(1)|skin(1)	2		Lung NSC(277;0.0908)		all cancers(265;0.00835)|Epithelial(280;0.0322)														---	---	---	---
GBP4	115361	broad.mit.edu	37	1	89655543	89655543	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89655543delA	uc001dnb.2	-							NM_052941	NP_443173			guanylate binding protein 4							cytoplasm	GTP binding|GTPase activity				0				all cancers(265;0.00723)|Epithelial(280;0.0291)														---	---	---	---
LRRC8B	23507	broad.mit.edu	37	1	90033299	90033300	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:90033299_90033300insA	uc001dni.2	+						LRRC8B_uc001dnh.2_Intron|LRRC8B_uc001dnj.2_Intron	NM_001134476	NP_001127948			leucine rich repeat containing 8 family, member							integral to membrane				ovary(2)	2		all_lung(203;0.17)		all cancers(265;0.00515)|Epithelial(280;0.0241)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	90776664	90776665	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:90776664_90776665delTT								ZNF326 (282570 upstream) : BARHL2 (400915 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	91071781	91071781	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91071781delA								ZNF326 (577687 upstream) : BARHL2 (105799 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	91340239	91340240	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91340239_91340240insT								BARHL2 (157445 upstream) : ZNF644 (40620 downstream)																																			---	---	---	---
TGFBR3	7049	broad.mit.edu	37	1	92162392	92162392	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92162392delT	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)														---	---	---	---
RPL5	6125	broad.mit.edu	37	1	93301568	93301569	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93301568_93301569insT	uc001doz.2	+						FAM69A_uc001dpc.2_Intron|RPL5_uc001dpa.2_Intron|RPL5_uc001dpb.2_Intron|RPL5_uc001dpd.2_5'Flank|SNORD21_uc001dpe.2_5'Flank	NM_000969	NP_000960			ribosomal protein L5						endocrine pancreas development|ribosomal large subunit biogenesis|rRNA processing|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit|nucleolus	5S rRNA binding|protein binding|structural constituent of ribosome				0		all_lung(203;0.00265)|Lung NSC(277;0.0056)|all_neural(321;0.185)|Melanoma(281;0.192)|Glioma(108;0.203)		GBM - Glioblastoma multiforme(16;0.000305)|all cancers(265;0.000343)|Epithelial(280;0.0927)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	93481503	93481503	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93481503delT								FAM69A (54424 upstream) : MTF2 (63289 downstream)																																			---	---	---	---
TMED5	50999	broad.mit.edu	37	1	93639521	93639522	+	Intron	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93639521_93639522delTG	uc001dpn.2	-						TMED5_uc001dpo.2_Intron|TMED5_uc001dpp.2_Intron	NM_016040	NP_057124			transmembrane emp24 protein transport domain						transport	endoplasmic reticulum membrane|ER-Golgi intermediate compartment|integral to membrane				ovary(1)	1		all_lung(203;0.0223)|Lung NSC(277;0.071)|Melanoma(281;0.147)|Glioma(108;0.188)		all cancers(265;0.00108)|GBM - Glioblastoma multiforme(16;0.00407)|Epithelial(280;0.0797)														---	---	---	---
BCAR3	8412	broad.mit.edu	37	1	94141263	94141263	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94141263delG	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	94233826	94233827	+	Intron	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94233826_94233827delTG	uc001dqb.2	-						uc001dqd.1_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)														---	---	---	---
ALG14	199857	broad.mit.edu	37	1	95539902	95539903	+	5'Flank	INS	-	T	T	rs10654501		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:95539902_95539903insT	uc001dra.2	-							NM_144988	NP_659425			asparagine-linked glycosylation 14 homolog						dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|integral to membrane	N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase activity				0		all_lung(203;0.0232)|Lung NSC(277;0.0739)		all cancers(265;0.0615)|Epithelial(280;0.139)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	96432551	96432551	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:96432551delT								RWDD3 (719778 upstream) : PTBP2 (754624 downstream)																																			---	---	---	---
DPYD	1806	broad.mit.edu	37	1	97596707	97596707	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:97596707delA	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	97893253	97893253	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:97893253delA	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	98190474	98190475	+	Intron	DEL	AG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:98190474_98190475delAG	uc001drv.2	-						DPYD_uc010oub.1_Intron|DPYD_uc001drw.2_Intron	NM_000110	NP_000101			dihydropyrimidine dehydrogenase isoform 1						'de novo' pyrimidine base biosynthetic process|purine base catabolic process|thymidine catabolic process|thymine catabolic process|UMP biosynthetic process|uracil catabolic process	cytosol	4 iron, 4 sulfur cluster binding|dihydroorotate oxidase activity|dihydropyrimidine dehydrogenase (NADP+) activity|electron carrier activity|flavin adenine dinucleotide binding|metal ion binding|NADP binding|protein homodimerization activity			ovary(3)|skin(3)|breast(2)	8		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Enfuvirtide(DB00109)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	98652749	98652749	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:98652749delT								MIR137 (141022 upstream) : SNX7 (474487 downstream)																																			---	---	---	---
SNX7	51375	broad.mit.edu	37	1	99163913	99163913	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:99163913delT	uc010ouc.1	+						SNX7_uc001dsa.2_Intron|SNX7_uc010oud.1_Intron	NM_015976	NP_057060			sorting nexin 7 isoform a						cell communication|protein transport	cytoplasmic vesicle membrane	phosphatidylinositol binding|protein binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)	3		all_epithelial(167;7.64e-07)|all_lung(203;0.0006)|Lung NSC(277;0.00137)		Epithelial(280;0.0521)|all cancers(265;0.0687)|COAD - Colon adenocarcinoma(174;0.15)|Lung(183;0.207)|Colorectal(170;0.234)														---	---	---	---
AGL	178	broad.mit.edu	37	1	100387359	100387359	+	3'UTR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100387359delT	uc001dsi.1	+	34					AGL_uc001dsj.1_3'UTR|AGL_uc001dsk.1_3'UTR|AGL_uc001dsl.1_3'UTR|AGL_uc001dsm.1_3'UTR|AGL_uc001dsn.1_3'UTR	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)														---	---	---	---
LRRC39	127495	broad.mit.edu	37	1	100624001	100624001	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100624001delT	uc001dsw.1	-						LRRC39_uc001dsx.1_Intron|LRRC39_uc001dsy.1_Intron|LRRC39_uc001dsz.1_Intron	NM_144620	NP_653221			leucine rich repeat containing 39											ovary(2)|skin(1)	3		all_epithelial(167;0.000542)|all_lung(203;0.0154)|Lung NSC(277;0.0155)		Epithelial(280;0.0826)|all cancers(265;0.135)|COAD - Colon adenocarcinoma(174;0.148)|Lung(183;0.195)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	100783116	100783116	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100783116delA								RTCD1 (24793 upstream) : CDC14A (27468 downstream)																																			---	---	---	---
EXTL2	2135	broad.mit.edu	37	1	101338119	101338119	+	3'UTR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:101338119delA	uc001dtk.1	-	5					EXTL2_uc001dtl.1_3'UTR|EXTL2_uc010ouk.1_3'UTR|EXTL2_uc001dtm.1_3'UTR	NM_001439	NP_001430			exostoses-like 2						N-acetylglucosamine metabolic process|UDP-N-acetylgalactosamine metabolic process	extracellular region|integral to membrane|intrinsic to endoplasmic reticulum membrane	alpha-1,4-N-acetylgalactosaminyltransferase activity|glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|metal ion binding			skin(1)	1		all_epithelial(167;2.48e-06)|all_lung(203;0.000414)|Lung NSC(277;0.000946)		Epithelial(280;0.0425)|all cancers(265;0.0628)|COAD - Colon adenocarcinoma(174;0.148)|Colorectal(144;0.167)|Lung(183;0.195)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	101836526	101836526	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:101836526delT								S1PR1 (129450 upstream) : OLFM3 (431601 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	101954245	101954245	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:101954245delT								S1PR1 (247169 upstream) : OLFM3 (313882 downstream)																																			---	---	---	---
OLFM3	118427	broad.mit.edu	37	1	102459510	102459511	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:102459510_102459511delAA	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	102500525	102500526	+	IGR	INS	-	TGTG	TGTG	rs138832420	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:102500525_102500526insTGTG								OLFM3 (37735 upstream) : COL11A1 (841498 downstream)																																			---	---	---	---
COL11A1	1301	broad.mit.edu	37	1	103364485	103364485	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:103364485delT	uc001dul.2	-						COL11A1_uc001duk.2_Intron|COL11A1_uc001dum.2_Intron|COL11A1_uc001dun.2_Intron|COL11A1_uc009weh.2_Intron	NM_001854	NP_001845			alpha 1 type XI collagen isoform A						collagen fibril organization|detection of mechanical stimulus involved in sensory perception of sound|visual perception	collagen type XI	extracellular matrix binding|extracellular matrix structural constituent|protein binding, bridging			ovary(6)|breast(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	12		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	103741398	103741399	+	IGR	DEL	AG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:103741398_103741399delAG								COL11A1 (167346 upstream) : RNPC3 (327179 downstream)																																			---	---	---	---
AMY2B	280	broad.mit.edu	37	1	104148727	104148727	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:104148727delA	uc001dus.1	+											Homo sapiens mRNA for KIAA1839 protein, partial cds.						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	104661371	104661371	+	IGR	DEL	A	-	-	rs111679818		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:104661371delA								AMY1A (454199 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	104878461	104878461	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:104878461delT								AMY1A (671289 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	105295244	105295244	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:105295244delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	105527529	105527529	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:105527529delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	106093053	106093053	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:106093053delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	107319516	107319516	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:107319516delA								None (None upstream) : PRMT6 (279751 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	107354872	107354872	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:107354872delA								None (None upstream) : PRMT6 (244395 downstream)																																			---	---	---	---
NTNG1	22854	broad.mit.edu	37	1	107830455	107830456	+	Intron	INS	-	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:107830455_107830456insC	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	107887209	107887209	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:107887209delT	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)														---	---	---	---
VAV3	10451	broad.mit.edu	37	1	108396586	108396586	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:108396586delT	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	108728319	108728319	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:108728319delA	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	108759110	108759110	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:108759110delC								SLC25A24 (16136 upstream) : NBPF4 (6853 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	109098328	109098328	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109098328delT								NBPF6 (85069 upstream) : FAM102B (4643 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	109596971	109596972	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109596971_109596972delAA								WDR47 (12121 upstream) : TAF13 (10026 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	109784407	109784410	+	IGR	DEL	TTTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109784407_109784410delTTTT								SARS (3622 upstream) : CELSR2 (8231 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	109988882	109988882	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109988882delA								PSMA5 (19845 upstream) : SYPL2 (20218 downstream)																																			---	---	---	---
UBL4B	164153	broad.mit.edu	37	1	110654377	110654377	+	5'Flank	DEL	A	-	-	rs72125367		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110654377delA	uc001dzc.2	+							NM_203412	NP_981957			ubiquitin-like 4B							cytoplasm				ovary(1)	1		all_cancers(81;1.14e-05)|all_epithelial(167;3.23e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0236)|all cancers(265;0.0823)|Epithelial(280;0.0917)|Colorectal(144;0.109)|LUSC - Lung squamous cell carcinoma(189;0.134)														---	---	---	---
DRAM2	128338	broad.mit.edu	37	1	111667640	111667640	+	Intron	DEL	A	-	-	rs146295738		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111667640delA	uc001ead.3	-						DRAM2_uc001eae.3_Intron|DRAM2_uc009wfy.2_Intron|DRAM2_uc001eaf.3_Intron	NM_178454	NP_848549			transmembrane protein 77						apoptosis|induction of apoptosis	Golgi apparatus|integral to membrane|lysosomal membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	111953278	111953279	+	IGR	DEL	AC	-	-	rs143157380		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111953278_111953279delAC								C1orf88 (57639 upstream) : OVGP1 (3659 downstream)																																			---	---	---	---
OVGP1	5016	broad.mit.edu	37	1	111959290	111959291	+	Intron	DEL	AA	-	-	rs34687982		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111959290_111959291delAA	uc001eba.2	-						OVGP1_uc001eaz.2_Intron|OVGP1_uc010owb.1_Intron	NM_002557	NP_002548			oviductal glycoprotein 1 precursor						chitin catabolic process|female pregnancy|single fertilization	transport vesicle	cation binding|chitinase activity			ovary(4)|large_intestine(1)	5		all_cancers(81;8.18e-06)|all_epithelial(167;5.64e-06)|all_lung(203;0.000152)|Lung NSC(277;0.000302)		Lung(183;0.0253)|Colorectal(144;0.033)|all cancers(265;0.0552)|Epithelial(280;0.0802)|COAD - Colon adenocarcinoma(174;0.123)|LUSC - Lung squamous cell carcinoma(189;0.14)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	112747606	112747606	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112747606delT								KCND3 (215829 upstream) : CTTNBP2NL (191194 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	112820206	112820206	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112820206delA								KCND3 (288429 upstream) : CTTNBP2NL (118594 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	113672521	113672521	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113672521delT								LRIG2 (5179 upstream) : MAGI3 (260954 downstream)																																			---	---	---	---
PTPN22	26191	broad.mit.edu	37	1	114377352	114377352	+	Intron	DEL	A	-	-	rs79608028		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114377352delA	uc001eds.2	-						PTPN22_uc009wgq.2_Intron|PTPN22_uc010owo.1_Intron|PTPN22_uc001edt.2_Intron|PTPN22_uc009wgr.2_Intron|PTPN22_uc009wgs.2_Intron|PTPN22_uc001edu.2_Intron	NM_015967	NP_057051			protein tyrosine phosphatase, non-receptor type						negative regulation of T cell activation|negative regulation of T cell receptor signaling pathway|phosphoanandamide dephosphorylation|regulation of B cell receptor signaling pathway|regulation of natural killer cell proliferation|T cell differentiation	internal side of plasma membrane|nucleus|perinuclear region of cytoplasm	kinase binding|protein tyrosine phosphatase activity|SH3 domain binding			kidney(2)|lung(1)|skin(1)	4	Lung SC(450;0.184)	all_cancers(81;1.93e-08)|all_epithelial(167;4.37e-08)|all_lung(203;5.22e-06)|Lung NSC(69;8.94e-06)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
BCL2L15	440603	broad.mit.edu	37	1	114429118	114429118	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114429118delA	uc001edw.2	-						uc001edv.1_Intron|BCL2L15_uc001edx.2_Intron|BCL2L15_uc001edy.2_Intron|BCL2L15_uc001edz.1_Intron	NM_001010922	NP_001010922			pro-apoptotic Bcl-2 protein						apoptosis					ovary(1)	1	Lung SC(450;0.184)	all_cancers(81;3.95e-08)|all_epithelial(167;9.95e-08)|all_lung(203;1.31e-05)|Lung NSC(69;2.46e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
HIPK1	204851	broad.mit.edu	37	1	114491357	114491357	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114491357delT	uc001eem.2	+						HIPK1_uc001eel.2_Intron|HIPK1_uc001een.2_Intron|HIPK1_uc001eeo.2_5'Flank	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)														---	---	---	---
DENND2C	163259	broad.mit.edu	37	1	115097485	115097485	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115097485delT	uc001eez.2	-							NM_198459				DENN/MADD domain containing 2C											skin(3)	3	all_epithelial(7;9.54e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
SYCP1	6847	broad.mit.edu	37	1	115516283	115516283	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115516283delT	uc001efr.2	+						SYCP1_uc010owt.1_Intron|SYCP1_uc001efq.2_Intron|SYCP1_uc009wgw.2_Intron	NM_003176	NP_003167			synaptonemal complex protein 1						cell division|reciprocal meiotic recombination|spermatogenesis|synaptonemal complex assembly		DNA binding			skin(1)	1	Lung SC(450;0.211)	all_cancers(81;8.65e-08)|all_epithelial(167;3.32e-07)|all_lung(203;6.55e-06)|Lung NSC(69;1.11e-05)|Acute lymphoblastic leukemia(138;0.221)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
FAM46C	54855	broad.mit.edu	37	1	118146621	118146621	+	5'Flank	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118146621delC	uc001ehe.2	+							NM_017709	NP_060179			hypothetical protein LOC54855												0	Lung SC(450;0.225)	all_cancers(81;0.000101)|all_lung(203;3.4e-06)|all_epithelial(167;4.98e-06)|Lung NSC(69;2.33e-05)		Lung(183;0.0576)|LUSC - Lung squamous cell carcinoma(189;0.192)|Colorectal(144;0.247)											Multiple Myeloma(3;1.13e-06)			---	---	---	---
Unknown	0	broad.mit.edu	37	1	118220189	118220190	+	IGR	DEL	AA	-	-	rs11365517		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118220189_118220190delAA								FAM46C (49179 upstream) : GDAP2 (185918 downstream)																																			---	---	---	---
SPAG17	200162	broad.mit.edu	37	1	118707031	118707034	+	Intron	DEL	GTCA	-	-	rs143482299		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118707031_118707034delGTCA	uc001ehk.2	-							NM_206996	NP_996879			sperm associated antigen 17							cilium|flagellar axoneme|microtubule				upper_aerodigestive_tract(2)|ovary(2)|large_intestine(1)|skin(1)	6	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)														---	---	---	---
TBX15	6913	broad.mit.edu	37	1	119428337	119428338	+	Intron	DEL	CA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:119428337_119428338delCA	uc001ehl.1	-						TBX15_uc009whj.1_Intron	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	120004263	120004263	+	IGR	DEL	A	-	-	rs145355901		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120004263delA								HSD3B2 (15143 upstream) : HSD3B1 (45563 downstream)																																			---	---	---	---
NOTCH2	4853	broad.mit.edu	37	1	120547404	120547404	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120547404delT	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	121108151	121108152	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:121108151_121108152delTT	uc001eis.2	+							NM_001042758	NP_001036223			SLIT-ROBO Rho GTPase activating protein 2																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	142572257	142572258	+	IGR	INS	-	G	G	rs145671478	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142572257_142572258insG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	142584437	142584438	+	IGR	INS	-	AA	AA	rs141047756		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142584437_142584438insAA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	142613621	142613622	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142613621_142613622delAA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	142796842	142796843	+	Intron	INS	-	T	T	rs145014686	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142796842_142796843insT	uc001eiw.1	+											Homo sapiens PNAS-130 mRNA, complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	142860697	142860697	+	Intron	DEL	A	-	-	rs139169457		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142860697delA	uc001eiw.1	+						uc001ejb.2_Intron|uc001ejd.1_Intron					Homo sapiens PNAS-130 mRNA, complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	143243132	143243133	+	Intron	DEL	AA	-	-	rs71582744		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143243132_143243133delAA	uc001eiw.1	+											Homo sapiens PNAS-130 mRNA, complete cds.																														---	---	---	---
PDE4DIP	9659	broad.mit.edu	37	1	144905993	144905995	+	Intron	DEL	AAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144905993_144905995delAAA	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	144908640	144908641	+	Intron	INS	-	G	G	rs149429786		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144908640_144908641insG	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	144941273	144941273	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144941273delA	uc001elw.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Intron|PDE4DIP_uc001emc.1_Intron|PDE4DIP_uc001emd.1_Intron	NM_014644	NP_055459			phosphodiesterase 4D interacting protein isoform						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)				T	PDGFRB	MPD								---	---	---	---
PDE4DIP	9659	broad.mit.edu	37	1	144990950	144990952	+	Intron	DEL	ATA	-	-	rs145512065		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144990950_144990952delATA	uc001elw.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Intron|PDE4DIP_uc001emc.1_Intron|PDE4DIP_uc001emd.1_Intron|PDE4DIP_uc001emg.1_Intron|PDE4DIP_uc001emh.2_Intron	NM_014644	NP_055459			phosphodiesterase 4D interacting protein isoform						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)				T	PDGFRB	MPD								---	---	---	---
PDE4DIP	9659	broad.mit.edu	37	1	145007452	145007453	+	Intron	INS	-	T	T	rs141963263		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145007452_145007453insT	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	145063046	145063047	+	Intron	INS	-	CTATA	CTATA	rs5777525		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145063046_145063047insCTATA	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001emh.2_Intron					RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0																		---	---	---	---
NBPF9	400818	broad.mit.edu	37	1	145077797	145077797	+	Intron	DEL	A	-	-	rs67787455		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145077797delA	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elo.2_5'Flank|PDE4DIP_uc001emh.2_5'Flank|PDE4DIP_uc001emk.2_5'Flank					RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0																		---	---	---	---
NBPF9	400818	broad.mit.edu	37	1	145180925	145180925	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145180925delG	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron					RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0																		---	---	---	---
NBPF10	100132406	broad.mit.edu	37	1	145419972	145419972	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145419972delT	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	146395722	146395722	+	Intron	DEL	A	-	-	rs142655742	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:146395722delA	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	146639187	146639187	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:146639187delA	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)													---	---	---	---
CHD1L	9557	broad.mit.edu	37	1	146727311	146727311	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:146727311delT	uc001epm.3	+						CHD1L_uc001epn.3_Intron|CHD1L_uc010ozo.1_Intron|CHD1L_uc009wjg.2_Intron|CHD1L_uc009wjh.2_Intron|CHD1L_uc010ozp.1_Intron|CHD1L_uc001epo.3_Intron	NM_004284	NP_004275			chromodomain helicase DNA binding protein						chromatin remodeling|DNA repair	cytoplasm|nucleus|plasma membrane	ATP binding|ATP-dependent DNA helicase activity|DNA binding|protein binding			ovary(3)|lung(2)|upper_aerodigestive_tract(1)	6	all_hematologic(923;0.0487)																	---	---	---	---
LOC200030	200030	broad.mit.edu	37	1	147767193	147767193	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:147767193delC	uc001eqf.2	-						LOC200030_uc010ozz.1_Intron|LOC200030_uc001eqe.2_Intron|LOC200030_uc001eqg.2_Intron	NM_017940	NP_060410			hypothetical protein LOC55672							cytoplasm					0																		---	---	---	---
LOC200030	200030	broad.mit.edu	37	1	148001285	148001286	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148001285_148001286insA	uc001eqf.2	-						LOC200030_uc010ozz.1_Intron|LOC200030_uc001eqe.2_Intron|LOC200030_uc001eqg.2_Intron|FLJ39739_uc001eqo.1_Intron	NM_017940	NP_060410			hypothetical protein LOC55672							cytoplasm					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	148768052	148768052	+	IGR	DEL	C	-	-	rs143218161		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148768052delC								NBPF16 (9741 upstream) : LOC645166 (160234 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	148850329	148850331	+	IGR	DEL	TCG	-	-	rs149713210		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148850329_148850331delTCG								NBPF16 (92018 upstream) : LOC645166 (77955 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	149028755	149028756	+	IGR	DEL	AT	-	-	rs141540912		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149028755_149028756delAT								LOC645166 (75701 upstream) : LOC388692 (250720 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	149234601	149234605	+	IGR	DEL	TTGTG	-	-	rs139770740		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149234601_149234605delTTGTG								LOC645166 (281547 upstream) : LOC388692 (44871 downstream)																																			---	---	---	---
FCGR1C	100132417	broad.mit.edu	37	1	149377284	149377285	+	Intron	DEL	TC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149377284_149377285delTC	uc010pbh.1	+							NR_027484				Homo sapiens cDNA FLJ77773 complete cds, highly similar to Homo sapiens Fc fragment of IgG, high affinity Ia, receptor (CD64) (FCGR1A), mRNA.												0																		---	---	---	---
TARS2	80222	broad.mit.edu	37	1	150462895	150462895	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150462895delT	uc001euq.2	+						TARS2_uc010pcd.1_Intron|TARS2_uc001eur.2_Intron|TARS2_uc009wlt.2_Intron|TARS2_uc009wls.2_Intron	NM_025150	NP_079426			threonyl-tRNA synthetase 2, mitochondrial						threonyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|threonine-tRNA ligase activity			ovary(1)	1	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0757)|all cancers(9;1.51e-21)|BRCA - Breast invasive adenocarcinoma(12;0.000734)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)		L-Threonine(DB00156)													---	---	---	---
GOLPH3L	55204	broad.mit.edu	37	1	150648453	150648454	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150648453_150648454delTT	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)															---	---	---	---
ARNT	405	broad.mit.edu	37	1	150834215	150834215	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150834215delA	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								---	---	---	---
FAM63A	55793	broad.mit.edu	37	1	150974465	150974466	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150974465_150974466delTT	uc001ewf.2	-						FAM63A_uc001ewc.2_Intron|FAM63A_uc010pcm.1_Intron|FAM63A_uc001ewd.2_Intron|FAM63A_uc001ewe.2_Intron|FAM63A_uc010pcn.1_Intron|FAM63A_uc001ewg.2_Intron	NM_018379	NP_001156731			hypothetical protein LOC55793 isoform 1								protein binding			ovary(1)	1	all_lung(15;1.09e-34)|Lung NSC(24;1.1e-30)|Lung SC(34;0.00202)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)															---	---	---	---
GABPB2	126626	broad.mit.edu	37	1	151079397	151079397	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151079397delT	uc001ewr.2	+						GABPB2_uc001ews.2_Intron|GABPB2_uc001ewt.2_Intron	NM_144618	NP_653219			GA repeat binding protein, beta 2						positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	protein heterodimerization activity|transcription regulatory region DNA binding				0				all cancers(107;7.17e-05)|GBM - Glioblastoma multiforme(94;0.000662)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	151993480	151993481	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151993480_151993481insA	uc001ezm.1	+											Homo sapiens cDNA FLJ43896 fis, clone TESTI4009752.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	152019157	152019157	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152019157delT								S100A11 (9646 upstream) : TCHHL1 (37463 downstream)																																			---	---	---	---
FLG	2312	broad.mit.edu	37	1	152291785	152291786	+	Intron	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152291785_152291786delTG	uc001ezu.1	-						uc001ezv.2_Intron	NM_002016	NP_002007			filaggrin						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				---	---	---	---
Unknown	0	broad.mit.edu	37	1	152310417	152310418	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152310417_152310418insT	uc001ezv.2	+											Homo sapiens cDNA FLJ31869 fis, clone NT2RP7002151.																														---	---	---	---
SPRR2D	6703	broad.mit.edu	37	1	153055233	153055233	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153055233delA	uc009wnz.2	-						SPRR2A_uc001fbf.2_Intron|SPRR2A_uc009woa.2_Intron					Homo sapiens cDNA FLJ76407 complete cds, highly similar to Homo sapiens small proline-rich protein 2D (SPRR2D), mRNA.						keratinization	cornified envelope|cytoplasm					0	Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	153419830	153419830	+	IGR	DEL	T	-	-	rs78325760		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153419830delT								S100A7L2 (7327 upstream) : S100A7 (10390 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	153549123	153549123	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153549123delA								S100A2 (10817 upstream) : S100A16 (30244 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	153760425	153760425	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153760425delA								SLC27A3 (7793 upstream) : GATAD2B (16779 downstream)																																			---	---	---	---
GATAD2B	57459	broad.mit.edu	37	1	153836107	153836107	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153836107delT	uc001fdb.3	-							NM_020699	NP_065750			GATA zinc finger domain containing 2B							nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0	all_lung(78;1.34e-32)|Lung NSC(65;1.04e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)															---	---	---	---
NUP210L	91181	broad.mit.edu	37	1	154094341	154094341	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154094341delA	uc001fdw.2	-						NUP210L_uc009woq.2_Intron|NUP210L_uc010peh.1_Intron	NM_207308	NP_997191			nucleoporin 210kDa-like isoform 1							integral to membrane				skin(5)|ovary(4)|large_intestine(1)|central_nervous_system(1)	11	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)		LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)															---	---	---	---
TPM3	7170	broad.mit.edu	37	1	154154502	154154505	+	Intron	DEL	ATTC	-	-	rs149264272		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154154502_154154505delATTC	uc001fec.1	-						TPM3_uc010pei.1_Intron|TPM3_uc001fdy.1_Intron|TPM3_uc001fdz.1_Intron|TPM3_uc001fea.1_Intron|TPM3_uc001feb.1_Intron|TPM3_uc010pej.1_Intron|TPM3_uc009wor.2_Intron|TPM3_uc001fed.1_Intron	NM_152263	NP_689476			tropomyosin 3 isoform 1						cellular component movement|muscle filament sliding|regulation of muscle contraction	cytosol|muscle thin filament tropomyosin|stress fiber	actin binding		TPM3/ALK(33)	haematopoietic_and_lymphoid_tissue(22)|soft_tissue(11)|skin(1)	34	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)							T	NTRK1|ALK	papillary thyroid|ALCL								---	---	---	---
UBAP2L	9898	broad.mit.edu	37	1	154239234	154239234	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154239234delA	uc001fep.3	+						UBAP2L_uc010pel.1_Intron|UBAP2L_uc001feq.2_Intron|UBAP2L_uc001fer.2_Intron	NM_014847	NP_055662			ubiquitin associated protein 2-like isoform a						binding of sperm to zona pellucida		protein binding			ovary(1)|central_nervous_system(1)	2	all_lung(78;1.09e-30)|Lung NSC(65;1.66e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)															---	---	---	---
UBAP2L	9898	broad.mit.edu	37	1	154242978	154242978	+	3'UTR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154242978delT	uc001fep.3	+	27					UBAP2L_uc010pel.1_Intron|UBAP2L_uc001feq.2_Intron|UBAP2L_uc001fer.2_3'UTR|HAX1_uc001fet.2_5'Flank|HAX1_uc001fes.2_5'Flank|HAX1_uc010peo.1_5'Flank|HAX1_uc009wou.2_5'Flank|HAX1_uc009wov.2_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)															---	---	---	---
TDRD10	126668	broad.mit.edu	37	1	154483088	154483088	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154483088delA	uc009wow.2	+						TDRD10_uc001ffd.2_Intron	NM_001098475	NP_001091945			tudor domain containing 10 isoform a								nucleotide binding|RNA binding			ovary(1)	1	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)															---	---	---	---
ZBTB7B	51043	broad.mit.edu	37	1	154974918	154974919	+	5'Flank	INS	-	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154974918_154974919insG	uc001fgk.3	+						ZBTB7B_uc009wpa.2_5'Flank|ZBTB7B_uc001fgj.3_5'Flank|ZBTB7B_uc010peq.1_5'Flank	NM_015872	NP_056956			zinc finger and BTB domain containing 7B						cell differentiation|ectoderm development|multicellular organismal development|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nucleus	DNA binding|zinc ion binding				0	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)															---	---	---	---
DCST2	127579	broad.mit.edu	37	1	154993288	154993290	+	Intron	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154993288_154993290delTTT	uc001fgm.2	-						DCST2_uc009wpb.2_Intron	NM_144622	NP_653223			DC-STAMP domain containing 2							integral to membrane				ovary(2)|central_nervous_system(1)	3	all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.00034)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	155065180	155065180	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155065180delG								EFNA3 (5174 upstream) : EFNA1 (35169 downstream)																																			---	---	---	---
ASH1L	55870	broad.mit.edu	37	1	155365459	155365459	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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)															---	---	---	---
SYT11	23208	broad.mit.edu	37	1	155851482	155851482	+	3'UTR	DEL	T	-	-	rs79837013		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155851482delT	uc001fmg.2	+	4					SYT11_uc010pgq.1_3'UTR	NM_152280	NP_689493			synaptotagmin XI							cell junction|synaptic vesicle membrane	protein binding|transporter activity			ovary(1)|skin(1)	2	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)		OV - Ovarian serous cystadenocarcinoma(3;0.000162)															---	---	---	---
RXFP4	339403	broad.mit.edu	37	1	155910624	155910625	+	5'Flank	INS	-	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155910624_155910625insG	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)																	---	---	---	---
ARHGEF2	9181	broad.mit.edu	37	1	155946210	155946210	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155946210delC	uc001fmt.2	-						ARHGEF2_uc001fmr.2_Intron|ARHGEF2_uc001fms.2_Intron|ARHGEF2_uc001fmu.2_Intron|ARHGEF2_uc010pgt.1_Intron|ARHGEF2_uc010pgu.1_Intron	NM_001162383	NP_001155855			Rho/Rac guanine nucleotide exchange factor 2						actin filament organization|apoptosis|cell division|cell morphogenesis|induction of apoptosis by extracellular signals|intracellular protein transport|mitosis|negative regulation of microtubule depolymerization|nerve growth factor receptor signaling pathway|positive regulation of NF-kappaB transcription factor activity|regulation of cell proliferation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|Golgi apparatus|microtubule|ruffle membrane|spindle|tight junction	microtubule binding|Rac GTPase binding|Rac guanyl-nucleotide exchange factor activity|zinc ion binding			ovary(1)	1	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)																	---	---	---	---
RAB25	57111	broad.mit.edu	37	1	156036862	156036862	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156036862delA	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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	156484819	156484820	+	IGR	DEL	TC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156484819_156484820delTC								MEF2D (14290 upstream) : IQGAP3 (10378 downstream)																																			---	---	---	---
APOA1BP	128240	broad.mit.edu	37	1	156562641	156562642	+	Intron	INS	-	CA	CA	rs148811958	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156562641_156562642insCA	uc001fph.2	+						APOA1BP_uc001fpg.2_Intron|APOA1BP_uc001fpi.2_Intron|APOA1BP_uc001fpj.2_Intron|APOA1BP_uc001fpk.2_Intron|APOA1BP_uc010php.1_Intron	NM_144772	NP_658985			apolipoprotein A-I binding protein precursor							extracellular region	protein binding			central_nervous_system(1)	1	all_hematologic(923;0.088)|Hepatocellular(266;0.158)																	---	---	---	---
PRCC	5546	broad.mit.edu	37	1	156768109	156768109	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156768109delT	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 								---	---	---	---
NTRK1	4914	broad.mit.edu	37	1	156841200	156841201	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156841200_156841201delAA	uc001fqh.1	+						NTRK1_uc001fqf.1_Intron|NTRK1_uc009wsi.1_Intron|NTRK1_uc001fqi.1_Intron|NTRK1_uc009wsk.1_Intron	NM_002529	NP_002520			neurotrophic tyrosine kinase, receptor, type 1						activation of adenylate cyclase activity|activation of MAPKK activity|activation of phospholipase C activity|cell differentiation|nerve growth factor receptor signaling pathway|nervous system development|phosphatidylinositol-mediated signaling|Ras protein signal transduction	endosome|integral to plasma membrane	ATP binding|neurotrophin receptor activity|transmembrane receptor protein serine/threonine kinase activity|transmembrane receptor protein tyrosine kinase activity			lung(9)|ovary(6)|stomach(1)|central_nervous_system(1)	17	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)				Imatinib(DB00619)			T	TPM3|TPR|TFG	papillary thyroid					TSP Lung(10;0.080)			---	---	---	---
ARHGEF11	9826	broad.mit.edu	37	1	156951985	156951987	+	Intron	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156951985_156951987delTTT	uc001fqo.2	-						ARHGEF11_uc001fqn.2_Intron	NM_014784	NP_055599			Rho guanine nucleotide exchange factor (GEF) 11						actin cytoskeleton organization|apoptosis|axon guidance|cellular component movement|cytokinesis|establishment of cell polarity|G-protein coupled receptor protein signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|positive regulation of transcription, DNA-dependent|regulation of cell growth|regulation of Rho protein signal transduction|Rho protein signal transduction|striated muscle contraction	cytosol|Golgi apparatus|plasma membrane	G-protein-coupled receptor binding|GTPase activator activity|Rho guanyl-nucleotide exchange factor activity|signal transducer activity			ovary(3)|skin(2)|pleura(1)|lung(1)|kidney(1)|pancreas(1)	9	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)																	---	---	---	---
KIRREL	55243	broad.mit.edu	37	1	157987171	157987171	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157987171delT	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)																	---	---	---	---
KIRREL	55243	broad.mit.edu	37	1	158024101	158024101	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158024101delT	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)																	---	---	---	---
CD1E	913	broad.mit.edu	37	1	158326836	158326836	+	3'UTR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158326836delT	uc001fse.2	+	6					CD1E_uc001fsd.2_3'UTR|CD1E_uc001fsk.2_3'UTR|CD1E_uc001fsj.2_3'UTR|CD1E_uc001fsc.2_3'UTR|CD1E_uc010pig.1_RNA|CD1E_uc001fsa.2_3'UTR|CD1E_uc001fsf.2_3'UTR|CD1E_uc001fry.2_3'UTR|CD1E_uc001fsg.2_3'UTR|CD1E_uc001fsh.2_3'UTR|CD1E_uc001fsi.2_3'UTR|CD1E_uc009wsv.2_3'UTR|CD1E_uc001frz.2_3'UTR|CD1E_uc009wsw.2_3'UTR	NM_030893	NP_112155			CD1E antigen isoform a precursor						antigen processing and presentation|immune response	early endosome|Golgi membrane|integral to plasma membrane|late endosome|lysosomal lumen				skin(3)	3	all_hematologic(112;0.0378)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	158494281	158494281	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158494281delA								OR10R2 (43607 upstream) : OR6Y1 (22639 downstream)																																			---	---	---	---
IFI16	3428	broad.mit.edu	37	1	158990400	158990400	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158990400delT	uc001ftg.2	+						IFI16_uc010pis.1_Intron	NM_005531	NP_005522			interferon, gamma-inducible protein 16						cell proliferation|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|monocyte differentiation|negative regulation of transcription, DNA-dependent|response to virus|transcription, DNA-dependent	cytoplasm|nuclear speck|nucleolus	double-stranded DNA binding|protein binding			ovary(1)	1	all_hematologic(112;0.0429)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	159717642	159717643	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159717642_159717643insT								CRP (33263 upstream) : DUSP23 (33116 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	160871980	160871983	+	IGR	DEL	GAGA	-	-	rs10700415		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160871980_160871983delGAGA								ITLN1 (17020 upstream) : ITLN2 (42834 downstream)																																			---	---	---	---
FCGR3B	2215	broad.mit.edu	37	1	161594823	161594823	+	Intron	DEL	A	-	-	rs66963969		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161594823delA	uc009wul.2	-							NM_000570	NP_000561			low affinity immunoglobulin gamma Fc region						immune response	anchored to membrane|extracellular region|plasma membrane	IgG binding|receptor activity				0	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Immune globulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)													---	---	---	---
FCRLB	127943	broad.mit.edu	37	1	161690064	161690064	+	5'Flank	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161690064delA	uc001gbh.2	+						FCRLB_uc009wus.2_5'Flank|FCRLB_uc001gbj.2_5'Flank|FCRLB_uc001gbk.2_5'Flank|FCRLB_uc001gbl.2_5'Flank|FCRLB_uc001gbm.2_5'Flank|FCRLB_uc001gbi.2_5'Flank	NM_001002901	NP_001002901			Fc receptor-like B							endoplasmic reticulum					0	all_hematologic(112;0.0359)		BRCA - Breast invasive adenocarcinoma(70;0.00634)															---	---	---	---
OLFML2B	25903	broad.mit.edu	37	1	161995690	161995690	+	5'Flank	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161995690delG	uc001gbu.2	-						OLFML2B_uc010pkq.1_5'Flank	NM_015441	NP_056256			olfactomedin-like 2B precursor											skin(1)	1	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.0172)															---	---	---	---
NOS1AP	9722	broad.mit.edu	37	1	162253361	162253361	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162253361delC	uc001gbv.2	+						NOS1AP_uc010pkr.1_Intron|NOS1AP_uc010pks.1_Intron|NOS1AP_uc001gbw.2_Intron	NM_014697	NP_055512			nitric oxide synthase 1 (neuronal) adaptor						regulation of apoptosis|regulation of nitric oxide biosynthetic process|regulation of nitric-oxide synthase activity		nitric-oxide synthase binding|PDZ domain binding			lung(2)|upper_aerodigestive_tract(1)	3	all_hematologic(112;0.203)		BRCA - Breast invasive adenocarcinoma(70;0.0537)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	162505692	162505692	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162505692delA								UHMK1 (11848 upstream) : UAP1 (25604 downstream)																																			---	---	---	---
UAP1	6675	broad.mit.edu	37	1	162558289	162558289	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162558289delT	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	162979045	162979045	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162979045delA								C1orf110 (140440 upstream) : RGS4 (59351 downstream)																																			---	---	---	---
RGS4	5999	broad.mit.edu	37	1	163038839	163038839	+	5'UTR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:163038839delT	uc009wuy.2	+	1					RGS4_uc001gcl.3_Intron|RGS4_uc009wuz.2_5'Flank|RGS4_uc009wva.2_5'Flank	NM_005613	NP_005604			regulator of G-protein signaling 4 isoform 2						inactivation of MAPK activity|regulation of G-protein coupled receptor protein signaling pathway	plasma membrane	calmodulin binding|GTPase activator activity|signal transducer activity			ovary(2)|central_nervous_system(1)	3																OREG0013952	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	163081561	163081562	+	IGR	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:163081561_163081562delTG								RGS4 (34970 upstream) : RGS5 (30536 downstream)																																			---	---	---	---
NUF2	83540	broad.mit.edu	37	1	163299948	163299949	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:163299948_163299949insA	uc001gcq.1	+						NUF2_uc001gcp.2_Intron|NUF2_uc001gcr.1_Intron|NUF2_uc009wvc.1_Intron	NM_145697	NP_663735			NUF2, NDC80 kinetochore complex component						cell division|chromosome segregation|mitotic prometaphase	condensed chromosome kinetochore|cytosol|Ndc80 complex|nucleus	protein binding			ovary(3)|skin(1)	4	all_hematologic(923;0.101)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	163471832	163471832	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:163471832delT								NUF2 (146279 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	164451497	164451497	+	IGR	DEL	A	-	-	rs76576249		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:164451497delA								None (None upstream) : PBX1 (77305 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	164483407	164483407	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:164483407delA								None (None upstream) : PBX1 (45395 downstream)																																			---	---	---	---
PBX1	5087	broad.mit.edu	37	1	164553601	164553602	+	Intron	DEL	AG	-	-	rs72455099		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:164553601_164553602delAG	uc001gct.2	+						PBX1_uc010pku.1_Intron|PBX1_uc010pkv.1_Intron|PBX1_uc001gcs.2_Intron	NM_002585	NP_002576			pre-B-cell leukemia homeobox 1						negative regulation of sequence-specific DNA binding transcription factor activity|sex differentiation|steroid biosynthetic process	cytoplasm|nucleus	sequence-specific DNA binding transcription factor activity|transcription factor binding		EWSR1/PBX1(3)	soft_tissue(3)|lung(1)|skin(1)	5								T	TCF3|EWSR1	pre B-ALL|myoepithelioma								---	---	---	---
Unknown	0	broad.mit.edu	37	1	165085518	165085523	+	IGR	DEL	CTCCTC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165085518_165085523delCTCCTC								PBX1 (231218 upstream) : LMX1A (85582 downstream)																																			---	---	---	---
LMX1A	4009	broad.mit.edu	37	1	165314757	165314770	+	Intron	DEL	CACCCACCAAAACA	-	-	rs66654553		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165314757_165314770delCACCCACCAAAACA	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)																	---	---	---	---
LOC400794	400794	broad.mit.edu	37	1	165450935	165450938	+	Intron	DEL	AGGA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165450935_165450938delAGGA	uc001gdc.2	-						LOC400794_uc001gdd.2_Intron	NR_026744				Homo sapiens cDNA FLJ35813 fis, clone TESTI2006067.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	166500916	166500917	+	IGR	DEL	TT	-	-	rs34779041		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166500916_166500917delTT								FAM78B (364710 upstream) : FMO9P (72236 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	166759921	166759921	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166759921delT								FMO9P (165450 upstream) : POGK (48803 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	167586956	167586956	+	IGR	DEL	C	-	-	rs76226400		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167586956delC								CREG1 (63900 upstream) : RCSD1 (12518 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	168600957	168600958	+	IGR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168600957_168600958insA								XCL1 (49642 upstream) : DPT (63749 downstream)																																			---	---	---	---
DPT	1805	broad.mit.edu	37	1	168698925	168698926	+	5'Flank	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168698925_168698926delTT	uc001gfp.2	-							NM_001937	NP_001928			dermatopontin precursor						cell adhesion	extracellular space|proteinaceous extracellular matrix				ovary(1)	1	all_hematologic(923;0.208)																	---	---	---	---
NME7	29922	broad.mit.edu	37	1	169140287	169140287	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169140287delA	uc001gfu.2	-						NME7_uc010plq.1_Intron|NME7_uc001gft.2_Intron	NM_013330	NP_037462			nucleoside diphosphate kinase 7 isoform a						CTP biosynthetic process|GTP biosynthetic process|UTP biosynthetic process	centrosome	ATP binding|metal ion binding|nucleoside diphosphate kinase activity			central_nervous_system(1)	1	all_hematologic(923;0.208)																	---	---	---	---
SELP	6403	broad.mit.edu	37	1	169585115	169585115	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169585115delT	uc001ggi.3	-						SELP_uc001ggh.2_Intron|SELP_uc009wvr.2_Intron	NM_003005	NP_002996			selectin P precursor						platelet activation|platelet degranulation|positive regulation of platelet activation	external side of plasma membrane|extracellular space|integral to plasma membrane|membrane fraction|platelet alpha granule membrane|platelet dense granule membrane|soluble fraction	fucose binding|glycosphingolipid binding|heparin binding|lipopolysaccharide binding|oligosaccharide binding|sialic acid binding			ovary(2)|skin(2)	4	all_hematologic(923;0.208)				Clopidogrel(DB00758)|Heparin(DB01109)|Tirofiban(DB00775)													---	---	---	---
SELL	6402	broad.mit.edu	37	1	169672196	169672196	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169672196delA	uc001ggk.2	-						C1orf112_uc001ggj.2_Intron|SELL_uc010pls.1_Intron|SELL_uc001ggl.1_Intron	NM_000655	NP_000646			selectin L precursor						blood coagulation|cell adhesion|leukocyte migration|regulation of immune response	integral to plasma membrane	glycosphingolipid binding|heparin binding|protease binding|sugar binding				0	all_hematologic(923;0.208)																	---	---	---	---
C1orf112	55732	broad.mit.edu	37	1	169817057	169817057	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169817057delA	uc001ggp.2	+						C1orf112_uc001ggj.2_Intron|C1orf112_uc001ggq.2_Intron|C1orf112_uc009wvt.2_Intron|C1orf112_uc009wvu.1_Intron|C1orf112_uc001ggr.2_Intron|C1orf112_uc010plv.1_Intron	NM_018186	NP_060656			hypothetical protein LOC55732												0	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)																	---	---	---	---
FMO3	2328	broad.mit.edu	37	1	171086114	171086115	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171086114_171086115insT	uc001ghi.2	+						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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	171643037	171643037	+	IGR	DEL	A	-	-	rs113896518		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171643037delA								MYOC (21214 upstream) : VAMP4 (26261 downstream)																																			---	---	---	---
DNM3	26052	broad.mit.edu	37	1	171855675	171855675	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171855675delT	uc001gie.2	+						DNM3_uc001gid.3_Intron|DNM3_uc009wwb.2_Intron|DNM3_uc001gif.2_Intron	NM_015569	NP_056384			dynamin 3 isoform a						endocytosis|filopodium assembly|synapse assembly	dendritic spine|microtubule|perinuclear region of cytoplasm|postsynaptic density	GTP binding|GTPase activity|protein binding			breast(1)	1																		---	---	---	---
DNM3	26052	broad.mit.edu	37	1	171972861	171972885	+	Intron	DEL	GAATAATTTATTGCCTATTGACATA	-	-	rs113762623		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171972861_171972885delGAATAATTTATTGCCTATTGACATA	uc001gie.2	+						DNM3_uc001gid.3_Intron|DNM3_uc009wwb.2_Intron|DNM3_uc001gif.2_Intron	NM_015569	NP_056384			dynamin 3 isoform a						endocytosis|filopodium assembly|synapse assembly	dendritic spine|microtubule|perinuclear region of cytoplasm|postsynaptic density	GTP binding|GTPase activity|protein binding			breast(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	172496703	172496706	+	IGR	DEL	AAAC	-	-	rs36166947		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172496703_172496706delAAAC								C1orf105 (58738 upstream) : C1orf9 (5554 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	172825869	172825869	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172825869delA								FASLG (189859 upstream) : TNFSF18 (184491 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	173657616	173657617	+	IGR	INS	-	CT	CT			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173657616_173657617insCT								ANKRD45 (18615 upstream) : KLHL20 (26463 downstream)																																			---	---	---	---
RC3H1	149041	broad.mit.edu	37	1	173930736	173930736	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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																		---	---	---	---
RABGAP1L	9910	broad.mit.edu	37	1	174491217	174491218	+	Intron	DEL	AA	-	-	rs72074759		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:174491217_174491218delAA	uc001gjx.2	+						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																		---	---	---	---
RFWD2	64326	broad.mit.edu	37	1	175949820	175949820	+	Intron	DEL	T	-	-	rs79160076		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175949820delT	uc001gku.1	-						RFWD2_uc001gkv.1_Intron|RFWD2_uc001gkw.1_Intron|RFWD2_uc009wwv.2_Intron|RFWD2_uc001gkt.1_Intron	NM_022457	NP_071902			ring finger and WD repeat domain 2 isoform a						DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest	centrosome|cytosol|focal adhesion|nuclear speck	protein binding|ubiquitin-protein ligase activity|zinc ion binding				0																		---	---	---	---
RFWD2	64326	broad.mit.edu	37	1	176081909	176081909	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176081909delT	uc001gku.1	-						RFWD2_uc001gkv.1_Intron|RFWD2_uc001gkw.1_Intron|RFWD2_uc009wwv.2_Intron|RFWD2_uc001gkt.1_Intron	NM_022457	NP_071902			ring finger and WD repeat domain 2 isoform a						DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest	centrosome|cytosol|focal adhesion|nuclear speck	protein binding|ubiquitin-protein ligase activity|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	176200270	176200273	+	IGR	DEL	TTTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176200270_176200273delTTTT								RFWD2 (23900 upstream) : PAPPA2 (232034 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	176231630	176231635	+	IGR	DEL	TTTTTG	-	-	rs12117041		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176231630_176231635delTTTTTG								RFWD2 (55260 upstream) : PAPPA2 (200672 downstream)																																			---	---	---	---
ASTN1	460	broad.mit.edu	37	1	176980964	176980964	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176980964delA	uc001glc.2	-						ASTN1_uc001glb.1_Intron|ASTN1_uc001gld.1_Intron|ASTN1_uc009wwx.1_Intron|ASTN1_uc001gle.3_Intron	NM_004319	NP_004310			astrotactin isoform 1						cell migration|neuron cell-cell adhesion	integral to membrane				ovary(6)|skin(5)|central_nervous_system(2)|large_intestine(1)|lung(1)	15																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	177688289	177688289	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177688289delG								FAM5B (436732 upstream) : SEC16B (209200 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	177810854	177810854	+	IGR	DEL	A	-	-	rs34769367		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177810854delA								FAM5B (559297 upstream) : SEC16B (86635 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	177881788	177881788	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177881788delT								FAM5B (630231 upstream) : SEC16B (15701 downstream)																																			---	---	---	---
C1orf49	84066	broad.mit.edu	37	1	178479880	178479880	+	5'Flank	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178479880delA	uc001glt.1	+						C1orf49_uc001glu.1_5'Flank|C1orf49_uc001glv.1_5'Flank|C1orf49_uc001glw.1_5'Flank	NM_032126	NP_115502			hypothetical protein LOC84066							microtubule cytoskeleton					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	178637598	178637599	+	IGR	INS	-	AG	AG	rs56404314		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178637598_178637599insAG								C1orf220 (119574 upstream) : RALGPS2 (56701 downstream)																																			---	---	---	---
ABL2	27	broad.mit.edu	37	1	179095896	179095896	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179095896delA	uc001gmj.3	-						ABL2_uc010pnf.1_Intron|ABL2_uc010png.1_Intron|ABL2_uc010pnh.1_Intron|ABL2_uc009wxe.2_Intron|ABL2_uc001gmg.3_Intron|ABL2_uc001gmi.3_Intron|ABL2_uc001gmh.3_Intron|ABL2_uc010pne.1_Intron|ABL2_uc009wxf.1_Intron|ABL2_uc001gmk.2_Intron	NM_007314	NP_009298			arg tyrosine kinase isoform b						axon guidance|cell adhesion|peptidyl-tyrosine phosphorylation|positive regulation of oxidoreductase activity|signal transduction	cytoskeleton|cytosol	ATP binding|magnesium ion binding|manganese ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding			lung(8)|breast(3)|ovary(2)|central_nervous_system(1)	14					Adenosine triphosphate(DB00171)|Dasatinib(DB01254)			T	ETV6	AML								---	---	---	---
Unknown	0	broad.mit.edu	37	1	179327071	179327072	+	IGR	INS	-	A	A	rs150286989	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179327071_179327072insA								SOAT1 (2619 upstream) : C1orf125 (8035 downstream)																																			---	---	---	---
ACBD6	84320	broad.mit.edu	37	1	180457717	180457717	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180457717delT	uc001gog.2	-							NM_032360	NP_115736			acyl-coenzyme A binding domain containing 6							cytoplasm|nucleus	fatty-acyl-CoA binding			ovary(1)	1																		---	---	---	---
XPR1	9213	broad.mit.edu	37	1	180613592	180613592	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180613592delT	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																		---	---	---	---
CACNA1E	777	broad.mit.edu	37	1	181514237	181514237	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181514237delA	uc001gow.2	+						CACNA1E_uc009wxr.2_Intron|CACNA1E_uc009wxs.2_Intron	NM_000721	NP_000712			calcium channel, voltage-dependent, R type,						energy reserve metabolic process|membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6																		---	---	---	---
CACNA1E	777	broad.mit.edu	37	1	181536795	181536795	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181536795delT	uc001gow.2	+						CACNA1E_uc009wxr.2_Intron|CACNA1E_uc009wxs.2_Intron	NM_000721	NP_000712			calcium channel, voltage-dependent, R type,						energy reserve metabolic process|membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	181789197	181789198	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181789197_181789198insT								CACNA1E (18484 upstream) : ZNF648 (234509 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	182305649	182305649	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182305649delA								ZNF648 (274802 upstream) : GLUL (46020 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	182328594	182328595	+	IGR	DEL	AG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182328594_182328595delAG								ZNF648 (297747 upstream) : GLUL (23074 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	182673659	182673659	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182673659delG								RGS8 (31592 upstream) : NPL (85213 downstream)																																			---	---	---	---
C1orf14	81626	broad.mit.edu	37	1	182881663	182881663	+	Intron	DEL	T	-	-	rs34803527		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182881663delT	uc001gpu.2	-						C1orf14_uc001gpv.2_Intron|C1orf14_uc010pnz.1_Intron|C1orf14_uc001gpw.2_Intron	NM_030933	NP_112195			chromosome 1 open reading frame 14												0				Colorectal(1306;1.64e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00267)														---	---	---	---
NMNAT2	23057	broad.mit.edu	37	1	183221068	183221069	+	3'UTR	DEL	GT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183221068_183221069delGT	uc001gqc.1	-	11					NMNAT2_uc009wye.1_RNA|NMNAT2_uc001gqb.1_3'UTR	NM_015039	NP_055854			nicotinamide mononucleotide adenylyltransferase						water-soluble vitamin metabolic process	Golgi membrane|nucleus	ATP binding|nicotinamide-nucleotide adenylyltransferase activity|nicotinate-nucleotide adenylyltransferase activity			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	184058860	184058860	+	IGR	DEL	A	-	-	rs113802996		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184058860delA								TSEN15 (15519 upstream) : C1orf21 (297290 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	184183174	184183174	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184183174delC								TSEN15 (139833 upstream) : C1orf21 (172976 downstream)																																			---	---	---	---
C1orf26	54823	broad.mit.edu	37	1	185245916	185245916	+	Intron	DEL	T	-	-	rs143251562		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185245916delT	uc001grg.3	+						C1orf26_uc001grh.3_Intron	NM_001105518	NP_001098988			hypothetical protein LOC54823												0																		---	---	---	---
HMCN1	83872	broad.mit.edu	37	1	185928909	185928910	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185928909_185928910delTT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	186177408	186177408	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186177408delA								HMCN1 (17323 upstream) : PRG4 (87997 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	186192132	186192132	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186192132delA								HMCN1 (32047 upstream) : PRG4 (73273 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	186249066	186249067	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186249066_186249067delTT								HMCN1 (88981 upstream) : PRG4 (16338 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	187262687	187262688	+	IGR	DEL	GA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:187262687_187262688delGA								PLA2G4A (304582 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	187695255	187695255	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:187695255delC								PLA2G4A (737150 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	188783822	188783822	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:188783822delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	188829206	188829206	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:188829206delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	189223023	189223028	+	IGR	DEL	TTTTTT	-	-	rs113290842		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:189223023_189223028delTTTTTT								None (None upstream) : FAM5C (843769 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	189580782	189580782	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:189580782delT								None (None upstream) : FAM5C (486015 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	189903975	189903975	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:189903975delA								None (None upstream) : FAM5C (162822 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	189916286	189916286	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:189916286delT								None (None upstream) : FAM5C (150511 downstream)																																			---	---	---	---
FAM5C	339479	broad.mit.edu	37	1	190366023	190366023	+	Intron	DEL	A	-	-	rs68091399		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:190366023delA	uc001gse.1	-						FAM5C_uc010pot.1_Intron	NM_199051	NP_950252			family with sequence similarity 5, member C							extracellular region				lung(2)|ovary(1)|kidney(1)|skin(1)	5	Prostate(682;0.198)																	---	---	---	---
FAM5C	339479	broad.mit.edu	37	1	190420709	190420710	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:190420709_190420710delTT	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	190847642	190847642	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:190847642delG								FAM5C (400883 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	191020788	191020789	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:191020788_191020789delTT								FAM5C (574029 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	191832880	191832880	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:191832880delA								None (None upstream) : RGS18 (294712 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	192155921	192155921	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:192155921delT								RGS18 (978 upstream) : RGS21 (130201 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	192697610	192697611	+	IGR	DEL	GT	-	-	rs61010412		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:192697610_192697611delGT								RGS13 (68223 upstream) : RGS2 (80558 downstream)																																			---	---	---	---
UCHL5	51377	broad.mit.edu	37	1	192997104	192997104	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:192997104delA	uc001gsm.2	-						UCHL5_uc001gsn.2_Intron|UCHL5_uc001gso.2_Intron|UCHL5_uc010pov.1_Intron|UCHL5_uc001gsp.2_Intron|UCHL5_uc001gsq.2_Intron|UCHL5_uc010pow.1_Intron|UCHL5_uc010pox.1_Intron	NM_015984	NP_057068			ubiquitin carboxyl-terminal hydrolase L5						DNA recombination|DNA repair|protein deubiquitination|regulation of proteasomal protein catabolic process|regulation of transcription, DNA-dependent|transcription, DNA-dependent|ubiquitin-dependent protein catabolic process	cytosol|Ino80 complex|proteasome complex	endopeptidase inhibitor activity|omega peptidase activity|proteasome binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			lung(2)|ovary(1)	3																		---	---	---	---
CDC73	79577	broad.mit.edu	37	1	193094121	193094121	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193094121delT	uc001gtb.2	+							NM_024529	NP_078805			parafibromin						cell cycle|histone H2B ubiquitination|histone monoubiquitination|transcription, DNA-dependent	Cdc73/Paf1 complex	protein binding			parathyroid(46)|ovary(1)|breast(1)|pancreas(1)	49														Hyperparathyroidism_Familial_Isolated|Hyperparathyroidism-Jaw_Tumor_Syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	1	193969324	193969324	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193969324delA								CDC73 (745384 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	194531397	194531397	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:194531397delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	194627578	194627579	+	IGR	INS	-	TTTG	TTTG	rs148256071	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:194627578_194627579insTTTG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	195394204	195394205	+	IGR	INS	-	A	A	rs137888484	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:195394204_195394205insA								None (None upstream) : KCNT2 (800708 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	195868336	195868336	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:195868336delT								None (None upstream) : KCNT2 (326577 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	196081576	196081578	+	IGR	DEL	TTC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196081576_196081578delTTC								None (None upstream) : KCNT2 (113335 downstream)																																			---	---	---	---
DENND1B	163486	broad.mit.edu	37	1	197610405	197610405	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197610405delA	uc001guf.3	-						DENND1B_uc010ppe.1_Intron|DENND1B_uc010ppf.1_Intron|DENND1B_uc001gue.3_Intron|DENND1B_uc001gug.3_Intron	NM_144977	NP_659414			DENN/MADD domain containing 1B isoform 2							clathrin-coated vesicle|cytosol	guanyl-nucleotide exchange factor activity				0																		---	---	---	---
NEK7	140609	broad.mit.edu	37	1	198143867	198143867	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:198143867delT	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	198399518	198399518	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:198399518delT								NEK7 (107972 upstream) : ATP6V1G3 (92838 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	198416506	198416506	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:198416506delA								NEK7 (124960 upstream) : ATP6V1G3 (75850 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	199967727	199967727	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:199967727delA								None (None upstream) : NR5A2 (29043 downstream)																																			---	---	---	---
KIF14	9928	broad.mit.edu	37	1	200534856	200534857	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200534856_200534857insA	uc010ppk.1	-						KIF14_uc010ppj.1_Intron	NM_014875	NP_055690			kinesin family member 14						microtubule-based movement	cytoplasm|microtubule|nucleus|spindle	ATP binding|microtubule motor activity|protein binding			breast(3)|ovary(2)|skin(2)	7																		---	---	---	---
CAMSAP1L1	23271	broad.mit.edu	37	1	200816521	200816521	+	Intron	DEL	G	-	-	rs2172666		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200816521delG	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	200828339	200828340	+	3'UTR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200828339_200828340insA	uc001gvl.2	+	18					CAMSAP1L1_uc001gvk.2_3'UTR|CAMSAP1L1_uc001gvm.2_3'UTR	NM_203459	NP_982284			calmodulin regulated spectrin-associated protein							cytoplasm|microtubule	protein binding			ovary(2)|large_intestine(1)|pancreas(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	201408816	201408816	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201408816delA								TNNI1 (9822 upstream) : PHLDA3 (25807 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	201428437	201428437	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201428437delC								TNNI1 (29443 upstream) : PHLDA3 (6186 downstream)																																			---	---	---	---
NAV1	89796	broad.mit.edu	37	1	201637681	201637681	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201637681delG	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	202083017	202083018	+	IGR	INS	-	TGTGTGTG	TGTGTGTG	rs145582764	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202083017_202083018insTGTGTGTG								ELF3 (96711 upstream) : GPR37L1 (9011 downstream)																																			---	---	---	---
LGR6	59352	broad.mit.edu	37	1	202162772	202162773	+	5'Flank	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202162772_202162773delTT	uc001gxu.2	+							NM_001017403	NP_001017403			leucine-rich repeat-containing G protein-coupled							integral to membrane|plasma membrane	protein-hormone receptor activity			large_intestine(4)|ovary(3)|skin(2)|pancreas(1)	10																		---	---	---	---
LGR6	59352	broad.mit.edu	37	1	202259707	202259707	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202259707delA	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																		---	---	---	---
PPP1R12B	4660	broad.mit.edu	37	1	202329305	202329306	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202329305_202329306insT	uc001gya.1	+						PPP1R12B_uc001gxy.2_Intron|PPP1R12B_uc009xad.1_Intron|PPP1R12B_uc009xae.1_Intron|PPP1R12B_uc001gxz.1_Intron	NM_002481	NP_002472			protein phosphatase 1, regulatory (inhibitor)						regulation of muscle contraction|signal transduction	cytoplasm	enzyme activator activity			ovary(3)	3			BRCA - Breast invasive adenocarcinoma(75;0.166)															---	---	---	---
PPP1R12B	4660	broad.mit.edu	37	1	202370325	202370325	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202370325delT	uc001gya.1	+						PPP1R12B_uc001gxy.2_Intron|PPP1R12B_uc009xad.1_Intron|PPP1R12B_uc009xae.1_Intron|PPP1R12B_uc001gxz.1_Intron	NM_002481	NP_002472			protein phosphatase 1, regulatory (inhibitor)						regulation of muscle contraction|signal transduction	cytoplasm	enzyme activator activity			ovary(3)	3			BRCA - Breast invasive adenocarcinoma(75;0.166)															---	---	---	---
PPP1R12B	4660	broad.mit.edu	37	1	202407190	202407190	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202407190delT	uc001gya.1	+						PPP1R12B_uc001gxy.2_Frame_Shift_Del_p.V499fs|PPP1R12B_uc009xad.1_Frame_Shift_Del_p.V305fs|PPP1R12B_uc009xae.1_3'UTR|PPP1R12B_uc001gxz.1_Intron	NM_002481	NP_002472			protein phosphatase 1, regulatory (inhibitor)						regulation of muscle contraction|signal transduction	cytoplasm	enzyme activator activity			ovary(3)	3			BRCA - Breast invasive adenocarcinoma(75;0.166)															---	---	---	---
PPP1R12B	4660	broad.mit.edu	37	1	202427071	202427071	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202427071delA	uc001gya.1	+						PPP1R12B_uc001gxz.1_Intron	NM_002481	NP_002472			protein phosphatase 1, regulatory (inhibitor)						regulation of muscle contraction|signal transduction	cytoplasm	enzyme activator activity			ovary(3)	3			BRCA - Breast invasive adenocarcinoma(75;0.166)															---	---	---	---
PPP1R12B	4660	broad.mit.edu	37	1	202513033	202513033	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202513033delT	uc001gya.1	+						PPP1R12B_uc001gxz.1_Intron|PPP1R12B_uc001gyb.1_Intron|PPP1R12B_uc001gyc.1_Intron	NM_002481	NP_002472			protein phosphatase 1, regulatory (inhibitor)						regulation of muscle contraction|signal transduction	cytoplasm	enzyme activator activity			ovary(3)	3			BRCA - Breast invasive adenocarcinoma(75;0.166)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	202789593	202789594	+	Intron	INS	-	TT	TT			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202789593_202789594insTT	uc001gyh.2	+											Homo sapiens hypothetical protein LOC641515, mRNA (cDNA clone MGC:33633 IMAGE:4827085), complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	203058785	203058785	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203058785delG								MYOG (3408 upstream) : ADORA1 (38051 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	203960762	203960764	+	IGR	DEL	ATT	-	-	rs10900535	by1000genomes;by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203960762_203960764delATT								SNRPE (120484 upstream) : C1orf157 (40811 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	203981755	203981755	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203981755delG								SNRPE (141477 upstream) : C1orf157 (19820 downstream)																																			---	---	---	---
NFASC	23114	broad.mit.edu	37	1	204902875	204902876	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204902875_204902876delAA	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)															---	---	---	---
CNTN2	6900	broad.mit.edu	37	1	205020828	205020829	+	Intron	DEL	TC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205020828_205020829delTC	uc001hbr.2	+						CNTN2_uc001hbq.1_Intron	NM_005076	NP_005067			contactin 2 precursor						axon guidance|clustering of voltage-gated potassium channels	anchored to membrane|juxtaparanode region of axon|myelin sheath|node of Ranvier|synapse part	identical protein binding			ovary(1)	1	all_cancers(21;0.144)|Breast(84;0.0437)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)															---	---	---	---
NUAK2	81788	broad.mit.edu	37	1	205293242	205293242	+	5'Flank	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205293242delT	uc001hce.2	-							NM_030952	NP_112214			NUAK family, SNF1-like kinase, 2						actin cytoskeleton organization|apoptosis|cellular response to glucose starvation|negative regulation of apoptosis		ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(3)|stomach(1)|breast(1)	5	Breast(84;0.186)		BRCA - Breast invasive adenocarcinoma(75;0.117)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	205423656	205423657	+	5'Flank	DEL	GT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205423656_205423657delGT	uc001hco.1	+											Homo sapiens cDNA FLJ38314 fis, clone FCBBF3022765.																														---	---	---	---
SLC45A3	85414	broad.mit.edu	37	1	205621503	205621503	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205621503delA	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 								---	---	---	---
PM20D1	148811	broad.mit.edu	37	1	205805011	205805011	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205805011delT	uc001hdj.2	-						PM20D1_uc009xbr.2_Intron	NM_152491	NP_689704			peptidase M20 domain containing 1 precursor							extracellular region	metal ion binding|peptidase activity			skin(1)	1	Breast(84;0.201)		BRCA - Breast invasive adenocarcinoma(75;0.0252)															---	---	---	---
CTSE	1510	broad.mit.edu	37	1	206328248	206328249	+	Intron	INS	-	A	A	rs150258638	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206328248_206328249insA	uc001hdu.2	+						CTSE_uc001hdv.2_Intron|CTSE_uc010prs.1_Intron	NM_001910	NP_001901			cathepsin E isoform a preproprotein						antigen processing and presentation of exogenous peptide antigen via MHC class II|digestion|proteolysis	endosome	aspartic-type endopeptidase activity			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(75;0.0754)															---	---	---	---
SRGAP2	23380	broad.mit.edu	37	1	206566603	206566604	+	Intron	INS	-	GG	GG	rs148368773		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206566603_206566604insGG	uc001hdy.2	+						SRGAP2_uc009xbt.2_Intron|SRGAP2_uc010prt.1_Intron|SRGAP2_uc001hdx.2_Intron|SRGAP2_uc010pru.1_Intron|SRGAP2_uc010prv.1_Intron	NM_015326	NP_056141			SLIT-ROBO Rho GTPase activating protein 2						axon guidance|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding				0	Breast(84;0.137)																	---	---	---	---
RASSF5	83593	broad.mit.edu	37	1	206699603	206699604	+	Intron	DEL	GT	-	-	rs66799325		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206699603_206699604delGT	uc001hed.2	+						RASSF5_uc001hec.1_Intron|RASSF5_uc001hee.2_Intron	NM_182663	NP_872604			Ras association (RalGDS/AF-6) domain family 5						apoptosis|intracellular signal transduction	cytoplasm|microtubule	metal ion binding|protein binding			ovary(1)	1	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.166)															---	---	---	---
PIGR	5284	broad.mit.edu	37	1	207107219	207107220	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207107219_207107220delTT	uc001hez.2	-						PIGR_uc009xbz.2_Intron	NM_002644	NP_002635			polymeric immunoglobulin receptor precursor							extracellular region|integral to plasma membrane	protein binding			ovary(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
CD46	4179	broad.mit.edu	37	1	207947554	207947554	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207947554delT	uc001hgc.2	+						CD46_uc001hgd.2_Intron|CD46_uc001hge.2_Intron|CD46_uc001hgf.2_Intron|CD46_uc001hgg.2_Intron|CD46_uc001hgh.2_Intron|CD46_uc001hgi.2_Intron|CD46_uc001hgj.2_Intron|CD46_uc001hgk.2_Intron|CD46_uc001hgl.2_Intron|CD46_uc001hgm.2_Intron|CD46_uc001hgn.2_Intron|CD46_uc001hgo.2_Intron|CD46_uc001hgp.2_Intron	NM_002389	NP_002380			CD46 antigen, complement regulatory protein						complement activation, classical pathway|innate immune response|interspecies interaction between organisms|single fertilization	inner acrosomal membrane|integral to plasma membrane	protein binding|receptor activity			large_intestine(2)|lung(1)|central_nervous_system(1)	4																		---	---	---	---
PLXNA2	5362	broad.mit.edu	37	1	208400424	208400424	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208400424delA	uc001hgz.2	-							NM_025179	NP_079455			plexin A2 precursor						axon guidance	integral to membrane|intracellular|plasma membrane				ovary(2)|central_nervous_system(1)	3				OV - Ovarian serous cystadenocarcinoma(81;0.199)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	208441726	208441727	+	IGR	DEL	GT	-	-	rs72366472		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208441726_208441727delGT								PLXNA2 (24061 upstream) : None (None downstream)																																			---	---	---	---
IRF6	3664	broad.mit.edu	37	1	209966562	209966562	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:209966562delT	uc001hhq.1	-						IRF6_uc010psm.1_Intron|IRF6_uc009xct.1_Intron	NM_006147	NP_006138			interferon regulatory factor 6						cell cycle arrest|interferon-gamma-mediated signaling pathway|mammary gland epithelial cell differentiation|negative regulation of cell proliferation|positive regulation of transcription, DNA-dependent|type I interferon-mediated signaling pathway	cytoplasm|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(81;0.0351)											HNSCC(57;0.16)			---	---	---	---
SYT14	255928	broad.mit.edu	37	1	210281974	210281974	+	Intron	DEL	A	-	-	rs141080366		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:210281974delA	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	210386338	210386338	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:210386338delT								SYT14 (48707 upstream) : C1orf133 (18466 downstream)																																			---	---	---	---
HHAT	55733	broad.mit.edu	37	1	210779604	210779604	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:210779604delT	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)														---	---	---	---
RCOR3	55758	broad.mit.edu	37	1	211445871	211445871	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:211445871delT	uc001hig.2	+						RCOR3_uc010psv.1_Intron|RCOR3_uc001hie.2_Intron|RCOR3_uc010psw.1_Intron|RCOR3_uc001hif.2_Intron	NM_018254	NP_060724			REST corepressor 3 isoform d						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(81;0.00961)|all cancers(67;0.0999)|Epithelial(68;0.171)														---	---	---	---
TRAF5	7188	broad.mit.edu	37	1	211508942	211508942	+	Intron	DEL	G	-	-	rs149345244	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:211508942delG	uc001hih.2	+						TRAF5_uc001hii.2_Intron|TRAF5_uc010psx.1_Intron|TRAF5_uc010psy.1_Intron	NM_004619	NP_004610			TNF receptor-associated factor 5						apoptosis|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|regulation of apoptosis	CD40 receptor complex|centrosome|internal side of plasma membrane	protein binding|ubiquitin-protein ligase activity|zinc ion binding			lung(2)|breast(2)|ovary(1)	5				OV - Ovarian serous cystadenocarcinoma(81;0.00946)|all cancers(67;0.0808)|Epithelial(68;0.144)														---	---	---	---
INTS7	25896	broad.mit.edu	37	1	212133854	212133854	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212133854delA	uc001hiw.1	-						INTS7_uc009xdb.1_Intron|INTS7_uc001hix.1_Intron|INTS7_uc001hiy.1_Intron|INTS7_uc010pta.1_Intron	NM_015434	NP_056249			integrator complex subunit 7						snRNA processing	integrator complex	protein binding				0				OV - Ovarian serous cystadenocarcinoma(81;0.00584)|all cancers(67;0.0318)|Epithelial(68;0.0852)														---	---	---	---
DTL	51514	broad.mit.edu	37	1	212272562	212272563	+	Intron	INS	-	TTTG	TTTG	rs138191220	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212272562_212272563insTTTG	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)														---	---	---	---
FLVCR1	28982	broad.mit.edu	37	1	213048258	213048259	+	Intron	INS	-	AC	AC	rs66892422		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:213048258_213048259insAC	uc001hjt.2	+							NM_014053	NP_054772			feline leukemia virus subgroup C cellular						cell death|cellular iron ion homeostasis|heme export|transmembrane transport	integral to plasma membrane	heme transporter activity|protein binding|receptor activity				0				OV - Ovarian serous cystadenocarcinoma(81;0.00733)|all cancers(67;0.013)|GBM - Glioblastoma multiforme(131;0.0845)|Epithelial(68;0.11)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	213528567	213528567	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:213528567delA								RPS6KC1 (81760 upstream) : PROX1 (632719 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	214422458	214422458	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214422458delA								PROX1 (212698 upstream) : SMYD2 (32107 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	214749657	214749657	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214749657delT								PTPN14 (25015 upstream) : CENPF (26875 downstream)																																			---	---	---	---
KCTD3	51133	broad.mit.edu	37	1	215765707	215765708	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215765707_215765708delTT	uc001hks.2	+						KCTD3_uc001hkt.2_Intron|KCTD3_uc010pub.1_Intron|KCTD3_uc009xdn.2_Intron	NM_016121	NP_057205			potassium channel tetramerisation domain							voltage-gated potassium channel complex	protein binding|voltage-gated potassium channel activity			ovary(3)	3				all cancers(67;0.0164)|OV - Ovarian serous cystadenocarcinoma(81;0.019)|GBM - Glioblastoma multiforme(131;0.0862)|Epithelial(68;0.13)														---	---	---	---
USH2A	7399	broad.mit.edu	37	1	216020447	216020447	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216020447delT	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	216295532	216295532	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216295532delT	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	216551083	216551083	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216551083delA	uc001hku.1	-						USH2A_uc001hkv.2_Intron	NM_206933	NP_996816			usherin isoform B						maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)											HNSCC(13;0.011)			---	---	---	---
Unknown	0	broad.mit.edu	37	1	216623259	216623259	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216623259delC								USH2A (26521 upstream) : ESRRG (53329 downstream)																																			---	---	---	---
ESRRG	2104	broad.mit.edu	37	1	216834309	216834309	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216834309delA	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	218141732	218141732	+	IGR	DEL	A	-	-	rs4636531	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:218141732delA								SPATA17 (101230 upstream) : RRP15 (316897 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	218930308	218930308	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:218930308delA								TGFB2 (312349 upstream) : LYPLAL1 (416884 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	219092632	219092633	+	IGR	INS	-	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:219092632_219092633insG								TGFB2 (474673 upstream) : LYPLAL1 (254559 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	219546246	219546247	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:219546246_219546247delAA								LYPLAL1 (160040 upstream) : SLC30A10 (312522 downstream)																																			---	---	---	---
RAB3GAP2	25782	broad.mit.edu	37	1	220379362	220379362	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220379362delA	uc010puk.1	-						RAB3GAP2_uc001hmf.2_Intron|RAB3GAP2_uc001hmg.2_Intron	NM_012414	NP_036546			rab3 GTPase-activating protein, non-catalytic						intracellular protein transport	cytoplasm|soluble fraction	GTPase activator activity|protein heterodimerization activity			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(131;0.0443)														---	---	---	---
MARK1	4139	broad.mit.edu	37	1	220749261	220749261	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220749261delA	uc001hmn.3	+						MARK1_uc001hml.2_Intron|MARK1_uc009xdw.2_Intron|MARK1_uc010pun.1_Intron|MARK1_uc001hmm.3_Intron	NM_018650	NP_061120			MAP/microtubule affinity-regulating kinase 1						intracellular protein kinase cascade	cytoplasm|microtubule cytoskeleton	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(4)|central_nervous_system(2)|skin(2)|stomach(1)|lung(1)	10				GBM - Glioblastoma multiforme(131;0.0407)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	221231946	221231946	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:221231946delT								HLX (173548 upstream) : LOC400804 (271324 downstream)																																			---	---	---	---
HHIPL2	79802	broad.mit.edu	37	1	222701953	222701953	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:222701953delA	uc001hnh.1	-							NM_024746	NP_079022			HHIP-like 2 precursor						carbohydrate metabolic process	extracellular region	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor|quinone binding			ovary(1)	1				GBM - Glioblastoma multiforme(131;0.0185)														---	---	---	---
HHIPL2	79802	broad.mit.edu	37	1	222722460	222722460	+	5'Flank	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:222722460delA	uc001hnh.1	-							NM_024746	NP_079022			HHIP-like 2 precursor						carbohydrate metabolic process	extracellular region	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor|quinone binding			ovary(1)	1				GBM - Glioblastoma multiforme(131;0.0185)														---	---	---	---
CAPN8	388743	broad.mit.edu	37	1	223804063	223804064	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223804063_223804064insT	uc009xee.2	-							NM_001143962	NP_001137434			calpain 8						proteolysis	Golgi apparatus	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	224200310	224200314	+	IGR	DEL	ACTCT	-	-	rs148290968		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:224200310_224200314delACTCT								TP53BP2 (166636 upstream) : FBXO28 (101477 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	224413658	224413658	+	IGR	DEL	T	-	-	rs11388032		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:224413658delT								DEGS1 (32518 upstream) : NVL (1379 downstream)																																			---	---	---	---
NVL	4931	broad.mit.edu	37	1	224488980	224488980	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:224488980delT	uc001hok.2	-						NVL_uc001hol.2_Intron|NVL_uc010pvd.1_Intron|NVL_uc010pve.1_Intron|NVL_uc010pvf.1_Intron	NM_002533	NP_002524			nuclear VCP-like isoform 1							aggresome|cytoplasm|nucleolus	ATP binding|nucleoside-triphosphatase activity			skin(2)	2				GBM - Glioblastoma multiforme(131;0.00501)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	225010604	225010604	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225010604delT								CNIH3 (82355 upstream) : DNAH14 (106752 downstream)																																			---	---	---	---
DNAH14	127602	broad.mit.edu	37	1	225253142	225253142	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225253142delA	uc001how.2	+							NM_001373	NP_001364			dynein, axonemal, heavy polypeptide 14 isoform						microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|microtubule motor activity			central_nervous_system(1)	1																		---	---	---	---
ENAH	55740	broad.mit.edu	37	1	225718042	225718042	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225718042delA	uc001hpc.1	-						ENAH_uc001hpd.1_Intron	NM_001008493	NP_001008493			enabled homolog isoform a						axon guidance|intracellular transport|T cell receptor signaling pathway	cytosol|filopodium|focal adhesion|lamellipodium|synapse	actin binding|SH3 domain binding|WW domain binding			ovary(1)|skin(1)	2	Breast(184;0.206)			GBM - Glioblastoma multiforme(131;0.19)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	226399624	226399624	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226399624delA								ACBD3 (25201 upstream) : MIXL1 (11759 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	226518885	226518886	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226518885_226518886delTT								LIN9 (21315 upstream) : PARP1 (29507 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	226522848	226522848	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226522848delT								LIN9 (25278 upstream) : PARP1 (25545 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	226635209	226635209	+	IGR	DEL	T	-	-	rs79892191		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226635209delT								PARP1 (39408 upstream) : C1orf95 (101292 downstream)																																			---	---	---	---
ITPKB	3707	broad.mit.edu	37	1	226909518	226909518	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226909518delT	uc010pvo.1	-						ITPKB_uc001hqh.2_Intron	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)																---	---	---	---
CDC42BPA	8476	broad.mit.edu	37	1	227203389	227203390	+	Intron	INS	-	A	A	rs148877902	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227203389_227203390insA	uc001hqr.2	-						CDC42BPA_uc001hqq.2_Intron|CDC42BPA_uc001hqs.2_Intron|CDC42BPA_uc009xes.2_Intron|CDC42BPA_uc010pvs.1_Intron|CDC42BPA_uc001hqp.2_Intron|CDC42BPA_uc001hqt.2_Intron	NM_003607	NP_003598			CDC42-binding protein kinase alpha isoform B						actin cytoskeleton reorganization|intracellular signal transduction	cell leading edge|cell-cell junction|cytoplasm	ATP binding|identical protein binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity			lung(6)|breast(2)|stomach(1)|ovary(1)|pancreas(1)	11		all_cancers(173;0.156)|Prostate(94;0.0792)																---	---	---	---
CDC42BPA	8476	broad.mit.edu	37	1	227292663	227292663	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227292663delA	uc001hqr.2	-						CDC42BPA_uc001hqs.2_Intron|CDC42BPA_uc009xes.2_Intron|CDC42BPA_uc010pvs.1_Intron	NM_003607	NP_003598			CDC42-binding protein kinase alpha isoform B						actin cytoskeleton reorganization|intracellular signal transduction	cell leading edge|cell-cell junction|cytoplasm	ATP binding|identical protein binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity			lung(6)|breast(2)|stomach(1)|ovary(1)|pancreas(1)	11		all_cancers(173;0.156)|Prostate(94;0.0792)																---	---	---	---
CDC42BPA	8476	broad.mit.edu	37	1	227372093	227372093	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227372093delT	uc001hqr.2	-						CDC42BPA_uc001hqs.2_Intron|CDC42BPA_uc009xes.2_Intron|CDC42BPA_uc010pvs.1_Intron	NM_003607	NP_003598			CDC42-binding protein kinase alpha isoform B						actin cytoskeleton reorganization|intracellular signal transduction	cell leading edge|cell-cell junction|cytoplasm	ATP binding|identical protein binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity			lung(6)|breast(2)|stomach(1)|ovary(1)|pancreas(1)	11		all_cancers(173;0.156)|Prostate(94;0.0792)																---	---	---	---
OBSCN	84033	broad.mit.edu	37	1	228561028	228561028	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228561028delG	uc009xez.1	+						OBSCN_uc001hsr.1_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	229032257	229032257	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229032257delT								RHOU (149848 upstream) : RAB4A (374622 downstream)																																			---	---	---	---
RAB4A	5867	broad.mit.edu	37	1	229419477	229419478	+	Intron	DEL	TT	-	-	rs112378440		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229419477_229419478delTT	uc001hth.2	+						RAB4A_uc001hti.2_Intron|RAB4A_uc001htj.2_Intron	NM_004578	NP_004569			RAB4A, member RAS oncogene family								GDP binding|GTP binding|GTPase activity			ovary(1)	1	Breast(184;0.0858)|Ovarian(103;0.103)	Prostate(94;0.178)																---	---	---	---
NUP133	55746	broad.mit.edu	37	1	229620119	229620120	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229620119_229620120delAA	uc001htn.2	-							NM_018230	NP_060700			nucleoporin 133kDa						carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA export from nucleus|nuclear pore organization|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|Nup107-160 complex	nucleocytoplasmic transporter activity|protein binding			breast(4)|skin(2)|ovary(1)	7	Breast(184;0.104)|Ovarian(103;0.249)	Prostate(94;0.167)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	229723392	229723392	+	IGR	DEL	T	-	-	rs67943718		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229723392delT								ABCB10 (28950 upstream) : TAF5L (5476 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	230017512	230017513	+	IGR	DEL	GT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230017512_230017513delGT								URB2 (221566 upstream) : GALNT2 (176023 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	230569582	230569582	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230569582delT								PGBD5 (56215 upstream) : COG2 (208620 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	230720055	230720055	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230720055delT								PGBD5 (206688 upstream) : COG2 (58147 downstream)																																			---	---	---	---
COG2	22796	broad.mit.edu	37	1	230796633	230796633	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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)																---	---	---	---
ARV1	64801	broad.mit.edu	37	1	231131337	231131341	+	Intron	DEL	AAAAC	-	-	rs58999793		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231131337_231131341delAAAAC	uc009xfl.1	+						ARV1_uc001huh.2_Intron	NM_022786	NP_073623			ARV1 homolog						sphingolipid metabolic process	integral to membrane				breast(2)	2	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.178)		COAD - Colon adenocarcinoma(196;0.211)|Colorectal(1306;0.233)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	231141906	231141907	+	IGR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231141906_231141907insA								ARV1 (5435 upstream) : FAM89A (12797 downstream)																																			---	---	---	---
TRIM67	440730	broad.mit.edu	37	1	231338076	231338079	+	Intron	DEL	GGAG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231338076_231338079delGGAG	uc009xfn.1	+							NM_001004342	NP_001004342			tripartite motif-containing 67							cytoplasm|cytoskeleton	zinc ion binding			ovary(2)|breast(1)|kidney(1)	4	Breast(184;0.0871)	all_cancers(173;0.189)|Prostate(94;0.167)																---	---	---	---
DISC1	27185	broad.mit.edu	37	1	231784018	231784020	+	Intron	DEL	TGT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231784018_231784020delTGT	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	231827175	231827176	+	Intron	INS	-	A	A	rs79065174		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231827175_231827176insA	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	232075495	232075496	+	Intron	INS	-	T	T	rs35479176		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232075495_232075496insT	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	232204868	232204868	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232204868delG								DISC1 (27852 upstream) : SIPA1L2 (328846 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	232983580	232983581	+	IGR	DEL	AG	-	-	rs144601359		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232983580_232983581delAG								KIAA1383 (37488 upstream) : C1orf57 (102789 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	234659370	234659370	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:234659370delT								TARBP1 (44521 upstream) : IRF2BP2 (80647 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	234784107	234784108	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:234784107_234784108delAA	uc001hwh.2	+											Homo sapiens cDNA clone IMAGE:4825891.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	234907498	234907499	+	IGR	INS	-	AC	AC	rs66542247	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:234907498_234907499insAC								IRF2BP2 (162227 upstream) : TOMM20 (365161 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	235042625	235042625	+	IGR	DEL	G	-	-	rs28585567		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235042625delG								IRF2BP2 (297354 upstream) : TOMM20 (230035 downstream)																																			---	---	---	---
ARID4B	51742	broad.mit.edu	37	1	235334961	235334961	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235334961delT	uc001hwq.2	-						ARID4B_uc001hwr.2_Intron|ARID4B_uc001hwp.2_Intron	NM_016374	NP_057458			AT rich interactive domain 4B isoform 1						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)															---	---	---	---
ARID4B	51742	broad.mit.edu	37	1	235451624	235451624	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235451624delA	uc001hwq.2	-						ARID4B_uc001hwr.2_Intron|ARID4B_uc001hws.3_Intron|ARID4B_uc001hwu.1_Intron	NM_016374	NP_057458			AT rich interactive domain 4B isoform 1						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)															---	---	---	---
ARID4B	51742	broad.mit.edu	37	1	235453041	235453044	+	Intron	DEL	AAAA	-	-	rs35163064		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235453041_235453044delAAAA	uc001hwq.2	-						ARID4B_uc001hwr.2_Intron|ARID4B_uc001hws.3_Intron|ARID4B_uc001hwu.1_Intron	NM_016374	NP_057458			AT rich interactive domain 4B isoform 1						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)															---	---	---	---
LYST	1130	broad.mit.edu	37	1	235913831	235913832	+	Intron	DEL	GT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235913831_235913832delGT	uc001hxj.2	-						LYST_uc009xga.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	236180690	236180690	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236180690delT	uc001hxo.2	-						NID1_uc009xgd.2_Intron	NM_002508	NP_002499			nidogen 1 precursor						cell-matrix adhesion	basement membrane	calcium ion binding			large_intestine(1)|pancreas(1)	2	Ovarian(103;0.0544)|Breast(184;0.23)	all_cancers(173;0.00491)|Prostate(94;0.184)|Acute lymphoblastic leukemia(190;0.229)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Becaplermin(DB00102)|Urokinase(DB00013)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	236465582	236465584	+	IGR	DEL	AAG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236465582_236465584delAAG								ERO1LB (20243 upstream) : EDARADD (92096 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	236542326	236542326	+	IGR	DEL	A	-	-	rs71954009		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236542326delA								ERO1LB (96987 upstream) : EDARADD (15354 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	238446221	238446221	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:238446221delT								LOC100130331 (354604 upstream) : LOC339535 (197465 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	239071535	239071541	+	IGR	DEL	CATTTAG	-	-	rs142569202		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:239071535_239071541delCATTTAG								LOC339535 (422218 upstream) : CHRM3 (478324 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	239238610	239238610	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:239238610delA								LOC339535 (589293 upstream) : CHRM3 (311255 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	239387174	239387174	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:239387174delT								LOC339535 (737857 upstream) : CHRM3 (162691 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	239539470	239539470	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:239539470delT								LOC339535 (890153 upstream) : CHRM3 (10395 downstream)																																			---	---	---	---
CHRM3	1131	broad.mit.edu	37	1	239585688	239585688	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:239585688delT	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	240249660	240249660	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240249660delG								CHRM3 (176945 upstream) : FMN2 (5525 downstream)																																			---	---	---	---
FMN2	56776	broad.mit.edu	37	1	240289665	240289665	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240289665delC	uc010pyd.1	+						FMN2_uc010pye.1_Intron	NM_020066	NP_064450			formin 2						actin cytoskeleton organization|establishment of meiotic spindle localization|intracellular signal transduction|meiotic chromosome movement towards spindle pole|meiotic metaphase I|multicellular organismal development|oogenesis|polar body extrusion after meiotic divisions		actin binding			ovary(4)|pancreas(3)|skin(3)|large_intestine(1)|central_nervous_system(1)	12	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)															---	---	---	---
RGS7	6000	broad.mit.edu	37	1	241348840	241348840	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241348840delT	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	241564956	241564957	+	IGR	INS	-	TG	TG	rs147570953	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241564956_241564957insTG								RGS7 (44478 upstream) : FH (95949 downstream)																																			---	---	---	---
KMO	8564	broad.mit.edu	37	1	241695116	241695116	+	5'Flank	DEL	A	-	-	rs74781744		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241695116delA	uc009xgp.2	+						KMO_uc001hyy.2_5'Flank|KMO_uc009xgo.1_5'Flank	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)															---	---	---	---
OPN3	23596	broad.mit.edu	37	1	241766775	241766776	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241766775_241766776delTT	uc001hza.2	-						OPN3_uc001hzb.2_Intron|OPN3_uc001hzc.2_Intron	NM_014322	NP_055137			opsin 3						phototransduction|protein-chromophore linkage|regulation of circadian rhythm|visual perception	integral to plasma membrane	G-protein coupled photoreceptor activity				0	Ovarian(103;0.103)|all_lung(81;0.23)	all_cancers(173;0.0231)	OV - Ovarian serous cystadenocarcinoma(106;0.0125)															---	---	---	---
OPN3	23596	broad.mit.edu	37	1	241777476	241777477	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241777476_241777477delAA	uc001hza.2	-						OPN3_uc001hzb.2_Intron|OPN3_uc001hzc.2_Intron	NM_014322	NP_055137			opsin 3						phototransduction|protein-chromophore linkage|regulation of circadian rhythm|visual perception	integral to plasma membrane	G-protein coupled photoreceptor activity				0	Ovarian(103;0.103)|all_lung(81;0.23)	all_cancers(173;0.0231)	OV - Ovarian serous cystadenocarcinoma(106;0.0125)															---	---	---	---
PLD5	200150	broad.mit.edu	37	1	242255126	242255127	+	Intron	INS	-	T	T	rs141764115	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242255126_242255127insT	uc001hzn.1	-						PLD5_uc001hzl.3_Intron|PLD5_uc001hzm.3_Intron|PLD5_uc001hzo.1_Intron					RecName: Full=Inactive phospholipase D5;          Short=Inactive PLD 5; AltName: Full=Inactive choline phosphatase 5; AltName: Full=Inactive phosphatidylcholine-hydrolyzing phospholipase D5; AltName: Full=PLDc;							integral to membrane	catalytic activity			ovary(6)	6	Melanoma(84;0.242)		OV - Ovarian serous cystadenocarcinoma(106;0.0329)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	242821967	242821967	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242821967delA								PLD5 (133969 upstream) : CEP170 (465764 downstream)																																			---	---	---	---
SDCCAG8	10806	broad.mit.edu	37	1	243561671	243561671	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:243561671delT	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	244499808	244499808	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244499808delA								ZNF238 (279032 upstream) : C1orf100 (16129 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	244963768	244963768	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244963768delA								PPPDE1 (91436 upstream) : FAM36A (34871 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	245310730	245310731	+	IGR	INS	-	TG	TG	rs138425820	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245310730_245310731insTG								EFCAB2 (22200 upstream) : KIF26B (7556 downstream)																																			---	---	---	---
KIF26B	55083	broad.mit.edu	37	1	245394821	245394821	+	Intron	DEL	G	-	-	rs7530998	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245394821delG	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	245766448	245766448	+	Intron	DEL	A	-	-	rs5782358		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245766448delA	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	246109485	246109486	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246109485_246109486insT	uc001ibl.2	-						SMYD3_uc001ibk.2_Intron	NM_022743	NP_073580			SET and MYND domain containing 3							cytoplasm|nucleus	histone-lysine N-methyltransferase activity|protein binding|zinc ion binding				0	all_cancers(71;0.000291)|all_epithelial(71;0.000174)|Ovarian(71;0.0377)|all_lung(81;0.0568)|Lung NSC(105;0.0804)|Breast(184;0.173)|Melanoma(84;0.242)	all_cancers(173;0.0496)|Acute lymphoblastic leukemia(190;0.164)	OV - Ovarian serous cystadenocarcinoma(106;0.0129)	all cancers(4;0.028)|GBM - Glioblastoma multiforme(49;0.0537)														---	---	---	---
SMYD3	64754	broad.mit.edu	37	1	246517319	246517319	+	Intron	DEL	A	-	-	rs66555956		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246517319delA	uc001ibl.2	-						SMYD3_uc001ibk.2_Intron	NM_022743	NP_073580			SET and MYND domain containing 3							cytoplasm|nucleus	histone-lysine N-methyltransferase activity|protein binding|zinc ion binding				0	all_cancers(71;0.000291)|all_epithelial(71;0.000174)|Ovarian(71;0.0377)|all_lung(81;0.0568)|Lung NSC(105;0.0804)|Breast(184;0.173)|Melanoma(84;0.242)	all_cancers(173;0.0496)|Acute lymphoblastic leukemia(190;0.164)	OV - Ovarian serous cystadenocarcinoma(106;0.0129)	all cancers(4;0.028)|GBM - Glioblastoma multiforme(49;0.0537)														---	---	---	---
SMYD3	64754	broad.mit.edu	37	1	246529463	246529463	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246529463delA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	246687585	246687586	+	IGR	DEL	GC	-	-	rs3129586	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246687585_246687586delGC								SMYD3 (16971 upstream) : TFB2M (16282 downstream)																																			---	---	---	---
SCCPDH	51097	broad.mit.edu	37	1	246908090	246908090	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246908090delT	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	247062420	247062421	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247062420_247062421delTT	uc001ibu.1	-						AHCTF1_uc001ibv.1_Intron|AHCTF1_uc009xgs.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)															---	---	---	---
AHCTF1	25909	broad.mit.edu	37	1	247076400	247076402	+	Intron	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247076400_247076402delTTT	uc001ibu.1	-						AHCTF1_uc001ibv.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)															---	---	---	---
ZNF124	7678	broad.mit.edu	37	1	247296104	247296105	+	Intron	INS	-	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247296104_247296105insC	uc001ici.2	-						uc001ich.2_Intron					Homo sapiens cDNA FLJ30085 fis, clone BGGI12001714, highly similar to Homo sapiens zinc finger protein 124 (HZF-16) (ZNF124), mRNA.						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(1)	1	all_cancers(71;5.07e-05)|all_epithelial(71;8.72e-06)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0488)|Lung NSC(105;0.053)		OV - Ovarian serous cystadenocarcinoma(106;0.00739)															---	---	---	---
NLRP3	114548	broad.mit.edu	37	1	247611571	247611579	+	Intron	DEL	TTTTTTTTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247611571_247611579delTTTTTTTTT	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	247997697	247997697	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247997697delT								OR14A16 (18666 upstream) : OR11L1 (6533 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	248070904	248070904	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248070904delT								OR2W3 (10762 upstream) : OR2T8 (13416 downstream)																																			---	---	---	---
OR2L13	284521	broad.mit.edu	37	1	248166157	248166159	+	Intron	DEL	AAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248166157_248166159delAAA	uc001ids.2	+							NM_175911	NP_787107			olfactory receptor, family 2, subfamily L,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity|protein binding			central_nervous_system(2)|ovary(1)|skin(1)	4	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0132)															---	---	---	---
OR2L13	284521	broad.mit.edu	37	1	248262524	248262524	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248262524delA	uc001ids.2	+							NM_175911	NP_787107			olfactory receptor, family 2, subfamily L,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity|protein binding			central_nervous_system(2)|ovary(1)|skin(1)	4	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0132)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	248844550	248844550	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248844550delT								OR2T27 (30365 upstream) : OR14I1 (120 downstream)																																			---	---	---	---
SNTG2	54221	broad.mit.edu	37	2	1285258	1285259	+	Intron	DEL	GT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1285258_1285259delGT	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	1466290	1466291	+	Intron	DEL	AC	-	-	rs35553172		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1466290_1466291delAC	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	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)													---	---	---	---
TPO	7173	broad.mit.edu	37	2	1479187	1479187	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1479187delT	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	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)													---	---	---	---
MYT1L	23040	broad.mit.edu	37	2	2069754	2069754	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:2069754delA	uc002qxe.2	-						MYT1L_uc002qxd.2_Intron|MYT1L_uc002qxf.1_Intron	NM_015025	NP_055840			myelin transcription factor 1-like						cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|central_nervous_system(1)	6	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	5456221	5456222	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:5456221_5456222insT								None (None upstream) : SOX11 (376577 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	5912349	5912350	+	IGR	DEL	TC	-	-	rs80300821		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:5912349_5912350delTC								SOX11 (70833 upstream) : LOC150622 (160469 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	6675502	6675502	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:6675502delT								LOC400940 (547138 upstream) : CMPK2 (305001 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	6756859	6756859	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:6756859delT								LOC400940 (628495 upstream) : CMPK2 (223644 downstream)																																			---	---	---	---
RSAD2	91543	broad.mit.edu	37	2	7031928	7031928	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:7031928delA	uc002qyp.1	+							NM_080657	NP_542388			radical S-adenosyl methionine domain containing						defense response to virus	endoplasmic reticulum membrane|Golgi apparatus	catalytic activity|iron-sulfur cluster binding|metal ion binding				0	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			OV - Ovarian serous cystadenocarcinoma(76;0.191)														---	---	---	---
RNF144A	9781	broad.mit.edu	37	2	7065591	7065591	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:7065591delC	uc002qys.2	+						RNF144A_uc002qyt.2_Intron	NM_014746	NP_055561			ring finger protein 144							Golgi apparatus|integral to membrane	ligase activity|zinc ion binding			ovary(1)|kidney(1)	2	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)	all_cancers(51;0.226)		OV - Ovarian serous cystadenocarcinoma(76;0.195)														---	---	---	---
RNF144A	9781	broad.mit.edu	37	2	7120207	7120207	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:7120207delG	uc002qys.2	+						RNF144A_uc002qyt.2_Intron	NM_014746	NP_055561			ring finger protein 144							Golgi apparatus|integral to membrane	ligase activity|zinc ion binding			ovary(1)|kidney(1)	2	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)	all_cancers(51;0.226)		OV - Ovarian serous cystadenocarcinoma(76;0.195)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	7204067	7204067	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:7204067delC								RNF144A (19760 upstream) : LOC339788 (858491 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	8543988	8543988	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:8543988delT								LOC339788 (427011 upstream) : ID2 (275352 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	8657988	8657988	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:8657988delT								LOC339788 (541011 upstream) : ID2 (161352 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	8731503	8731507	+	IGR	DEL	TTGTT	-	-	rs112105639	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:8731503_8731507delTTGTT								LOC339788 (614526 upstream) : ID2 (87833 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	8779284	8779287	+	IGR	DEL	TCAG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:8779284_8779287delTCAG								LOC339788 (662307 upstream) : ID2 (40053 downstream)																																			---	---	---	---
MBOAT2	129642	broad.mit.edu	37	2	9134370	9134370	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9134370delA	uc002qzg.1	-						MBOAT2_uc010yix.1_Intron	NM_138799	NP_620154			O-acyltransferase (membrane bound) domain						phospholipid biosynthetic process	integral to membrane	1-acylglycerol-3-phosphate O-acyltransferase activity				0	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
ADAM17	6868	broad.mit.edu	37	2	9665429	9665432	+	Intron	DEL	AAAA	-	-	rs79556534		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9665429_9665432delAAAA	uc002qzu.2	-						ADAM17_uc010ewy.2_Intron|ADAM17_uc010ewz.2_Intron|ADAM17_uc010exa.2_5'Flank	NM_003183	NP_003174			a disintegrin and metalloprotease domain 17						B cell differentiation|cell adhesion mediated by integrin|epidermal growth factor receptor signaling pathway|epidermal growth factor receptor transactivation by G-protein coupled receptor signaling pathway|germinal center formation|membrane protein intracellular domain proteolysis|negative regulation of interleukin-8 production|nerve growth factor receptor signaling pathway|Notch signaling pathway|PMA-inducible membrane protein ectodomain proteolysis|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of chemokine production|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of protein phosphorylation|positive regulation of T cell chemotaxis|positive regulation of transforming growth factor beta receptor signaling pathway|regulation of mast cell apoptosis|response to drug|response to high density lipoprotein particle stimulus|response to hypoxia|response to lipopolysaccharide|spleen development|T cell differentiation in thymus|wound healing, spreading of epidermal cells	actin cytoskeleton|apical plasma membrane|cell surface|cytoplasm|integral to plasma membrane|membrane raft	integrin binding|interleukin-6 receptor binding|metalloendopeptidase activity|PDZ domain binding|SH3 domain binding|zinc ion binding			lung(1)|kidney(1)	2	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.225)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	10077013	10077013	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10077013delA								TAF1B (2470 upstream) : GRHL1 (14779 downstream)																																			---	---	---	---
HPCAL1	3241	broad.mit.edu	37	2	10455419	10455419	+	Intron	DEL	A	-	-	rs34894261		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10455419delA	uc002raj.2	+						HPCAL1_uc002rak.2_Intron|HPCAL1_uc002ral.2_Intron	NM_002149	NP_002140			hippocalcin-like 1								calcium ion binding			pancreas(1)	1	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.214)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	10628866	10628866	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10628866delT								ODC1 (40413 upstream) : NOL10 (82028 downstream)																																			---	---	---	---
NOL10	79954	broad.mit.edu	37	2	10726728	10726728	+	Intron	DEL	C	-	-	rs77661523		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10726728delC	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)														---	---	---	---
ATP6V1C2	245973	broad.mit.edu	37	2	10900496	10900496	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10900496delA	uc002ras.2	+						ATP6V1C2_uc002rat.2_Intron	NM_001039362	NP_001034451			vacuolar H+ ATPase C2 isoform a						ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	cytosol|proton-transporting V-type ATPase, V1 domain				ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.15)|OV - Ovarian serous cystadenocarcinoma(76;0.152)														---	---	---	---
C2orf50	130813	broad.mit.edu	37	2	11280501	11280501	+	Intron	DEL	A	-	-	rs150566091		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11280501delA	uc010yji.1	+						C2orf50_uc010yjj.1_Intron	NM_182500	NP_872306			hypothetical protein LOC130813												0	all_hematologic(175;0.0797)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.0997)|OV - Ovarian serous cystadenocarcinoma(76;0.134)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	11788617	11788617	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11788617delG								GREB1 (5705 upstream) : NTSR2 (9688 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	12293343	12293351	+	Intron	DEL	TTCCTTCCC	-	-	rs112549370		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:12293343_12293351delTTCCTTCCC	uc002rbu.1	+											Homo sapiens cDNA FLJ10696 fis, clone NT2RP3000484.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	12467385	12467385	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:12467385delA	uc002rbu.1	+											Homo sapiens cDNA FLJ10696 fis, clone NT2RP3000484.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	12774246	12774246	+	IGR	DEL	A	-	-	rs66800406		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:12774246delA								LPIN1 (806715 upstream) : TRIB2 (82752 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	12783330	12783330	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:12783330delT								LPIN1 (815799 upstream) : TRIB2 (73668 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	13926120	13926120	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:13926120delA								None (None upstream) : FAM84A (846736 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	14448425	14448426	+	Intron	INS	-	GG	GG	rs148807373	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:14448425_14448426insGG	uc002rby.2	-											Homo sapiens cDNA clone IMAGE:5263003.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	14465331	14465331	+	Intron	DEL	A	-	-	rs112694258		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:14465331delA	uc002rby.2	-											Homo sapiens cDNA clone IMAGE:5263003.																														---	---	---	---
DDX1	1653	broad.mit.edu	37	2	15743791	15743792	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15743791_15743792insT	uc002rce.2	+						DDX1_uc010yjq.1_Intron	NM_004939	NP_004930			DEAD (Asp-Glu-Ala-Asp) box polypeptide 1						DNA duplex unwinding|double-strand break repair|multicellular organismal development|regulation of transcription, DNA-dependent|regulation of translational initiation|spliceosome assembly|transcription, DNA-dependent	cleavage body|stress granule|tRNA-splicing ligase complex	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding|DNA/RNA helicase activity|exonuclease activity|poly(A) RNA binding|protein binding|RNA helicase activity|transcription cofactor activity			central_nervous_system(2)|upper_aerodigestive_tract(1)|ovary(1)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.197)	all_epithelial(98;2.96e-07)|Acute lymphoblastic leukemia(84;4.24e-05)|Ovarian(717;0.0694)	GBM - Glioblastoma multiforme(3;0.00969)	Epithelial(75;4.35e-05)|OV - Ovarian serous cystadenocarcinoma(76;0.133)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	16134251	16134266	+	IGR	DEL	CTTCCTTCCTTCCTTC	-	-	rs71938919		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:16134251_16134266delCTTCCTTCCTTCCTTC								MYCN (47123 upstream) : FAM49A (599635 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	16152645	16152646	+	IGR	INS	-	A	A	rs143275221	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:16152645_16152646insA								MYCN (65517 upstream) : FAM49A (581255 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	17269683	17269684	+	IGR	INS	-	A	A	rs140544821	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17269683_17269684insA								FAM49A (422587 upstream) : RAD51AP2 (422302 downstream)																																			---	---	---	---
SMC6	79677	broad.mit.edu	37	2	17906640	17906640	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17906640delA	uc002rco.2	-						SMC6_uc010exo.2_Intron|SMC6_uc002rcn.2_Intron|SMC6_uc002rcp.1_Intron|SMC6_uc002rcq.2_Intron|SMC6_uc002rcr.1_Intron	NM_001142286	NP_001135758			SMC6 protein						DNA recombination|DNA repair	chromosome|nucleus	ATP binding			breast(4)|upper_aerodigestive_tract(1)|kidney(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	18024281	18024281	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:18024281delA								MSGN1 (25915 upstream) : KCNS3 (34833 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	19460647	19460647	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:19460647delA								NT5C1B (689809 upstream) : OSR1 (90600 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	19525494	19525495	+	IGR	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:19525494_19525495delAC								NT5C1B (754656 upstream) : OSR1 (25752 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	19686748	19686748	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:19686748delT								OSR1 (128376 upstream) : TTC32 (409770 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	19882419	19882420	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:19882419_19882420delTT								OSR1 (324047 upstream) : TTC32 (214098 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	19890319	19890332	+	IGR	DEL	AGGGAGGGAGAGAC	-	-	rs5010858	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:19890319_19890332delAGGGAGGGAGAGAC								OSR1 (331947 upstream) : TTC32 (206186 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	19934739	19934742	+	IGR	DEL	GAAC	-	-	rs72577630	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:19934739_19934742delGAAC								OSR1 (376367 upstream) : TTC32 (161776 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	20254893	20254893	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20254893delT								LAPTM4A (3104 upstream) : SDC1 (145665 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	20433976	20433976	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20433976delT								SDC1 (8782 upstream) : PUM2 (14477 downstream)																																			---	---	---	---
PUM2	23369	broad.mit.edu	37	2	20511470	20511470	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20511470delA	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	20625975	20625975	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20625975delT								PUM2 (75512 upstream) : RHOB (20860 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	22052297	22052297	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:22052297delG								APOB (785352 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	23023590	23023590	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:23023590delA								None (None upstream) : KLHL29 (731865 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	23309425	23309425	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:23309425delA								None (None upstream) : KLHL29 (446030 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	23524418	23524418	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:23524418delG								None (None upstream) : KLHL29 (231037 downstream)																																			---	---	---	---
FKBP1B	2281	broad.mit.edu	37	2	24282996	24282996	+	Intron	DEL	A	-	-	rs111905080		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24282996delA	uc002rer.2	+						FKBP1B_uc002res.2_Intron|FKBP1B_uc002ret.2_Intron|FKBP1B_uc002reu.2_Intron	NM_004116	NP_004107			FK506 binding protein 1B, 12.6 kDa isoform a						'de novo' protein folding|negative regulation of heart rate|negative regulation of protein phosphatase type 2B activity|protein maturation by protein folding|protein refolding|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|regulation of ryanodine-sensitive calcium-release channel activity|response to redox state	calcium channel complex|sarcoplasmic reticulum membrane	FK506 binding|peptidyl-prolyl cis-trans isomerase activity|receptor binding				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	24651349	24651350	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24651349_24651350delAA								ITSN2 (67952 upstream) : NCOA1 (135829 downstream)																																			---	---	---	---
ADCY3	109	broad.mit.edu	37	2	25106978	25106978	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25106978delT	uc002rfs.3	-						ADCY3_uc010ykm.1_Intron	NM_004036	NP_004027			adenylate cyclase 3						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|sensory perception of smell|synaptic transmission|transmembrane transport|water transport	cytoplasm|integral to plasma membrane	ATP binding|calmodulin binding|metal ion binding			breast(3)|ovary(1)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.203)																	---	---	---	---
DNMT3A	1788	broad.mit.edu	37	2	25549366	25549366	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25549366delT	uc002rgc.2	-						DNMT3A_uc002rgd.2_Intron|DNMT3A_uc010eyi.2_Intron|DNMT3A_uc002rge.2_Intron|DNMT3A_uc002rgf.2_Intron	NM_022552	NP_072046			DNA cytosine methyltransferase 3 alpha isoform						regulation of gene expression by genetic imprinting	cytoplasm|euchromatin|nuclear matrix	DNA (cytosine-5-)-methyltransferase activity|DNA binding|metal ion binding|protein binding			haematopoietic_and_lymphoid_tissue(133)|lung(4)|ovary(3)	140	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)							Mis|F|N|S		AML								---	---	---	---
DTNB	1838	broad.mit.edu	37	2	25741365	25741366	+	Intron	DEL	CA	-	-	rs142189511	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25741365_25741366delCA	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)																	---	---	---	---
KIF3C	3797	broad.mit.edu	37	2	26173804	26173804	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26173804delA	uc002rgu.2	-						KIF3C_uc010eyj.1_Intron|KIF3C_uc010ykr.1_Intron	NM_002254	NP_002245			kinesin family member 3C						blood coagulation|microtubule-based movement	cytosol|kinesin complex|microtubule	ATP binding|microtubule motor activity			ovary(3)|skin(1)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)															OREG0014505	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
HADHB	3032	broad.mit.edu	37	2	26503128	26503128	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26503128delA	uc002rgz.2	+						HADHB_uc010ykv.1_Intron|HADHB_uc010ykw.1_Intron|HADHB_uc002rha.2_Intron|HADHB_uc010ykx.1_Intron	NM_000183	NP_000174			mitochondrial trifunctional protein, beta						fatty acid beta-oxidation	mitochondrial nucleoid	3-hydroxyacyl-CoA dehydrogenase activity|acetyl-CoA C-acyltransferase activity|enoyl-CoA hydratase activity|protein binding			ovary(1)|breast(1)	2	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
C2orf39	92749	broad.mit.edu	37	2	26646887	26646888	+	Intron	DEL	TG	-	-	rs67134348		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26646887_26646888delTG	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)																	---	---	---	---
CIB4	130106	broad.mit.edu	37	2	26839988	26839989	+	Intron	INS	-	TGTGTGTG	TGTGTGTG	rs146713738	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26839988_26839989insTGTGTGTG	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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	27061061	27061061	+	IGR	DEL	A	-	-	rs11452674		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27061061delA								CENPA (37129 upstream) : DPYSL5 (9908 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	27935735	27935735	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27935735delA	uc002rll.1	-											SubName: Full=Putative uncharacterized protein ENSP00000368999;																														---	---	---	---
MRPL33	9553	broad.mit.edu	37	2	27999178	27999178	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27999178delG	uc002rlm.1	+						MRPL33_uc002rln.1_Intron	NM_004891	NP_004882			mitochondrial ribosomal protein L33 isoform a						translation	mitochondrion|ribosome	structural constituent of ribosome				0	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
PLB1	151056	broad.mit.edu	37	2	28781573	28781574	+	Intron	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28781573_28781574delTG	uc002rmb.1	+						PLB1_uc010ezj.1_Intron|PLB1_uc002rmc.2_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)																	---	---	---	---
FAM179A	165186	broad.mit.edu	37	2	29274578	29274579	+	Intron	DEL	GA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29274578_29274579delGA	uc010ezl.2	+						FAM179A_uc010ymm.1_Intron|FAM179A_uc002rmr.3_Intron	NM_199280	NP_954974			hypothetical protein LOC165186								binding			ovary(3)|skin(1)	4																		---	---	---	---
ALK	238	broad.mit.edu	37	2	30008779	30008796	+	Intron	DEL	ACACACACACACACACAC	-	-	rs10548432		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:30008779_30008796delACACACACACACACACAC	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	30227764	30227767	+	IGR	DEL	CTCA	-	-	rs150970555		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:30227764_30227767delCTCA								ALK (83332 upstream) : YPEL5 (141983 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	30350252	30350252	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:30350252delA								ALK (205820 upstream) : YPEL5 (19498 downstream)																																			---	---	---	---
SPAST	6683	broad.mit.edu	37	2	32363421	32363421	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32363421delT	uc002roc.2	+						SPAST_uc002rod.2_Intron	NM_014946	NP_055761			spastin isoform 1						cell cycle|cell death|cell differentiation|cytokinesis, completion of separation|ER to Golgi vesicle-mediated transport|microtubule bundle formation|microtubule severing|nervous system development|protein hexamerization|protein homooligomerization	endoplasmic reticulum|endosome|integral to membrane|microtubule|microtubule organizing center|nucleus|perinuclear region of cytoplasm|spindle	alpha-tubulin binding|ATP binding|beta-tubulin binding|microtubule binding|microtubule-severing ATPase activity			breast(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)																	---	---	---	---
SLC30A6	55676	broad.mit.edu	37	2	32397457	32397457	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32397457delT	uc002roe.1	+						SLC30A6_uc002rof.1_Intron|SLC30A6_uc010ymw.1_Intron|SLC30A6_uc010ezr.1_Intron|SLC30A6_uc002rog.1_Intron|SLC30A6_uc010ezs.1_Intron|SLC30A6_uc002roh.1_Intron	NM_017964	NP_060434			solute carrier family 30 (zinc transporter),							Golgi membrane|integral to membrane	zinc ion transmembrane transporter activity				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)																	---	---	---	---
BIRC6	57448	broad.mit.edu	37	2	32617877	32617877	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32617877delT	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	32675530	32675530	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32675530delA	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	32690110	32690111	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32690110_32690111delTT	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-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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)																	---	---	---	---
TTC27	55622	broad.mit.edu	37	2	32989514	32989515	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32989514_32989515insA	uc002rom.2	+						TTC27_uc010ymx.1_Intron|TTC27_uc002ron.2_Intron	NM_017735	NP_060205			tetratricopeptide repeat domain 27								protein binding			central_nervous_system(1)	1																		---	---	---	---
LTBP1	4052	broad.mit.edu	37	2	33177711	33177711	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33177711delT	uc002ros.2	+							NM_206943	NP_996826			latent transforming growth factor beta binding						negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta	proteinaceous extracellular matrix	calcium ion binding|growth factor binding|transforming growth factor beta receptor activity			ovary(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|central_nervous_system(1)	8	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)																---	---	---	---
Unknown	0	broad.mit.edu	37	2	34256217	34256217	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:34256217delT								MYADML (302933 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	34749969	34749969	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:34749969delT								MYADML (796685 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	34854249	34854249	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:34854249delA								MYADML (900965 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	35429203	35429204	+	IGR	DEL	TC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:35429203_35429204delTC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	35504797	35504797	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:35504797delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	35941781	35941782	+	IGR	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:35941781_35941782delAC								None (None upstream) : CRIM1 (641615 downstream)																																			---	---	---	---
CRIM1	51232	broad.mit.edu	37	2	36659942	36659943	+	Intron	DEL	AT	-	-	rs77459787	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:36659942_36659943delAT	uc002rpd.2	+							NM_016441	NP_057525			cysteine-rich motor neuron 1 precursor						nervous system development|regulation of cell growth	extracellular region|integral to membrane|plasma membrane	insulin-like growth factor binding|insulin-like growth factor receptor activity|serine-type endopeptidase inhibitor activity			ovary(2)|skin(1)	3		all_hematologic(82;0.131)|Acute lymphoblastic leukemia(82;0.154)																---	---	---	---
CRIM1	51232	broad.mit.edu	37	2	36737453	36737453	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:36737453delA	uc002rpd.2	+							NM_016441	NP_057525			cysteine-rich motor neuron 1 precursor						nervous system development|regulation of cell growth	extracellular region|integral to membrane|plasma membrane	insulin-like growth factor binding|insulin-like growth factor receptor activity|serine-type endopeptidase inhibitor activity			ovary(2)|skin(1)	3		all_hematologic(82;0.131)|Acute lymphoblastic leukemia(82;0.154)																---	---	---	---
Unknown	0	broad.mit.edu	37	2	36779350	36779350	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:36779350delA								CRIM1 (1073 upstream) : FEZ2 (54 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	37605549	37605549	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37605549delA								QPCT (5085 upstream) : CDC42EP3 (265194 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	37649396	37649396	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37649396delG								QPCT (48932 upstream) : CDC42EP3 (221347 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	37862321	37862322	+	IGR	INS	-	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37862321_37862322insG								QPCT (261857 upstream) : CDC42EP3 (8421 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	38060398	38060399	+	IGR	DEL	TA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38060398_38060399delTA								CDC42EP3 (161072 upstream) : FAM82A1 (92063 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	38739082	38739082	+	IGR	DEL	T	-	-	rs72364091		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38739082delT								ATL2 (134650 upstream) : HNRPLL (51246 downstream)																																			---	---	---	---
GALM	130589	broad.mit.edu	37	2	38907855	38907855	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38907855delA	uc002rqy.2	+							NM_138801	NP_620156			galactose mutarotase						hexose metabolic process	cytoplasm	aldose 1-epimerase activity|carbohydrate binding				0		all_hematologic(82;0.248)																---	---	---	---
SOS1	6654	broad.mit.edu	37	2	39299051	39299054	+	Intron	DEL	TTTT	-	-	rs75838859		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39299051_39299054delTTTT	uc002rrk.3	-						SOS1_uc010ynr.1_Intron	NM_005633	NP_005624			son of sevenless homolog 1						apoptosis|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|induction of apoptosis by extracellular signals|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction	cytosol	DNA binding|protein binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			ovary(4)|breast(3)|lung(2)|central_nervous_system(1)	10		all_hematologic(82;0.21)												Noonan_syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	2	41072770	41072770	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:41072770delT								SLC8A1 (333195 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	41422125	41422128	+	IGR	DEL	ACAC	-	-	rs60096813		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:41422125_41422128delACAC								SLC8A1 (682550 upstream) : PKDCC (853033 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	42133292	42133292	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42133292delA								None (None upstream) : PKDCC (141869 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	42303492	42303499	+	IGR	DEL	AAAGAAAA	-	-	rs34530202		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42303492_42303499delAAAGAAAA								PKDCC (17826 upstream) : EML4 (92991 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	42375356	42375356	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42375356delA								PKDCC (89690 upstream) : EML4 (21134 downstream)																																			---	---	---	---
EML4	27436	broad.mit.edu	37	2	42523612	42523613	+	Intron	DEL	TA	-	-	rs10604697		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42523612_42523613delTA	uc002rsi.2	+						EML4_uc010fap.2_Intron|EML4_uc002rsj.2_Intron	NM_019063	NP_061936			echinoderm microtubule associated protein like 4						microtubule-based process|mitosis	cytoplasm|microtubule	protein binding		EML4/ALK(246)	lung(246)|ovary(2)|central_nervous_system(1)|skin(1)	250								T	ALK	NSCLC								---	---	---	---
THADA	63892	broad.mit.edu	37	2	43476231	43476231	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43476231delT	uc002rsw.3	-						THADA_uc010far.2_Intron|THADA_uc002rsx.3_Intron|THADA_uc002rsy.3_Intron	NM_001083953	NP_001077422			thyroid adenoma associated								binding			ovary(2)|skin(1)	3		Acute lymphoblastic leukemia(82;0.00361)|all_hematologic(82;0.00837)																---	---	---	---
THADA	63892	broad.mit.edu	37	2	43518926	43518926	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43518926delA	uc002rsw.3	-						THADA_uc010far.2_Intron|THADA_uc002rsx.3_Intron|THADA_uc002rsy.3_Intron	NM_001083953	NP_001077422			thyroid adenoma associated								binding			ovary(2)|skin(1)	3		Acute lymphoblastic leukemia(82;0.00361)|all_hematologic(82;0.00837)																---	---	---	---
DYNC2LI1	51626	broad.mit.edu	37	2	44013493	44013493	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44013493delT	uc002rtk.2	+						DYNC2LI1_uc002rth.2_Intron|DYNC2LI1_uc002rti.2_Intron|DYNC2LI1_uc002rtj.2_Intron|DYNC2LI1_uc002rtl.2_Intron|DYNC2LI1_uc010ynz.1_Intron	NM_016008	NP_057092			dynein 2 light intermediate chain isoform 1							apical part of cell|axonemal dynein complex|cilium axoneme|cytoplasm|microtubule|motile primary cilium	motor activity			ovary(1)	1		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)																---	---	---	---
ABCG5	64240	broad.mit.edu	37	2	44054969	44054969	+	Intron	DEL	A	-	-	rs112929080	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44054969delA	uc002rtn.2	-						ABCG5_uc002rtm.2_Intron|ABCG5_uc002rto.2_Intron|ABCG5_uc002rtp.2_Intron	NM_022436	NP_071881			ATP-binding cassette sub-family G member 5						cholesterol efflux|cholesterol homeostasis|excretion|lipid metabolic process|negative regulation of intestinal cholesterol absorption|negative regulation of intestinal phytosterol absorption	apical plasma membrane|integral to membrane	ATP binding|ATPase activity|protein heterodimerization activity			ovary(1)|skin(1)	2		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)																---	---	---	---
ABCG8	64241	broad.mit.edu	37	2	44101418	44101418	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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)																---	---	---	---
C2orf34	79823	broad.mit.edu	37	2	44970716	44970716	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44970716delA	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	45093163	45093163	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45093163delA								C2orf34 (93434 upstream) : SIX3 (75874 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	45297373	45297373	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45297373delA								SIX2 (60830 upstream) : SRBD1 (318447 downstream)																																			---	---	---	---
PRKCE	5581	broad.mit.edu	37	2	45890002	45890003	+	Intron	INS	-	CAAG	CAAG	rs147813647	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45890002_45890003insCAAG	uc002rut.2	+							NM_005400	NP_005391			protein kinase C, epsilon						activation of phospholipase C activity|induction of apoptosis|intracellular signal transduction|nerve growth factor receptor signaling pathway|platelet activation	cytosol|endoplasmic reticulum|plasma membrane	ATP binding|enzyme activator activity|metal ion binding|signal transducer activity			lung(4)|ovary(3)|kidney(1)|breast(1)|large_intestine(1)	10		all_hematologic(82;0.155)|Acute lymphoblastic leukemia(82;0.209)	LUSC - Lung squamous cell carcinoma(58;0.171)															---	---	---	---
TTC7A	57217	broad.mit.edu	37	2	47164525	47164525	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47164525delA	uc002rvm.2	+						MCFD2_uc010fba.2_Intron|MCFD2_uc010yof.1_Intron	NM_020458	NP_065191			tetratricopeptide repeat domain 7A								binding			breast(1)|skin(1)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18)	Lung(47;0.0792)|LUSC - Lung squamous cell carcinoma(58;0.114)															---	---	---	---
EPCAM	4072	broad.mit.edu	37	2	47594015	47594015	+	5'Flank	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47594015delA	uc002rvx.2	+						EPCAM_uc002rvw.2_Intron	NM_002354	NP_002345			epithelial cell adhesion molecule precursor						positive regulation of cell proliferation	apical plasma membrane|basolateral plasma membrane|integral to membrane|lateral plasma membrane|tight junction	protein binding			skin(1)	1														Lynch_syndrome				---	---	---	---
MSH2	4436	broad.mit.edu	37	2	47858767	47858770	+	Intron	DEL	GCGT	-	-	rs57437001	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47858767_47858770delGCGT	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				---	---	---	---
Unknown	0	broad.mit.edu	37	2	48177642	48177644	+	IGR	DEL	GAC	-	-	rs2348491		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48177642_48177644delGAC								FBXO11 (44828 upstream) : FOXN2 (364151 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	49968084	49968093	+	IGR	DEL	TGTGTGTGTG	-	-	rs113208871		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:49968084_49968093delTGTGTGTGTG								FSHR (586454 upstream) : NRXN1 (177551 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	50016537	50016537	+	IGR	DEL	A	-	-	rs149986850		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:50016537delA								FSHR (634907 upstream) : NRXN1 (129107 downstream)																																			---	---	---	---
NRXN1	9378	broad.mit.edu	37	2	50387681	50387682	+	Intron	DEL	AA	-	-	rs78203257		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:50387681_50387682delAA	uc010fbp.2	-						NRXN1_uc002rxb.3_Intron|NRXN1_uc010fbq.2_Intron|NRXN1_uc002rxe.3_Intron	NM_138735	NP_620072			neurexin 1 isoform beta precursor						angiogenesis|neuron cell-cell adhesion|neuronal signal transduction	cell surface|endocytic vesicle|integral to membrane|presynaptic membrane	cell adhesion molecule binding|receptor binding			ovary(2)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)															---	---	---	---
NRXN1	9378	broad.mit.edu	37	2	50504634	50504652	+	Intron	DEL	CTTTTTCCTTCCTTCCTTC	-	-	rs147518619		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:50504634_50504652delCTTTTTCCTTCCTTCCTTC	uc010fbp.2	-						NRXN1_uc002rxb.3_Intron|NRXN1_uc010fbq.2_Intron|NRXN1_uc002rxe.3_Intron|NRXN1_uc002rxc.1_Intron	NM_138735	NP_620072			neurexin 1 isoform beta precursor						angiogenesis|neuron cell-cell adhesion|neuronal signal transduction	cell surface|endocytic vesicle|integral to membrane|presynaptic membrane	cell adhesion molecule binding|receptor binding			ovary(2)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)															---	---	---	---
NRXN1	9378	broad.mit.edu	37	2	50606256	50606256	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:50606256delA	uc010fbq.2	-						NRXN1_uc002rxb.3_Intron|NRXN1_uc002rxe.3_Intron|NRXN1_uc002rxc.1_Intron	NM_001135659	NP_001129131			neurexin 1 isoform alpha2 precursor						angiogenesis|neuron cell-cell adhesion|neuronal signal transduction	cell surface|endocytic vesicle|integral to membrane|presynaptic membrane	cell adhesion molecule binding|receptor binding			ovary(2)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	51532350	51532350	+	IGR	DEL	T	-	-	rs11327305		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:51532350delT								NRXN1 (272676 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	52131303	52131304	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:52131303_52131304delAA								NRXN1 (871629 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	53048096	53048096	+	IGR	DEL	G	-	-	rs11125446	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:53048096delG								None (None upstream) : ASB3 (849022 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	53095258	53095258	+	IGR	DEL	A	-	-	rs72381897		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:53095258delA								None (None upstream) : ASB3 (801860 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	54674683	54674683	+	IGR	DEL	A	-	-	rs113764417		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54674683delA								C2orf73 (85969 upstream) : SPTBN1 (8771 downstream)																																			---	---	---	---
CCDC88A	55704	broad.mit.edu	37	2	55621097	55621098	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55621097_55621098insT	uc002ryv.2	-						CCDC88A_uc010yoz.1_Intron|CCDC88A_uc010ypa.1_Intron	NM_001135597	NP_001129069			coiled-coil domain containing 88A isoform 1						activation of protein kinase B activity|cell migration|cellular membrane organization|DNA replication|lamellipodium assembly|microtubule cytoskeleton organization|regulation of actin cytoskeleton organization|regulation of cell proliferation|regulation of DNA replication|regulation of neuron projection development|TOR signaling cascade	cytoplasmic membrane-bounded vesicle|cytosol|endoplasmic reticulum|Golgi apparatus|lamellipodium|plasma membrane	actin binding|microtubule binding|phosphatidylinositol binding|protein homodimerization activity|protein kinase B binding			ovary(2)|skin(2)	4																		---	---	---	---
CCDC88A	55704	broad.mit.edu	37	2	55642520	55642520	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55642520delG	uc002ryv.2	-						CCDC88A_uc010yoz.1_Intron|CCDC88A_uc010ypa.1_Intron|CCDC88A_uc010fbz.2_Intron	NM_001135597	NP_001129069			coiled-coil domain containing 88A isoform 1						activation of protein kinase B activity|cell migration|cellular membrane organization|DNA replication|lamellipodium assembly|microtubule cytoskeleton organization|regulation of actin cytoskeleton organization|regulation of cell proliferation|regulation of DNA replication|regulation of neuron projection development|TOR signaling cascade	cytoplasmic membrane-bounded vesicle|cytosol|endoplasmic reticulum|Golgi apparatus|lamellipodium|plasma membrane	actin binding|microtubule binding|phosphatidylinositol binding|protein homodimerization activity|protein kinase B binding			ovary(2)|skin(2)	4																		---	---	---	---
CCDC104	112942	broad.mit.edu	37	2	55756167	55756167	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55756167delT	uc002ryy.2	+						CCDC104_uc002ryx.2_Intron	NM_080667	NP_542398			coiled-coil domain containing 104											ovary(1)	1			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	55931430	55931430	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55931430delT								PNPT1 (10419 upstream) : EFEMP1 (161673 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	55953989	55953991	+	IGR	DEL	AAC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55953989_55953991delAAC								PNPT1 (32978 upstream) : EFEMP1 (139112 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	56640436	56640436	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:56640436delA								CCDC85A (27128 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	57286697	57286697	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:57286697delA								CCDC85A (673389 upstream) : VRK2 (848089 downstream)																																			---	---	---	---
VRK2	7444	broad.mit.edu	37	2	58139561	58139561	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:58139561delT	uc002rzo.2	+						VRK2_uc010fcb.2_Intron	NM_001130482	NP_001123954			vaccinia related kinase 2 isoform 2							integral to membrane	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(1)	1																		---	---	---	---
FANCL	55120	broad.mit.edu	37	2	58455067	58455067	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:58455067delA	uc002rzw.3	-						FANCL_uc002rzx.3_Intron|FANCL_uc010fce.2_Intron|FANCL_uc010fcf.1_Intron	NM_018062	NP_060532			Fanconi anemia, complementation group L isoform						DNA repair	cytoplasm|nucleoplasm	ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2													Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				---	---	---	---
Unknown	0	broad.mit.edu	37	2	59746025	59746026	+	IGR	INS	-	T	T	rs141969297		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:59746025_59746026insT								None (None upstream) : BCL11A (932277 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	59841574	59841575	+	IGR	INS	-	G	G	rs138964582	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:59841574_59841575insG								None (None upstream) : BCL11A (836728 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	59847204	59847204	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:59847204delT								None (None upstream) : BCL11A (831099 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	60399248	60399255	+	IGR	DEL	TGGATGGA	-	-	rs72098867		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60399248_60399255delTGGATGGA								None (None upstream) : BCL11A (279048 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	60925452	60925452	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60925452delT								BCL11A (144819 upstream) : PAPOLG (57931 downstream)																																			---	---	---	---
PAPOLG	64895	broad.mit.edu	37	2	60997758	60997758	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60997758delT	uc002sai.2	+						PAPOLG_uc002saj.2_Intron|PAPOLG_uc002sak.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)															---	---	---	---
PUS10	150962	broad.mit.edu	37	2	61222225	61222225	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61222225delA	uc010fci.2	-						PUS10_uc002sao.2_Intron|PUS10_uc010ypk.1_Intron	NM_144709	NP_653310			pseudouridylate synthase 10						pseudouridine synthesis|tRNA processing		pseudouridine synthase activity|RNA binding			ovary(2)|large_intestine(1)|kidney(1)	4			LUSC - Lung squamous cell carcinoma(5;1.56e-06)|Lung(5;2.48e-05)|Epithelial(17;0.113)															---	---	---	---
XPO1	7514	broad.mit.edu	37	2	61755067	61755067	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61755067delT	uc002sbj.2	-						XPO1_uc010fcl.2_Intron|XPO1_uc010ypn.1_Intron|XPO1_uc002sbk.2_Intron	NM_003400	NP_003391			exportin 1						intracellular protein transport|mitotic prometaphase|mRNA metabolic process|mRNA transport|viral genome transport in host cell|viral infectious cycle	annulate lamellae|Cajal body|cytosol|kinetochore|nuclear envelope|nucleolus|ribonucleoprotein complex	protein binding|protein transporter activity|RNA binding			ovary(1)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1)	4			LUSC - Lung squamous cell carcinoma(7;5.71e-05)|Epithelial(17;0.0662)|all cancers(80;0.226)															---	---	---	---
XPO1	7514	broad.mit.edu	37	2	61759969	61759969	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61759969delA	uc002sbj.2	-						XPO1_uc010fcl.2_Intron|XPO1_uc010ypn.1_Intron|XPO1_uc002sbk.2_Intron	NM_003400	NP_003391			exportin 1						intracellular protein transport|mitotic prometaphase|mRNA metabolic process|mRNA transport|viral genome transport in host cell|viral infectious cycle	annulate lamellae|Cajal body|cytosol|kinetochore|nuclear envelope|nucleolus|ribonucleoprotein complex	protein binding|protein transporter activity|RNA binding			ovary(1)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1)	4			LUSC - Lung squamous cell carcinoma(7;5.71e-05)|Epithelial(17;0.0662)|all cancers(80;0.226)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	61903886	61903886	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61903886delT								XPO1 (138468 upstream) : FAM161A (148099 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	61986275	61986277	+	IGR	DEL	AAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61986275_61986277delAAA								XPO1 (220857 upstream) : FAM161A (65708 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	62379580	62379583	+	IGR	DEL	TTTT	-	-	rs11377971		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62379580_62379583delTTTT								COMMD1 (16376 upstream) : B3GNT2 (43679 downstream)																																			---	---	---	---
B3GNT2	10678	broad.mit.edu	37	2	62425940	62425941	+	Intron	INS	-	A	A	rs7606275		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62425940_62425941insA	uc002sbs.2	+							NM_006577	NP_006568			UDP-GlcNAc:betaGal							Golgi membrane|integral to membrane	UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity			ovary(1)	1	Lung NSC(7;0.031)|all_lung(7;0.0634)		LUSC - Lung squamous cell carcinoma(7;3.55e-06)|Epithelial(17;0.0963)															---	---	---	---
B3GNT2	10678	broad.mit.edu	37	2	62437456	62437456	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62437456delT	uc002sbs.2	+							NM_006577	NP_006568			UDP-GlcNAc:betaGal							Golgi membrane|integral to membrane	UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity			ovary(1)	1	Lung NSC(7;0.031)|all_lung(7;0.0634)		LUSC - Lung squamous cell carcinoma(7;3.55e-06)|Epithelial(17;0.0963)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	62891564	62891564	+	5'Flank	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62891564delT	uc002sbw.1	-											Homo sapiens cDNA clone IMAGE:5271366.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	63322511	63322511	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:63322511delT								OTX1 (38208 upstream) : C2orf86 (26026 downstream)																																			---	---	---	---
C2orf86	51057	broad.mit.edu	37	2	63777749	63777750	+	Intron	INS	-	G	G	rs141508326	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:63777749_63777750insG	uc002sch.2	-						C2orf86_uc002sci.1_Intron	NM_015910	NP_056994			hypothetical protein LOC51057 isoform 2						cilium morphogenesis|regulation of embryonic cell shape|regulation of protein localization|septin cytoskeleton organization	cilium axoneme|cytoplasm|cytoskeleton|plasma membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	64050656	64050656	+	IGR	DEL	C	-	-	rs147495277	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64050656delC								LOC388955 (200497 upstream) : UGP2 (17442 downstream)																																			---	---	---	---
UGP2	7360	broad.mit.edu	37	2	64096100	64096100	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64096100delA	uc002scm.2	+						UGP2_uc002scl.2_Intron|UGP2_uc010ypx.1_Intron	NM_006759	NP_006750			UDP-glucose pyrophosphorylase 2 isoform a						glycogen biosynthetic process|phosphorylation|UDP-glucose metabolic process|UDP-glucuronate biosynthetic process|xenobiotic metabolic process	cytosol	metal ion binding|protein binding|UTP:glucose-1-phosphate uridylyltransferase activity				0																		---	---	---	---
AFTPH	54812	broad.mit.edu	37	2	64810590	64810590	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64810590delT	uc002sdc.2	+						AFTPH_uc002scz.2_Intron|AFTPH_uc002sda.2_Intron|AFTPH_uc002sdb.2_Intron	NM_203437	NP_982261			aftiphilin protein isoform a						protein transport	AP-1 adaptor complex|cytosol|nucleus	clathrin binding			ovary(2)	2																		---	---	---	---
SERTAD2	9792	broad.mit.edu	37	2	64872526	64872527	+	Intron	INS	-	A	A	rs146130816	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64872526_64872527insA	uc002sde.1	-							NM_014755	NP_055570			SERTA domain containing 2						negative regulation of cell growth|transcription, DNA-dependent	cytoplasm|nucleus					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	65256771	65256771	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65256771delA								SLC1A4 (5774 upstream) : CEP68 (26724 downstream)																																			---	---	---	---
RAB1A	5861	broad.mit.edu	37	2	65325970	65325971	+	Intron	INS	-	TTT	TTT	rs76500247		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65325970_65325971insTTT	uc002sdm.2	-						RAB1A_uc002sdn.2_Intron|RAB1A_uc010yqe.1_Intron|RAB1A_uc002sdo.2_Intron	NM_004161	NP_004152			RAB1A, member RAS oncogene family isoform 1						protein transport|small GTPase mediated signal transduction|vesicle-mediated transport	endoplasmic reticulum|Golgi apparatus	GTP binding|GTPase activity				0																		---	---	---	---
ACTR2	10097	broad.mit.edu	37	2	65476834	65476834	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65476834delA	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	65770388	65770389	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65770388_65770389delTT	uc010fcy.1	+											Homo sapiens cDNA FLJ16124 fis, clone BRACE2011677.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	66806298	66806299	+	IGR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:66806298_66806299insA								MEIS1 (6408 upstream) : ETAA1 (818143 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	66874194	66874195	+	IGR	INS	-	TCT	TCT	rs145977963		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:66874194_66874195insTCT								MEIS1 (74304 upstream) : ETAA1 (750247 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	67416702	67416702	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:67416702delA	uc002sdx.2	+						uc002sdy.1_Intron					Homo sapiens, clone IMAGE:5541055, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	67444704	67444706	+	Intron	DEL	ATG	-	-	rs139034223		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:67444704_67444706delATG	uc002sdx.2	+						uc002sdy.1_5'Flank					Homo sapiens, clone IMAGE:5541055, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	67545965	67545965	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:67545965delA								MEIS1 (746075 upstream) : ETAA1 (78477 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	67748742	67748742	+	IGR	DEL	T	-	-	rs66621583		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:67748742delT								ETAA1 (111209 upstream) : C1D (520591 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	68252186	68252186	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:68252186delT								ETAA1 (614653 upstream) : C1D (17147 downstream)																																			---	---	---	---
ANTXR1	84168	broad.mit.edu	37	2	69323616	69323623	+	Intron	DEL	GAGGGAGG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69323616_69323623delGAGGGAGG	uc002sfg.2	+						ANTXR1_uc002sfe.2_Intron|ANTXR1_uc002sff.2_Intron|ANTXR1_uc002sfd.2_Intron	NM_032208	NP_115584			anthrax toxin receptor 1 isoform 1 precursor						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				---	---	---	---
ANTXR1	84168	broad.mit.edu	37	2	69452725	69452725	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69452725delG	uc002sfg.2	+							NM_032208	NP_115584			anthrax toxin receptor 1 isoform 1 precursor						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				---	---	---	---
Unknown	0	broad.mit.edu	37	2	69482166	69482166	+	IGR	DEL	T	-	-	rs111422416		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69482166delT								ANTXR1 (5709 upstream) : GFPT1 (64739 downstream)																																			---	---	---	---
AAK1	22848	broad.mit.edu	37	2	69708179	69708179	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69708179delT	uc002sfp.2	-							NM_014911	NP_055726			AP2 associated kinase 1							coated pit|mitochondrion|plasma membrane	ATP binding|protein serine/threonine kinase activity				0																		---	---	---	---
AAK1	22848	broad.mit.edu	37	2	69824840	69824840	+	Intron	DEL	A	-	-	rs34117119		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69824840delA	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	69950515	69950515	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69950515delA								AAK1 (79538 upstream) : ANXA4 (18612 downstream)																																			---	---	---	---
NAGK	55577	broad.mit.edu	37	2	71292963	71292964	+	5'Flank	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71292963_71292964insA	uc002shp.3	+						NAGK_uc010fea.2_5'Flank|NAGK_uc002shq.3_5'Flank|NAGK_uc002shr.2_5'Flank	NM_017567	NP_060037			N-Acetylglucosamine kinase						N-acetylglucosamine metabolic process|N-acetylmannosamine metabolic process		ATP binding|N-acetylglucosamine kinase activity|protein binding				0					N-Acetyl-D-glucosamine(DB00141)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	72401778	72401779	+	IGR	INS	-	AC	AC	rs151272403	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:72401778_72401779insAC								CYP26B1 (26815 upstream) : EXOC6B (4666 downstream)																																			---	---	---	---
EXOC6B	23233	broad.mit.edu	37	2	72659158	72659158	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:72659158delT	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	72739457	72739496	+	Intron	DEL	GAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAA	-	-	rs143739965		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:72739457_72739496delGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAA	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																		---	---	---	---
EMX1	2016	broad.mit.edu	37	2	73151153	73151154	+	Intron	INS	-	G	G	rs149137911	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73151153_73151154insG	uc002sin.1	+						EMX1_uc002sim.1_Intron	NM_004097	NP_004088			empty spiracles homolog 1							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	73363266	73363266	+	IGR	DEL	T	-	-	rs75794996		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73363266delT								RAB11FIP5 (23120 upstream) : NOTO (66120 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	73604840	73604840	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73604840delT								EGR4 (84011 upstream) : ALMS1 (8046 downstream)																																			---	---	---	---
ALMS1	7840	broad.mit.edu	37	2	73787336	73787336	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73787336delA	uc002sje.1	+						ALMS1_uc002sjf.1_Intron|ALMS1_uc002sjg.2_Intron|ALMS1_uc002sjh.1_Intron	NM_015120	NP_055935			Alstrom syndrome 1						G2/M transition of mitotic cell cycle	centrosome|cilium|cytosol|microtubule basal body|spindle pole				skin(3)|ovary(2)|breast(2)|pancreas(1)|lung(1)	9																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	73846512	73846512	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73846512delA								ALMS1 (9466 upstream) : NAT8 (21338 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	73913287	73913288	+	IGR	DEL	TC	-	-	rs146543150		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73913287_73913288delTC								ALMS1P (595 upstream) : NAT8B (14348 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	74340730	74340730	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74340730delA								TET3 (5430 upstream) : BOLA3 (21798 downstream)																																			---	---	---	---
HK2	3099	broad.mit.edu	37	2	75081242	75081245	+	Intron	DEL	TTTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75081242_75081245delTTTT	uc002snd.2	+							NM_000189	NP_000180			hexokinase 2						apoptotic mitochondrial changes|glucose transport|glycolysis|transmembrane transport	cytosol|mitochondrial outer membrane	ATP binding|glucokinase activity			ovary(1)|lung(1)	2																		---	---	---	---
C2orf3	6936	broad.mit.edu	37	2	75923212	75923212	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75923212delC	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																		---	---	---	---
LRRTM4	80059	broad.mit.edu	37	2	77408867	77408867	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:77408867delA	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	78888562	78888562	+	IGR	DEL	G	-	-	rs11126679	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:78888562delG								SNAR-H (706410 upstream) : REG3G (364264 downstream)																																			---	---	---	---
CTNNA2	1496	broad.mit.edu	37	2	79707049	79707050	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:79707049_79707050delAA	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	80494003	80494003	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:80494003delC	uc010ysh.1	+						CTNNA2_uc010yse.1_Intron|CTNNA2_uc010ysf.1_Intron|CTNNA2_uc010ysg.1_Intron	NM_004389	NP_004380			catenin, alpha 2 isoform 1						axonogenesis|brain morphogenesis|cell-cell adhesion|dendrite morphogenesis|muscle cell differentiation|positive regulation of muscle cell differentiation|prepulse inhibition|radial glia guided migration of Purkinje cell|regulation of synapse structural plasticity	actin cytoskeleton|axon|cytosol	cadherin binding|structural constituent of cytoskeleton			pancreas(4)|lung(3)|breast(1)|skin(1)	9																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	81864687	81864687	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:81864687delT								CTNNA2 (988783 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	82092712	82092712	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:82092712delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	82381376	82381377	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:82381376_82381377insT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	83549559	83549559	+	IGR	DEL	T	-	-	rs78094986		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:83549559delT								None (None upstream) : FUNDC2P2 (968247 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	84023454	84023455	+	IGR	INS	-	GAAGA	GAAGA	rs145519142	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:84023454_84023455insGAAGA								None (None upstream) : FUNDC2P2 (494351 downstream)																																			---	---	---	---
TCF7L1	83439	broad.mit.edu	37	2	85510389	85510389	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85510389delC	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	85529268	85529268	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85529268delA	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	85615275	85615275	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85615275delA	uc002spf.3	+						ELMOD3_uc002spg.3_Intron|ELMOD3_uc002sph.3_Intron|ELMOD3_uc010ysn.1_Intron|ELMOD3_uc010yso.1_Intron|ELMOD3_uc010ysp.1_Intron	NM_001135021	NP_001128493			ELMO/CED-12 domain containing 3 isoform b						phagocytosis	cytoskeleton				ovary(2)	2																		---	---	---	---
USP39	10713	broad.mit.edu	37	2	85860253	85860253	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85860253delT	uc002sqe.2	+						USP39_uc002sqb.2_Intron|USP39_uc010ysu.1_Intron|USP39_uc010ysv.1_Intron|USP39_uc010fgn.1_Intron|USP39_uc002sqf.2_Intron|USP39_uc002sqg.2_Intron|USP39_uc010fgo.2_Intron	NM_006590	NP_006581			ubiquitin specific protease 39						spliceosome assembly|ubiquitin-dependent protein catabolic process	nucleus	protein binding|ubiquitin thiolesterase activity|zinc ion binding			ovary(1)	1																		---	---	---	---
USP39	10713	broad.mit.edu	37	2	85862683	85862683	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85862683delA	uc002sqe.2	+						USP39_uc002sqb.2_Intron|USP39_uc010ysu.1_Intron|USP39_uc010ysv.1_Intron|USP39_uc010fgn.1_Intron|USP39_uc002sqf.2_Intron|USP39_uc002sqg.2_Intron|USP39_uc010fgo.2_Intron	NM_006590	NP_006581			ubiquitin specific protease 39						spliceosome assembly|ubiquitin-dependent protein catabolic process	nucleus	protein binding|ubiquitin thiolesterase activity|zinc ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	86228872	86228873	+	IGR	DEL	AC	-	-	rs71712370		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86228872_86228873delAC								ST3GAL5 (112715 upstream) : LOC90784 (18466 downstream)																																			---	---	---	---
RMND5A	64795	broad.mit.edu	37	2	87104818	87104819	+	Intron	INS	-	AA	AA			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87104818_87104819insAA	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	87556408	87556408	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87556408delT	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	88310126	88310127	+	IGR	INS	-	G	G	rs143868716	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88310126_88310127insG								RMND5A (271360 upstream) : KRCC1 (16597 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	88496058	88496059	+	IGR	INS	-	ACAC	ACAC	rs148067375	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88496058_88496059insACAC								THNSL2 (9913 upstream) : FOXI3 (251667 downstream)																																			---	---	---	---
FLJ40330	645784	broad.mit.edu	37	2	89073098	89073099	+	Intron	INS	-	A	A	rs145200928	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89073098_89073099insA	uc002stf.2	+						FLJ40330_uc010fhf.2_Intron|FLJ40330_uc010fhg.2_Intron|FLJ40330_uc010fhh.2_Intron					Homo sapiens mRNA; cDNA DKFZp434J1630 (from clone DKFZp434J1630).												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	89917336	89917337	+	Intron	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89917336_89917337delAC	uc010fhm.2	+											Parts of antibodies, mostly variable regions.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	90415153	90415157	+	Intron	DEL	AAAAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90415153_90415157delAAAAA	uc010fhm.2	+											Parts of antibodies, mostly variable regions.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	90470953	90470954	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90470953_90470954delAA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	91696135	91696136	+	IGR	INS	-	GCTGGCTTGGCTGGATTG	GCTGGCTTGGCTGGATTG	rs141780744	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91696135_91696136insGCTGGCTTGGCTGGATTG								None (None upstream) : LOC654342 (109056 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	91798818	91798818	+	IGR	DEL	C	-	-	rs71380648		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91798818delC								None (None upstream) : LOC654342 (6374 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	92041822	92041823	+	IGR	DEL	AC	-	-	rs74533162		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92041822_92041823delAC								GGT8P (71669 upstream) : FKSG73 (87336 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	92116753	92116754	+	IGR	DEL	CA	-	-	rs150080836		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92116753_92116754delCA								GGT8P (146600 upstream) : FKSG73 (12405 downstream)																																			---	---	---	---
FKSG73	440888	broad.mit.edu	37	2	92127217	92127218	+	5'Flank	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92127217_92127218delTG	uc010yuc.1	+							NR_027714				SubName: Full=FKSG73; SubName: Full=FKSG73 protein, isoform CRA_a;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	92317890	92317890	+	IGR	DEL	T	-	-	rs7597972		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92317890delT								FKSG73 (187396 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	95396056	95396056	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:95396056delT								None (None upstream) : ANKRD20B (30619 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	96517671	96517672	+	IGR	INS	-	T	T	rs74850741		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96517671_96517672insT								TRIM43 (252204 upstream) : LOC729234 (158627 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	96910125	96910126	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96910125_96910126delAA								LOC285033 (2424 upstream) : TMEM127 (6188 downstream)																																			---	---	---	---
FAHD2B	151313	broad.mit.edu	37	2	97749725	97749725	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97749725delG	uc002sxm.2	-	7	993	c.842delC	c.(841-843)CCAfs	p.P281fs		NM_199336	NP_955368	Q6P2I3	FAH2B_HUMAN	fumarylacetoacetate hydrolase domain containing	281							hydrolase activity|metal ion binding				0																		---	---	---	---
TMEM131	23505	broad.mit.edu	37	2	98573575	98573576	+	Intron	INS	-	T	T	rs34518893		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98573575_98573576insT	uc002syh.3	-						TMEM131_uc010yvg.1_Intron|TMEM131_uc002syi.2_Intron	NM_015348	NP_056163			RW1 protein							integral to membrane				ovary(4)|central_nervous_system(2)	6																		---	---	---	---
INPP4A	3631	broad.mit.edu	37	2	99139234	99139234	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99139234delA	uc002syy.2	+						INPP4A_uc010yvj.1_Intron|INPP4A_uc010yvk.1_Intron|INPP4A_uc002syx.2_Intron|INPP4A_uc010fik.2_Intron	NM_001134224	NP_001127696			inositol polyphosphate-4-phosphatase, type 1						signal transduction		phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity			kidney(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	99556621	99556621	+	IGR	DEL	C	-	-	rs66483342		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99556621delC								C2orf55 (3937 upstream) : TSGA10 (57104 downstream)																																			---	---	---	---
TSGA10	80705	broad.mit.edu	37	2	99685334	99685334	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99685334delA	uc002szg.3	-						TSGA10_uc002szh.3_Intron|TSGA10_uc002szi.3_Intron|TSGA10_uc010fin.1_Intron	NM_182911	NP_878915			testis specific, 10						spermatogenesis	cytoplasm|nuclear membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
AFF3	3899	broad.mit.edu	37	2	100758672	100758673	+	Intron	INS	-	CA	CA	rs142910842	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100758672_100758673insCA	uc002tag.2	-							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	100819764	100819764	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100819764delT								AFF3 (60727 upstream) : LONRF2 (69990 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	101143858	101143858	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101143858delC								NMS (44116 upstream) : PDCL3 (35560 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	101172784	101172784	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101172784delA								NMS (73042 upstream) : PDCL3 (6634 downstream)																																			---	---	---	---
NPAS2	4862	broad.mit.edu	37	2	101582515	101582515	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101582515delT	uc002tap.1	+						NPAS2_uc010yvt.1_Intron	NM_002518	NP_002509			neuronal PAS domain protein 2						central nervous system development|positive regulation of transcription from RNA polymerase II promoter|rhythmic process	transcription factor complex	DNA binding|Hsp90 protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			ovary(3)|upper_aerodigestive_tract(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	101960899	101960899	+	IGR	DEL	A	-	-	rs141875732	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101960899delA								RNF149 (35747 upstream) : CREG2 (3917 downstream)																																			---	---	---	---
RFX8	731220	broad.mit.edu	37	2	102027051	102027051	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102027051delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	102157638	102157638	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102157638delT								RFX8 (66473 upstream) : MAP4K4 (156850 downstream)																																			---	---	---	---
MAP4K4	9448	broad.mit.edu	37	2	102383074	102383075	+	Intron	DEL	TT	-	-	rs68091332		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102383074_102383075delTT	uc002tbg.2	+						MAP4K4_uc002tbc.2_Intron|MAP4K4_uc002tbd.2_Intron|MAP4K4_uc002tbe.2_Intron|MAP4K4_uc002tbf.2_Intron|MAP4K4_uc010yvy.1_Intron|MAP4K4_uc002tbh.2_Intron|MAP4K4_uc002tbi.2_Intron	NM_145687	NP_663720			mitogen-activated protein kinase kinase kinase						intracellular protein kinase cascade|regulation of JNK cascade|response to stress	cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			stomach(1)|lung(1)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
MAP4K4	9448	broad.mit.edu	37	2	102453562	102453564	+	Intron	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102453562_102453564delTTT	uc002tbg.2	+						MAP4K4_uc002tbc.2_Intron|MAP4K4_uc002tbd.2_Intron|MAP4K4_uc002tbe.2_Intron|MAP4K4_uc002tbf.2_Intron|MAP4K4_uc010yvy.1_Intron|MAP4K4_uc002tbh.2_Intron|MAP4K4_uc002tbi.2_Intron|MAP4K4_uc010yvz.1_Intron|MAP4K4_uc010fiw.1_Intron|MAP4K4_uc002tbj.1_Intron	NM_145687	NP_663720			mitogen-activated protein kinase kinase kinase						intracellular protein kinase cascade|regulation of JNK cascade|response to stress	cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			stomach(1)|lung(1)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
MAP4K4	9448	broad.mit.edu	37	2	102503487	102503487	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102503487delA	uc002tbg.2	+						MAP4K4_uc002tbc.2_Intron|MAP4K4_uc002tbd.2_Intron|MAP4K4_uc002tbe.2_Intron|MAP4K4_uc002tbf.2_Intron|MAP4K4_uc010yvy.1_Intron|MAP4K4_uc002tbh.2_Intron|MAP4K4_uc002tbi.2_Intron|MAP4K4_uc010yvz.1_Intron|MAP4K4_uc002tbk.2_Intron|MAP4K4_uc002tbl.2_Intron	NM_145687	NP_663720			mitogen-activated protein kinase kinase kinase						intracellular protein kinase cascade|regulation of JNK cascade|response to stress	cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			stomach(1)|lung(1)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	102665336	102665336	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102665336delA								IL1R2 (20456 upstream) : IL1R1 (21500 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	104619544	104619547	+	IGR	DEL	GAAG	-	-	rs138274633		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:104619544_104619547delGAAG								None (None upstream) : LOC150568 (431258 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	104657212	104657212	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:104657212delT								None (None upstream) : LOC150568 (393593 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	104704577	104704577	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:104704577delT								None (None upstream) : LOC150568 (346228 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	105387605	105387605	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105387605delA								LOC150568 (258391 upstream) : POU3F3 (84364 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	105488532	105488533	+	Intron	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105488532_105488533delAC	uc002tcm.1	-											Homo sapiens cDNA FLJ38179 fis, clone FCBBF1000118.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	105551026	105551027	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105551026_105551027delTT								POU3F3 (77556 upstream) : MRPS9 (103456 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	106961891	106961891	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106961891delT								UXS1 (151096 upstream) : PLGLA (40878 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	107316764	107316766	+	IGR	DEL	AAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:107316764_107316766delAAA								RGPD3 (231963 upstream) : ST6GAL2 (101292 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	107897810	107897810	+	IGR	DEL	T	-	-	rs75512445		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:107897810delT								ST6GAL2 (394247 upstream) : LOC729121 (541710 downstream)																																			---	---	---	---
LIMS1	3987	broad.mit.edu	37	2	109231556	109231558	+	Intron	DEL	TGG	-	-	rs150651782		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109231556_109231558delTGG	uc002teg.2	+						LIMS1_uc002tef.2_Intron|LIMS1_uc002teh.2_Intron|LIMS1_uc002tei.2_Intron	NM_004987	NP_004978			LIM and senescent cell antigen-like domains 1						cell aging|cell junction assembly|cellular response to transforming growth factor beta stimulus|negative regulation of transcription, DNA-dependent	cytosol|focal adhesion|perinuclear region of cytoplasm	protein binding|zinc ion binding				0																		---	---	---	---
LIMS1	3987	broad.mit.edu	37	2	109269375	109269375	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109269375delA	uc002teg.2	+						LIMS1_uc002tef.2_Intron|LIMS1_uc002teh.2_Intron|LIMS1_uc002tei.2_Intron|LIMS1_uc002tej.2_Intron|LIMS1_uc002tek.3_5'Flank	NM_004987	NP_004978			LIM and senescent cell antigen-like domains 1						cell aging|cell junction assembly|cellular response to transforming growth factor beta stimulus|negative regulation of transcription, DNA-dependent	cytosol|focal adhesion|perinuclear region of cytoplasm	protein binding|zinc ion binding				0																		---	---	---	---
CCDC138	165055	broad.mit.edu	37	2	109409518	109409518	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109409518delA	uc002ten.1	+						CCDC138_uc002teo.1_Intron|CCDC138_uc002tep.1_Intron|CCDC138_uc010fjm.1_Intron	NM_144978	NP_659415			coiled-coil domain containing 138												0																		---	---	---	---
MALL	7851	broad.mit.edu	37	2	110854288	110854289	+	Intron	DEL	AC	-	-	rs71383860		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:110854288_110854289delAC	uc002tfk.2	-						MALL_uc010fju.2_Intron	NM_005434	NP_005425			mal, T-cell differentiation protein-like						cholesterol homeostasis	clathrin-coated vesicle|Golgi membrane|integral to membrane|membrane raft|plasma membrane	protein binding			ovary(1)|skin(1)	2				Epithelial(1;0.0546)|STAD - Stomach adenocarcinoma(1;0.18)														---	---	---	---
ACOXL	55289	broad.mit.edu	37	2	111622605	111622606	+	Intron	INS	-	GTTTT	GTTTT	rs147073924	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:111622605_111622606insGTTTT	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	112475539	112475540	+	IGR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112475539_112475540insA								LOC541471 (222847 upstream) : ANAPC1 (51101 downstream)																																			---	---	---	---
ANAPC1	64682	broad.mit.edu	37	2	112576822	112576822	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112576822delA	uc002thi.2	-							NM_022662	NP_073153			anaphase promoting complex subunit 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|cytosol|nucleoplasm				skin(2)	2																		---	---	---	---
MERTK	10461	broad.mit.edu	37	2	112721976	112721979	+	Intron	DEL	GCGC	-	-	rs70962969		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112721976_112721979delGCGC	uc002thk.1	+						MERTK_uc002thl.1_Intron	NM_006343	NP_006334			MER receptor tyrosine kinase precursor						cell surface receptor linked signaling pathway|cell-cell signaling|leukocyte migration	integral to plasma membrane|soluble fraction	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(6)|upper_aerodigestive_tract(1)|stomach(1)|kidney(1)	9																		---	---	---	---
MERTK	10461	broad.mit.edu	37	2	112770607	112770607	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112770607delT	uc002thk.1	+						MERTK_uc002thl.1_Intron	NM_006343	NP_006334			MER receptor tyrosine kinase precursor						cell surface receptor linked signaling pathway|cell-cell signaling|leukocyte migration	integral to plasma membrane|soluble fraction	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(6)|upper_aerodigestive_tract(1)|stomach(1)|kidney(1)	9																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	112789564	112789564	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112789564delA								MERTK (2619 upstream) : TMEM87B (23236 downstream)																																			---	---	---	---
TMEM87B	84910	broad.mit.edu	37	2	112809991	112809992	+	5'Flank	INS	-	AC	AC	rs147016510	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112809991_112809992insAC	uc002thm.2	+						TMEM87B_uc010fkg.2_5'Flank|TMEM87B_uc010fkh.2_5'Flank	NM_032824	NP_116213			transmembrane protein 87B precursor							integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	113022776	113022776	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113022776delA								ZC3H8 (10112 upstream) : ZC3H6 (10402 downstream)																																			---	---	---	---
ZC3H6	376940	broad.mit.edu	37	2	113052558	113052558	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113052558delT	uc002thq.1	+							NM_198581	NP_940983			zinc finger CCCH-type domain containing 6								nucleic acid binding|zinc ion binding			ovary(3)|central_nervous_system(1)	4																		---	---	---	---
POLR1B	84172	broad.mit.edu	37	2	113323526	113323526	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113323526delT	uc002thw.2	+						POLR1B_uc010fkn.2_Intron|POLR1B_uc002thx.2_Intron|POLR1B_uc010fko.2_Intron|POLR1B_uc010fkp.2_Intron|POLR1B_uc010yxn.1_Intron|POLR1B_uc002thy.2_Intron|POLR1B_uc010yxo.1_Intron	NM_019014	NP_061887			RNA polymerase I polypeptide B isoform 1						termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	nucleoplasm	DNA binding|DNA-directed RNA polymerase activity|metal ion binding|protein binding|ribonucleoside binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	113546225	113546225	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113546225delA								IL1A (3254 upstream) : IL1B (41112 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	114147233	114147233	+	IGR	DEL	A	-	-	rs35307977		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114147233delA								PAX8 (110735 upstream) : CBWD2 (48035 downstream)																																			---	---	---	---
DPP10	57628	broad.mit.edu	37	2	115459880	115459880	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:115459880delT	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	116051289	116051289	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:116051289delT	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	117189382	117189384	+	IGR	DEL	ATT	-	-	rs139098997		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:117189382_117189384delATT								DPP10 (587446 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	117280265	117280265	+	IGR	DEL	T	-	-	rs112044137		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:117280265delT								DPP10 (678329 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	117353191	117353191	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:117353191delT								DPP10 (751255 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	117593740	117593741	+	IGR	INS	-	GAGAAAA	GAGAAAA	rs149160785	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:117593740_117593741insGAGAAAA								DPP10 (991804 upstream) : DDX18 (978514 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	118220057	118220057	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:118220057delA								None (None upstream) : DDX18 (352198 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	119425044	119425044	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:119425044delT								INSIG2 (557448 upstream) : EN1 (174704 downstream)																																			---	---	---	---
MARCO	8685	broad.mit.edu	37	2	119730962	119730963	+	Intron	DEL	TC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:119730962_119730963delTC	uc002tln.1	+						MARCO_uc010yyf.1_Intron	NM_006770	NP_006761			macrophage receptor with collagenous structure						cell surface receptor linked signaling pathway|innate immune response	collagen|integral to plasma membrane	pattern recognition receptor activity|scavenger receptor activity			ovary(3)|skin(2)|central_nervous_system(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	119796492	119796492	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:119796492delA								MARCO (44256 upstream) : C1QL2 (117327 downstream)																																			---	---	---	---
PTPN4	5775	broad.mit.edu	37	2	120620318	120620318	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120620318delT	uc002tmf.1	+							NM_002830	NP_002821			protein tyrosine phosphatase, non-receptor type							cytoplasm|cytoskeleton|internal side of plasma membrane	cytoskeletal protein binding|non-membrane spanning protein tyrosine phosphatase activity			ovary(2)	2					Alendronate(DB00630)													---	---	---	---
PTPN4	5775	broad.mit.edu	37	2	120651481	120651481	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120651481delA	uc002tmf.1	+						PTPN4_uc010flj.1_Intron	NM_002830	NP_002821			protein tyrosine phosphatase, non-receptor type							cytoplasm|cytoskeleton|internal side of plasma membrane	cytoskeletal protein binding|non-membrane spanning protein tyrosine phosphatase activity			ovary(2)	2					Alendronate(DB00630)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	121179705	121179705	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121179705delA								INHBB (70322 upstream) : LOC84931 (42206 downstream)																																			---	---	---	---
GLI2	2736	broad.mit.edu	37	2	121711889	121711889	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121711889delG	uc010flp.2	+						GLI2_uc002tmq.1_Intron|GLI2_uc002tmr.1_Intron|GLI2_uc002tmt.3_Intron|GLI2_uc002tmu.3_Intron|GLI2_uc002tmv.1_Intron|GLI2_uc010flo.1_Intron|GLI2_uc002tmw.1_Intron	NM_005270	NP_005261			GLI-Kruppel family member GLI2						axon guidance|branching morphogenesis of a tube|cell proliferation|cerebellar cortex morphogenesis|developmental growth|embryonic digestive tract development|epidermal cell differentiation|floor plate formation|heart development|hindgut morphogenesis|kidney development|lung development|negative regulation of transcription from RNA polymerase II promoter|odontogenesis of dentine-containing tooth|osteoblast development|osteoblast differentiation|pituitary gland development|positive regulation of DNA replication|positive regulation of T cell differentiation in thymus|positive regulation of transcription from RNA polymerase II promoter|proximal/distal pattern formation|skeletal system development|smoothened signaling pathway involved in ventral spinal cord interneuron specification|spinal cord ventral commissure morphogenesis	nucleus|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|lung(2)|breast(1)|central_nervous_system(1)|pancreas(1)	13	Renal(3;0.0496)	Prostate(154;0.0623)																---	---	---	---
Unknown	0	broad.mit.edu	37	2	122538490	122538490	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122538490delC								TSN (13064 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	122637102	122637103	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122637102_122637103delTT								TSN (111676 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	122695147	122695147	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122695147delT								TSN (169721 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	122927499	122927499	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122927499delG								TSN (402073 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	123340828	123340829	+	IGR	INS	-	AAAG	AAAG	rs139779224	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:123340828_123340829insAAAG								TSN (815402 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	124332028	124332031	+	IGR	DEL	TGTG	-	-	rs141638548		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:124332028_124332031delTGTG								None (None upstream) : CNTNAP5 (450833 downstream)																																			---	---	---	---
CNTNAP5	129684	broad.mit.edu	37	2	124918102	124918102	+	Intron	DEL	T	-	-	rs66939847		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:124918102delT	uc002tno.2	+						CNTNAP5_uc010flu.2_Intron	NM_130773	NP_570129			contactin associated protein-like 5 precursor						cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(10)	10				BRCA - Breast invasive adenocarcinoma(221;0.248)														---	---	---	---
CNTNAP5	129684	broad.mit.edu	37	2	125521222	125521222	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:125521222delT	uc002tno.2	+						CNTNAP5_uc010flu.2_Intron	NM_130773	NP_570129			contactin associated protein-like 5 precursor						cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(10)	10				BRCA - Breast invasive adenocarcinoma(221;0.248)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	125688904	125688904	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:125688904delG								CNTNAP5 (16043 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	126047358	126047358	+	IGR	DEL	T	-	-	rs116580998	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:126047358delT								CNTNAP5 (374497 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	127176683	127176683	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:127176683delT								None (None upstream) : GYPC (237001 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	127544655	127544655	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:127544655delA								GYPC (90410 upstream) : BIN1 (260952 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	127747434	127747435	+	IGR	INS	-	T	T	rs148595908	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:127747434_127747435insT								GYPC (293189 upstream) : BIN1 (58172 downstream)																																			---	---	---	---
BIN1	274	broad.mit.edu	37	2	127864113	127864113	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:127864113delG	uc002tns.1	-						BIN1_uc010yzg.1_Intron|BIN1_uc002tnu.1_Intron|BIN1_uc002toa.1_Intron|BIN1_uc002tnt.1_Intron|BIN1_uc002tnv.1_Intron|BIN1_uc002tnw.1_Intron|BIN1_uc002tnx.1_Intron|BIN1_uc002tny.1_Intron|BIN1_uc002tnz.1_Intron|BIN1_uc002tob.1_Intron|BIN1_uc002toc.1_Intron	NM_139343	NP_647593			bridging integrator 1 isoform 1						cell proliferation|endocytosis|interspecies interaction between organisms|multicellular organismal development	actin cytoskeleton|nucleus				ovary(2)|central_nervous_system(2)|skin(2)|lung(1)	7	Colorectal(110;0.0831)			BRCA - Breast invasive adenocarcinoma(221;0.073)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	127916376	127916376	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:127916376delG								BIN1 (51512 upstream) : CYP27C1 (25036 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	128218685	128218685	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128218685delA								PROC (31869 upstream) : IWS1 (19698 downstream)																																			---	---	---	---
MYO7B	4648	broad.mit.edu	37	2	128305995	128305996	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128305995_128305996delTT	uc002top.2	+							NM_001080527	NP_001073996			myosin VIIB							apical plasma membrane|myosin complex	actin binding|ATP binding|motor activity			ovary(1)|pancreas(1)	2	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)														---	---	---	---
WDR33	55339	broad.mit.edu	37	2	128543782	128543782	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128543782delT	uc002tpg.1	-						WDR33_uc002tph.1_Intron|WDR33_uc002tpi.1_Intron	NM_018383	NP_060853			WD repeat domain 33 isoform 1						postreplication repair|spermatogenesis	collagen|nucleus	protein binding				0	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0695)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	128795015	128795016	+	IGR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128795015_128795016insA								SAP130 (9382 upstream) : UGGT1 (53738 downstream)																																			---	---	---	---
UGGT1	56886	broad.mit.edu	37	2	128905186	128905186	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128905186delT	uc002tps.2	+						UGGT1_uc010fme.1_Intron|UGGT1_uc002tpr.2_Intron	NM_020120	NP_064505			UDP-glucose ceramide glucosyltransferase-like 1						'de novo' posttranslational protein folding|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum lumen|ER-Golgi intermediate compartment	UDP-glucose:glycoprotein glucosyltransferase activity|unfolded protein binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	129315937	129315940	+	IGR	DEL	TTTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:129315937_129315940delTTTT								HS6ST1 (239766 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	129776761	129776761	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:129776761delA								HS6ST1 (700590 upstream) : LOC389033 (903674 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	130732402	130732404	+	Intron	DEL	AAA	-	-	rs112393341		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130732402_130732404delAAA	uc002tpw.1	-											Homo sapiens cDNA FLJ41458 fis, clone BRSTN2014490.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	130754030	130754031	+	IGR	INS	-	G	G	rs143208718	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130754030_130754031insG								RAB6C (13719 upstream) : LOC440905 (29541 downstream)																																			---	---	---	---
FAM128A	653784	broad.mit.edu	37	2	132246571	132246571	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132246571delC	uc002tsw.3	-						FAM128A_uc002tsv.3_Intron	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	133026488	133026488	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133026488delG								NCRNA00164 (10946 upstream) : GPR39 (147659 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	133030572	133030572	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133030572delA								NCRNA00164 (15030 upstream) : GPR39 (143575 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	133035721	133035721	+	IGR	DEL	A	-	-	rs144002658		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133035721delA								NCRNA00164 (20179 upstream) : GPR39 (138426 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	133052910	133052911	+	IGR	INS	-	T	T	rs138624541	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133052910_133052911insT								NCRNA00164 (37368 upstream) : GPR39 (121236 downstream)																																			---	---	---	---
GPR39	2863	broad.mit.edu	37	2	133307360	133307360	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133307360delA	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	134068980	134068980	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:134068980delA	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	134090948	134090948	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:134090948delG	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	134441309	134441310	+	IGR	DEL	CA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:134441309_134441310delCA								NCKAP5 (115278 upstream) : MGAT5 (570520 downstream)																																			---	---	---	---
YSK4	80122	broad.mit.edu	37	2	135737014	135737015	+	Intron	DEL	GT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135737014_135737015delGT	uc002tue.1	-						YSK4_uc002tuf.1_Intron|YSK4_uc010fnc.1_Intron|YSK4_uc010fnd.1_Intron|YSK4_uc010zbg.1_Intron	NM_025052	NP_079328			Yeast Sps1/Ste20-related kinase 4 isoform 1								ATP binding|protein serine/threonine kinase activity			stomach(2)|urinary_tract(1)|ovary(1)|breast(1)	5				BRCA - Breast invasive adenocarcinoma(221;0.112)														---	---	---	---
ZRANB3	84083	broad.mit.edu	37	2	136041957	136041958	+	Intron	DEL	TA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136041957_136041958delTA	uc002tum.2	-						ZRANB3_uc002tuk.2_Intron|ZRANB3_uc002tul.2_Intron|ZRANB3_uc002tun.1_Intron	NM_032143	NP_115519			zinc finger, RAN-binding domain containing 3							intracellular	ATP binding|DNA binding|endonuclease activity|helicase activity|zinc ion binding			lung(2)	2				BRCA - Breast invasive adenocarcinoma(221;0.135)														---	---	---	---
ZRANB3	84083	broad.mit.edu	37	2	136072323	136072323	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136072323delT	uc002tum.2	-						ZRANB3_uc002tuk.2_Intron|ZRANB3_uc002tul.2_Intron|ZRANB3_uc002tun.1_Intron	NM_032143	NP_115519			zinc finger, RAN-binding domain containing 3							intracellular	ATP binding|DNA binding|endonuclease activity|helicase activity|zinc ion binding			lung(2)	2				BRCA - Breast invasive adenocarcinoma(221;0.135)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	137368187	137368187	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:137368187delT								CXCR4 (492462 upstream) : THSD7B (154928 downstream)																																			---	---	---	---
THSD7B	80731	broad.mit.edu	37	2	137751392	137751393	+	Intron	DEL	AT	-	-	rs77004886		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:137751392_137751393delAT	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)														---	---	---	---
THSD7B	80731	broad.mit.edu	37	2	138157865	138157865	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:138157865delT	uc002tva.1	+						THSD7B_uc010zbj.1_Intron|THSD7B_uc002tvb.2_Intron	NM_001080427	NP_001073896			thrombospondin, type I, domain containing 7B											ovary(4)|central_nervous_system(2)|pancreas(1)	7				BRCA - Breast invasive adenocarcinoma(221;0.19)														---	---	---	---
THSD7B	80731	broad.mit.edu	37	2	138254783	138254786	+	Intron	DEL	ACAC	-	-	rs138624375		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:138254783_138254786delACAC	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	138850652	138850652	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:138850652delA								HNMT (76719 upstream) : SPOPL (408698 downstream)																																			---	---	---	---
NXPH2	11249	broad.mit.edu	37	2	139450684	139450684	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:139450684delC	uc002tvi.2	-							NM_007226	NP_009157			neurexophilin 2 precursor						neuropeptide signaling pathway	extracellular region				ovary(3)|skin(1)	4				BRCA - Breast invasive adenocarcinoma(221;0.101)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	139890270	139890271	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:139890270_139890271delAA								NXPH2 (352459 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	140038185	140038185	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:140038185delT								NXPH2 (500374 upstream) : LRP1B (950811 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	140092725	140092728	+	IGR	DEL	TCCC	-	-	rs60402279		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:140092725_140092728delTCCC								NXPH2 (554914 upstream) : LRP1B (896268 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	140838792	140838795	+	IGR	DEL	CAAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:140838792_140838795delCAAA								None (None upstream) : LRP1B (150201 downstream)																																			---	---	---	---
LRP1B	53353	broad.mit.edu	37	2	141023708	141023708	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141023708delT	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	141044503	141044503	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141044503delT	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	141167919	141167919	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141167919delT	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	142405661	142405661	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:142405661delG	uc002tvj.1	-						LRP1B_uc010fnl.1_Intron	NM_018557	NP_061027			low density lipoprotein-related protein 1B						protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)											TSP Lung(27;0.18)			---	---	---	---
LRP1B	53353	broad.mit.edu	37	2	142414654	142414654	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:142414654delT	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	142922620	142922620	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:142922620delA								LRP1B (33350 upstream) : KYNU (712575 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	143613435	143613435	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:143613435delA								LRP1B (724165 upstream) : KYNU (21760 downstream)																																			---	---	---	---
KYNU	8942	broad.mit.edu	37	2	143667633	143667634	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:143667633_143667634insT	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)													---	---	---	---
ARHGAP15	55843	broad.mit.edu	37	2	144022690	144022690	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:144022690delA	uc002tvm.3	+						ARHGAP15_uc010zbl.1_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)														---	---	---	---
ARHGAP15	55843	broad.mit.edu	37	2	144200998	144200998	+	Intron	DEL	C	-	-	rs71915524		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:144200998delC	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)														---	---	---	---
ARHGAP15	55843	broad.mit.edu	37	2	144270967	144270967	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:144270967delC	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)														---	---	---	---
ARHGAP15	55843	broad.mit.edu	37	2	144400441	144400441	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:144400441delA	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)														---	---	---	---
ARHGAP15	55843	broad.mit.edu	37	2	144479761	144479762	+	Intron	DEL	CA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:144479761_144479762delCA	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	144546383	144546383	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:144546383delT								ARHGAP15 (20463 upstream) : GTDC1 (157200 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	144596569	144596569	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:144596569delA								ARHGAP15 (70649 upstream) : GTDC1 (107014 downstream)																																			---	---	---	---
GTDC1	79712	broad.mit.edu	37	2	144893962	144893962	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:144893962delA	uc002tvp.2	-						GTDC1_uc002tvo.2_Intron|GTDC1_uc002tvq.2_Intron|GTDC1_uc002tvr.2_Intron|GTDC1_uc010fnn.2_Intron|GTDC1_uc002tvs.2_Intron|GTDC1_uc010fno.2_Intron|GTDC1_uc002tvt.1_Intron	NM_001006636	NP_001006637			glycosyltransferase-like domain containing 1						biosynthetic process		transferase activity, transferring glycosyl groups			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.0914)														---	---	---	---
GTDC1	79712	broad.mit.edu	37	2	145005927	145005927	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:145005927delT	uc002tvp.2	-						GTDC1_uc002tvq.2_Intron|GTDC1_uc002tvr.2_Intron|GTDC1_uc010fnn.2_Intron|GTDC1_uc002tvs.2_Intron|GTDC1_uc010fno.2_Intron|GTDC1_uc002tvt.1_Intron	NM_001006636	NP_001006637			glycosyltransferase-like domain containing 1						biosynthetic process		transferase activity, transferring glycosyl groups			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.0914)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	145348525	145348525	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:145348525delT								ZEB2 (70594 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	145836829	145836829	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:145836829delT	uc002twd.2	+						uc002twe.2_Intron					Homo sapiens, clone IMAGE:5538654, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	145845708	145845708	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:145845708delA	uc002twd.2	+						uc002twe.2_Intron					Homo sapiens, clone IMAGE:5538654, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	146093625	146093625	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:146093625delT								ZEB2 (815694 upstream) : None (None downstream)																																			---	---	---	---
MBD5	55777	broad.mit.edu	37	2	149204838	149204841	+	Intron	DEL	GAAA	-	-	rs3955149		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:149204838_149204841delGAAA	uc002twm.3	+							NM_018328	NP_060798			methyl-CpG binding domain protein 5							chromosome|nucleus	chromatin binding|DNA binding			skin(3)|ovary(2)	5				BRCA - Breast invasive adenocarcinoma(221;0.0569)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	149591652	149591653	+	IGR	INS	-	CTTT	CTTT			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:149591652_149591653insCTTT								EPC2 (46517 upstream) : KIF5C (41166 downstream)																																			---	---	---	---
KIF5C	3800	broad.mit.edu	37	2	149663677	149663678	+	Intron	DEL	GA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:149663677_149663678delGA	uc010zbu.1	+							NM_004522	NP_004513			kinesin family member 5C						microtubule-based movement|organelle organization	cytoplasm|kinesin complex|microtubule	ATP binding|microtubule motor activity			skin(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.108)														---	---	---	---
KIF5C	3800	broad.mit.edu	37	2	149791406	149791407	+	Intron	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:149791406_149791407delAC	uc010zbu.1	+							NM_004522	NP_004513			kinesin family member 5C						microtubule-based movement|organelle organization	cytoplasm|kinesin complex|microtubule	ATP binding|microtubule motor activity			skin(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.108)														---	---	---	---
LYPD6	130574	broad.mit.edu	37	2	150301169	150301169	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:150301169delT	uc002twy.2	+						LYPD6_uc010fnt.2_Intron|LYPD6_uc002twz.2_Intron|LYPD6_uc002txa.2_Intron	NM_194317	NP_919298			LY6/PLAUR domain containing 6 precursor							extracellular region					0				BRCA - Breast invasive adenocarcinoma(221;0.0667)														---	---	---	---
RND3	390	broad.mit.edu	37	2	151344614	151344614	+	5'Flank	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:151344614delT	uc002txe.2	-						RND3_uc002txf.2_5'Flank|RND3_uc002txg.2_5'Flank|RND3_uc010zbv.1_5'Flank|RND3_uc010zbw.1_5'Flank	NM_005168	NP_005159			ras homolog gene family, member E precursor						actin cytoskeleton organization|cell adhesion|small GTPase mediated signal transduction	Golgi membrane	GTP binding|GTPase activity			lung(2)	2				BRCA - Breast invasive adenocarcinoma(221;0.106)												OREG0015012	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	151795725	151795725	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:151795725delT								RND3 (451545 upstream) : RBM43 (309004 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	152007478	152007485	+	IGR	DEL	TTTTTTTA	-	-	rs488574		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152007478_152007485delTTTTTTTA								RND3 (663298 upstream) : RBM43 (97244 downstream)																																			---	---	---	---
RIF1	55183	broad.mit.edu	37	2	152302071	152302071	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152302071delT	uc002txm.2	+						RIF1_uc002txl.2_Intron|RIF1_uc010fnv.1_Intron|RIF1_uc002txn.2_Intron|RIF1_uc002txo.2_Intron	NM_018151	NP_060621			RAP1 interacting factor 1						cell cycle|response to DNA damage stimulus	chromosome, telomeric region|cytoplasm|nucleus|spindle	binding			ovary(5)|breast(4)|skin(3)|lung(2)|kidney(1)	15				BRCA - Breast invasive adenocarcinoma(221;0.0429)														---	---	---	---
NEB	4703	broad.mit.edu	37	2	152358902	152358902	+	Intron	DEL	A	-	-	rs72175331		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152358902delA	uc010fnx.2	-						NEB_uc002txr.2_Intron|RIF1_uc002txp.2_Intron|NEB_uc002txq.2_Intron|NEB_uc010zca.1_Intron|NEB_uc010zcb.1_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	152370226	152370226	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152370226delA	uc010fnx.2	-						NEB_uc002txr.2_Intron|NEB_uc002txt.3_Intron	NM_004543	NP_004534			nebulin isoform 3						muscle filament sliding|muscle organ development|regulation of actin filament length|somatic muscle development	actin cytoskeleton|cytosol|Z disc	actin binding|structural constituent of muscle			ovary(8)|large_intestine(5)|breast(3)|central_nervous_system(2)|skin(1)|pancreas(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.219)														---	---	---	---
FMNL2	114793	broad.mit.edu	37	2	153189300	153189301	+	5'Flank	INS	-	T	T	rs145026643	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:153189300_153189301insT	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	153532455	153532455	+	Intron	DEL	T	-	-	rs79704915		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:153532455delT	uc002tyi.2	-						PRPF40A_uc002tyh.3_Intron|PRPF40A_uc010zcd.1_Intron|PRPF40A_uc002tyj.2_Intron	NM_017892	NP_060362			formin binding protein 3						mRNA processing|RNA splicing	nuclear matrix|nuclear speck	protein binding				0																		---	---	---	---
ARL6IP6	151188	broad.mit.edu	37	2	153595501	153595502	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:153595501_153595502delTT	uc002tyn.2	+						ARL6IP6_uc002tym.2_Intron|ARL6IP6_uc002tyo.2_Intron	NM_152522	NP_689735			ADP-ribosylation-like factor 6 interacting							integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	153699643	153699643	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:153699643delT								ARL6IP6 (81876 upstream) : RPRM (634209 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	154333362	154333362	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:154333362delC								ARL6IP6 (715595 upstream) : RPRM (490 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	154654376	154654376	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:154654376delT								RPRM (319054 upstream) : GALNT13 (74050 downstream)																																			---	---	---	---
GALNT13	114805	broad.mit.edu	37	2	154996135	154996136	+	Intron	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:154996135_154996136delAC	uc002tyr.3	+						GALNT13_uc002tyt.3_Intron|GALNT13_uc010foc.1_5'Flank	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	155515138	155515138	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:155515138delT								GALNT13 (204650 upstream) : KCNJ3 (39955 downstream)																																			---	---	---	---
KCNJ3	3760	broad.mit.edu	37	2	155621984	155621984	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:155621984delC	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	156698882	156698882	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:156698882delA								KCNJ3 (985868 upstream) : NR4A2 (482064 downstream)																																			---	---	---	---
GPD2	2820	broad.mit.edu	37	2	157303091	157303092	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:157303091_157303092delTT	uc002tzf.3	+						GPD2_uc010zch.1_Intron|GPD2_uc002tzd.3_Intron	NM_001083112	NP_001076581			glycerol-3-phosphate dehydrogenase 2,						cellular lipid metabolic process	glycerol-3-phosphate dehydrogenase complex|mitochondrial inner membrane	calcium ion binding|sn-glycerol-3-phosphate:ubiquinone-8 oxidoreductase activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	157640485	157640486	+	IGR	DEL	AG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:157640485_157640486delAG								GPD2 (170238 upstream) : GALNT5 (473854 downstream)																																			---	---	---	---
ACVR1C	130399	broad.mit.edu	37	2	158406602	158406602	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:158406602delT	uc002tzk.3	-						ACVR1C_uc002tzl.3_Intron|ACVR1C_uc010fof.2_Intron|ACVR1C_uc010foe.2_Intron	NM_145259	NP_660302			activin A receptor, type IC isoform 1						apoptosis|cell differentiation|regulation of apoptosis	activin receptor complex	activin receptor activity, type I|ATP binding|transforming growth factor beta receptor activity			lung(3)|ovary(2)|skin(2)	7																		---	---	---	---
ACVR1	90	broad.mit.edu	37	2	158649121	158649122	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:158649121_158649122insT	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	158826546	158826547	+	IGR	DEL	TG	-	-	rs70990627		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:158826546_158826547delTG								ACVR1 (94172 upstream) : UPP2 (25144 downstream)																																			---	---	---	---
CCDC148	130940	broad.mit.edu	37	2	159107284	159107284	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:159107284delT	uc002tzq.2	-	10	1514	c.1251delA	c.(1249-1251)AAAfs	p.K417fs	CCDC148_uc002tzr.2_Frame_Shift_Del_p.K265fs|CCDC148_uc010foh.2_Frame_Shift_Del_p.K130fs	NM_138803	NP_620158	Q8NFR7	CC148_HUMAN	coiled-coil domain containing 148	417	Potential.|Glu/Lys-rich.									ovary(2)	2																		---	---	---	---
PKP4	8502	broad.mit.edu	37	2	159326718	159326721	+	Intron	DEL	TACT	-	-	rs143724945		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:159326718_159326721delTACT	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)			---	---	---	---
PKP4	8502	broad.mit.edu	37	2	159488063	159488063	+	Intron	DEL	T	-	-	rs75092706		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:159488063delT	uc002tzv.2	+						PKP4_uc002tzt.1_Intron|PKP4_uc002tzu.2_Intron|PKP4_uc002tzw.2_Intron|PKP4_uc002tzx.2_Intron|PKP4_uc002tzy.1_Intron|PKP4_uc002tzz.1_Intron|PKP4_uc002uaa.2_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	159876960	159876960	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:159876960delT	uc002uag.2	+						TANC1_uc010fol.1_Intron|TANC1_uc010zcm.1_Intron	NM_033394	NP_203752			tetratricopeptide repeat, ankyrin repeat and							cell junction|postsynaptic density|postsynaptic membrane	binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
TANC1	85461	broad.mit.edu	37	2	159940389	159940389	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:159940389delT	uc002uag.2	+						TANC1_uc010fol.1_Intron|TANC1_uc010zcm.1_Intron|TANC1_uc010fom.1_Intron	NM_033394	NP_203752			tetratricopeptide repeat, ankyrin repeat and							cell junction|postsynaptic density|postsynaptic membrane	binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
TANC1	85461	broad.mit.edu	37	2	160006760	160006760	+	Intron	DEL	T	-	-	rs111498713		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160006760delT	uc002uag.2	+						TANC1_uc010fol.1_Intron|TANC1_uc010zcm.1_Intron|TANC1_uc010fom.1_Intron|TANC1_uc002uah.1_3'UTR	NM_033394	NP_203752			tetratricopeptide repeat, ankyrin repeat and							cell junction|postsynaptic density|postsynaptic membrane	binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
BAZ2B	29994	broad.mit.edu	37	2	160242852	160242853	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160242852_160242853insT	uc002uao.2	-						BAZ2B_uc002uap.2_Intron	NM_013450	NP_038478			bromodomain adjacent to zinc finger domain, 2B						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(3)|skin(1)	4																		---	---	---	---
BAZ2B	29994	broad.mit.edu	37	2	160494588	160494589	+	Intron	DEL	AG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160494588_160494589delAG	uc002uau.1	-											SubName: Full=Putative uncharacterized protein DKFZp686H10114;						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	160651736	160651737	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160651736_160651737delAA	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)														---	---	---	---
PLA2R1	22925	broad.mit.edu	37	2	160843569	160843569	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160843569delA	uc002ube.1	-						PLA2R1_uc010zcp.1_Intron|PLA2R1_uc002ubf.2_Intron	NM_007366	NP_031392			phospholipase A2 receptor 1 isoform 1 precursor						endocytosis	extracellular space|integral to plasma membrane	receptor activity|sugar binding			skin(2)|ovary(1)	3																		---	---	---	---
ITGB6	3694	broad.mit.edu	37	2	161030923	161030924	+	Intron	INS	-	GT	GT	rs141343115	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:161030923_161030924insGT	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																		---	---	---	---
RBMS1	5937	broad.mit.edu	37	2	161282846	161282847	+	Intron	INS	-	AAGG	AAGG	rs138498508	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:161282846_161282847insAAGG	uc002ubo.2	-						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																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	161362923	161362923	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:161362923delT								RBMS1 (12605 upstream) : TANK (630543 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	161366765	161366766	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:161366765_161366766delAA								RBMS1 (16447 upstream) : TANK (626700 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	161623728	161623728	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:161623728delC								RBMS1 (273410 upstream) : TANK (369738 downstream)																																			---	---	---	---
PSMD14	10213	broad.mit.edu	37	2	162199131	162199132	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162199131_162199132delTT	uc002ubu.2	+						uc002ubv.3_5'Flank	NM_005805	NP_005796			proteasome 26S subunit, non-ATPase 14						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K63-linked deubiquitination|regulation of apoptosis|regulation of cellular amino acid metabolic process|regulation of proteasomal protein catabolic process|S phase of mitotic cell cycle|viral reproduction	proteasome complex	endopeptidase activator activity|metal ion binding|metallopeptidase activity|proteasome binding|ubiquitin thiolesterase activity			breast(1)	1																		---	---	---	---
KCNH7	90134	broad.mit.edu	37	2	163399795	163399796	+	Intron	DEL	CA	-	-	rs66895789		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:163399795_163399796delCA	uc002uch.1	-						KCNH7_uc002uci.2_Intron	NM_033272	NP_150375			potassium voltage-gated channel, subfamily H,						regulation of transcription, DNA-dependent	integral to membrane	protein binding|signal transducer activity			ovary(3)|skin(2)	5					Ibutilide(DB00308)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	164297200	164297200	+	IGR	DEL	G	-	-	rs111683121		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:164297200delG								KCNH7 (601960 upstream) : FIGN (166918 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	164873512	164873512	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:164873512delT								FIGN (280999 upstream) : GRB14 (475821 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	165324242	165324243	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165324242_165324243delAA								FIGN (731729 upstream) : GRB14 (25090 downstream)																																			---	---	---	---
COBLL1	22837	broad.mit.edu	37	2	165543108	165543108	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165543108delT	uc010zcw.1	-						COBLL1_uc002ucp.2_Intron|COBLL1_uc002ucq.2_Intron|COBLL1_uc010zcx.1_Intron|COBLL1_uc002ucn.2_Intron|COBLL1_uc002uco.2_Intron	NM_014900	NP_055715			COBL-like 1											ovary(2)|pancreas(1)	3																		---	---	---	---
COBLL1	22837	broad.mit.edu	37	2	165551296	165551296	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165551296delA	uc010zcw.1	-	15	3045	c.2921delT	c.(2920-2922)TTGfs	p.L974fs	COBLL1_uc002ucp.2_Frame_Shift_Del_p.L907fs|COBLL1_uc002ucq.2_Frame_Shift_Del_p.L869fs|COBLL1_uc010zcx.1_Frame_Shift_Del_p.L915fs|COBLL1_uc002ucn.2_Frame_Shift_Del_p.L335fs|COBLL1_uc002uco.2_Frame_Shift_Del_p.L638fs	NM_014900	NP_055715	Q53SF7	COBL1_HUMAN	COBL-like 1	945										ovary(2)|pancreas(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	165859215	165859217	+	IGR	DEL	AAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165859215_165859217delAAA								SLC38A11 (47180 upstream) : SCN3A (84815 downstream)																																			---	---	---	---
SCN2A	6326	broad.mit.edu	37	2	166231096	166231097	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166231096_166231097insT	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	166700711	166700711	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166700711delT								GALNT3 (49542 upstream) : TTC21B (13277 downstream)																																			---	---	---	---
TTC21B	79809	broad.mit.edu	37	2	166756519	166756524	+	Intron	DEL	AAAAAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166756519_166756524delAAAAAA	uc002udk.2	-							NM_024753	NP_079029			tetratricopeptide repeat domain 21B							cilium axoneme|cytoplasm|cytoskeleton	binding			ovary(2)|pancreas(2)|breast(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	167460910	167460911	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:167460910_167460911insT								SCN7A (110193 upstream) : XIRP2 (284086 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	167593690	167593690	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:167593690delT								SCN7A (242973 upstream) : XIRP2 (151307 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	168328171	168328171	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168328171delA								XIRP2 (211912 upstream) : B3GALT1 (347011 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	168777252	168777252	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168777252delA								B3GALT1 (49886 upstream) : STK39 (33279 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	168779262	168779262	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168779262delA								B3GALT1 (51896 upstream) : STK39 (31269 downstream)																																			---	---	---	---
ABCB11	8647	broad.mit.edu	37	2	169824641	169824642	+	Intron	INS	-	TTTC	TTTC	rs10699842		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:169824641_169824642insTTTC	uc002ueo.1	-						ABCB11_uc010zda.1_Intron|ABCB11_uc010zdb.1_Intron	NM_003742	NP_003733			ATP-binding cassette, sub-family B (MDR/TAP),						bile acid biosynthetic process	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus|membrane fraction	ATP binding|bile acid-exporting ATPase activity|canalicular bile acid transmembrane transporter activity|sodium-exporting ATPase activity, phosphorylative mechanism			ovary(2)|large_intestine(2)|breast(1)	5					Adenosine triphosphate(DB00171)|Bosentan(DB00559)|Glibenclamide(DB01016)													---	---	---	---
LRP2	4036	broad.mit.edu	37	2	170075855	170075855	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170075855delA	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	170621792	170621793	+	IGR	DEL	TC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170621792_170621793delTC								KLHL23 (15354 upstream) : SSB (33596 downstream)																																			---	---	---	---
UBR3	130507	broad.mit.edu	37	2	170938525	170938525	+	3'UTR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170938525delT	uc010zdi.1	+	39					UBR3_uc002ufr.3_RNA|UBR3_uc010fqa.2_3'UTR|UBR3_uc002uft.3_3'UTR|UBR3_uc010zdj.1_3'UTR|UBR3_uc002ufu.3_3'UTR	NM_172070	NP_742067			E3 ubiquitin-protein ligase UBR3						sensory perception of smell|suckling behavior|ubiquitin-dependent protein catabolic process	integral to membrane	ubiquitin-protein ligase activity|zinc ion binding				0																		---	---	---	---
MYO3B	140469	broad.mit.edu	37	2	171185914	171185914	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171185914delT	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																		---	---	---	---
TLK1	9874	broad.mit.edu	37	2	172041675	172041675	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172041675delT	uc002ugp.2	-							NM_001136554	NP_001130026			tousled-like kinase 1 isoform 2						cell cycle|chromatin modification|intracellular protein transport|intracellular signal transduction|regulation of chromatin assembly or disassembly|response to DNA damage stimulus	nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(1)	1																		---	---	---	---
TLK1	9874	broad.mit.edu	37	2	172056021	172056023	+	Intron	DEL	AAA	-	-	rs71401411		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172056021_172056023delAAA	uc002ugp.2	-							NM_001136554	NP_001130026			tousled-like kinase 1 isoform 2						cell cycle|chromatin modification|intracellular protein transport|intracellular signal transduction|regulation of chromatin assembly or disassembly|response to DNA damage stimulus	nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(1)	1																		---	---	---	---
METTL8	79828	broad.mit.edu	37	2	172194307	172194309	+	Intron	DEL	AAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172194307_172194309delAAA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	172957568	172957568	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172957568delT								DLX1 (3169 upstream) : DLX2 (6599 downstream)																																			---	---	---	---
DLX2	1746	broad.mit.edu	37	2	172966448	172966449	+	Intron	INS	-	G	G	rs145477323	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172966448_172966449insG	uc002uhn.2	-						DLX2_uc010zdx.1_Intron	NM_004405	NP_004396			distal-less homeobox 2							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.216)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	172994505	172994505	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172994505delT								DLX2 (27027 upstream) : ITGA6 (297577 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	173101751	173101751	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:173101751delC								DLX2 (134273 upstream) : ITGA6 (190331 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	173143743	173143743	+	IGR	DEL	T	-	-	rs67200748		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:173143743delT								DLX2 (176265 upstream) : ITGA6 (148339 downstream)																																			---	---	---	---
ZAK	51776	broad.mit.edu	37	2	174024130	174024131	+	Intron	INS	-	T	T	rs72081014		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174024130_174024131insT	uc002uhz.2	+						ZAK_uc002uhx.2_Intron|ZAK_uc002uhy.2_Intron|ZAK_uc010zei.1_Intron|ZAK_uc002uia.1_Intron	NM_016653	NP_057737			MLK-related kinase isoform 1						activation of JUN kinase activity|activation of MAPKK activity|cell cycle arrest|cell death|cell differentiation|cell proliferation|DNA damage checkpoint|positive regulation of apoptosis|response to radiation	cytoplasm|nucleus	ATP binding|identical protein binding|magnesium ion binding|MAP kinase kinase kinase activity|protein binding			lung(3)|stomach(1)|ovary(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(117;0.176)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	174414005	174414005	+	IGR	DEL	T	-	-	rs112517738		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174414005delT								CDCA7 (180287 upstream) : SP3 (359254 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	174638475	174638475	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174638475delA								CDCA7 (404757 upstream) : SP3 (134784 downstream)																																			---	---	---	---
SCRN3	79634	broad.mit.edu	37	2	175277273	175277273	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:175277273delT	uc002uiq.2	+						SCRN3_uc010zen.1_Intron|SCRN3_uc010zeo.1_Intron|SCRN3_uc002uis.2_Intron	NM_024583	NP_078859			secernin 3						proteolysis		dipeptidase activity			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.229)															---	---	---	---
WIPF1	7456	broad.mit.edu	37	2	175528866	175528867	+	Intron	DEL	CA	-	-	rs6738986	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:175528866_175528867delCA	uc010fqt.1	-						uc002uiw.2_Intron|uc002uix.1_Intron|WIPF1_uc002uja.2_Intron|WIPF1_uc002ujc.1_Intron	NM_003387	NP_003378			WAS/WASL interacting protein family, member 1						actin polymerization or depolymerization|protein complex assembly	cytoplasmic membrane-bounded vesicle	actin binding|profilin binding			ovary(1)|skin(1)	2																		---	---	---	---
ATF2	1386	broad.mit.edu	37	2	176007443	176007456	+	Intron	DEL	GAGAGAGTGTGTGT	-	-	rs71407178		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:176007443_176007456delGAGAGAGTGTGTGT	uc002ujl.2	-						ATF2_uc010fqv.2_Intron|ATF2_uc002ujv.2_Intron|ATF2_uc002ujm.2_Intron|ATF2_uc002ujn.2_Intron|ATF2_uc002ujo.2_Intron|ATF2_uc002ujp.2_Intron|ATF2_uc002ujq.2_Intron|ATF2_uc002ujr.2_Intron|ATF2_uc010fqu.2_Intron|ATF2_uc002ujs.2_Intron|ATF2_uc002ujt.2_Intron|ATF2_uc002uju.2_Intron|ATF2_uc002ujw.1_Intron|ATF2_uc002ujx.1_Intron|ATF2_uc002ujy.1_Intron	NM_001880	NP_001871			activating transcription factor 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	nucleoplasm	protein dimerization activity|sequence-specific DNA binding|transcription coactivator activity|zinc ion binding			lung(1)|breast(1)|pancreas(1)	3			OV - Ovarian serous cystadenocarcinoma(117;0.125)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	176526703	176526703	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:176526703delT								ATP5G3 (480213 upstream) : KIAA1715 (263707 downstream)																																			---	---	---	---
HOXD9	3235	broad.mit.edu	37	2	176987334	176987334	+	5'Flank	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:176987334delT	uc010zex.1	+							NM_014213	NP_055028			homeobox D9							nucleus	sequence-specific DNA binding				0			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.195)	Colorectal(32;0.0226)|READ - Rectum adenocarcinoma(9;0.0556)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	177521713	177521713	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:177521713delG								MIR1246 (55933 upstream) : HNRNPA3 (555709 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	177684178	177684179	+	IGR	INS	-	CCCCA	CCCCA	rs144654706	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:177684178_177684179insCCCCA								MIR1246 (218398 upstream) : HNRNPA3 (393243 downstream)																																			---	---	---	---
NFE2L2	4780	broad.mit.edu	37	2	178124030	178124030	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178124030delA	uc002ulh.3	-						NFE2L2_uc002ulg.3_Intron|NFE2L2_uc010zfa.1_Intron|NFE2L2_uc002uli.3_Intron|NFE2L2_uc010fra.2_Intron|NFE2L2_uc010frb.2_Intron	NM_006164	NP_006155			nuclear factor erythroid 2-like 2 isoform 1						transcription from RNA polymerase II promoter	centrosome|cytosol|nucleus|plasma membrane	protein dimerization activity|protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)	1			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)					Mis		NSCLC|HNSCC					HNSCC(56;0.16)			---	---	---	---
NFE2L2	4780	broad.mit.edu	37	2	178214280	178214281	+	Intron	DEL	GT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178214280_178214281delGT	uc002uli.3	-						LOC100130691_uc002ulk.1_Intron	NM_001145412	NP_001138884			nuclear factor erythroid 2-like 2 isoform 2						transcription from RNA polymerase II promoter	centrosome|cytosol|nucleus|plasma membrane	protein dimerization activity|protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)	1			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)					Mis		NSCLC|HNSCC					HNSCC(56;0.16)			---	---	---	---
PLEKHA3	65977	broad.mit.edu	37	2	179366809	179366809	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179366809delT	uc002umn.2	+							NM_019091	NP_061964			pleckstrin homology domain containing, family A							cytoplasm|membrane				ovary(1)|kidney(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.0266)|all cancers(119;0.0865)															---	---	---	---
CCDC141	285025	broad.mit.edu	37	2	179727182	179727182	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179727182delT	uc002unf.1	-							NM_173648	NP_775919			coiled-coil domain containing 141								protein binding			ovary(7)|pancreas(2)|skin(1)	10			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.0531)|all cancers(119;0.147)															---	---	---	---
ZNF385B	151126	broad.mit.edu	37	2	180408685	180408685	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:180408685delT	uc002unn.3	-						ZNF385B_uc002unj.2_Intron|ZNF385B_uc002unk.2_Intron|ZNF385B_uc002unl.2_Intron|ZNF385B_uc002unm.2_Intron	NM_152520	NP_689733			zinc finger protein 385B isoform 1							nucleus	nucleic acid binding|zinc ion binding			ovary(1)	1			Epithelial(96;0.174)|OV - Ovarian serous cystadenocarcinoma(117;0.201)															---	---	---	---
PPP1R1C	151242	broad.mit.edu	37	2	182864604	182864605	+	Intron	INS	-	TA	TA			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:182864604_182864605insTA	uc002uoo.2	+						PPP1R1C_uc002uon.2_Intron|PPP1R1C_uc002uop.1_Intron|PPP1R1C_uc010frm.1_Intron|PPP1R1C_uc010frn.1_Intron	NM_001080545	NP_001074014			protein phosphatase 1, regulatory (inhibitor)						signal transduction	cytoplasm	protein phosphatase inhibitor activity				0			OV - Ovarian serous cystadenocarcinoma(117;0.0628)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	183508990	183508991	+	IGR	INS	-	TG	TG	rs147464053	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:183508990_183508991insTG								PDE1A (121483 upstream) : DNAJC10 (72008 downstream)																																			---	---	---	---
DNAJC10	54431	broad.mit.edu	37	2	183593883	183593883	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:183593883delT	uc002uow.1	+						DNAJC10_uc002uox.1_Intron|DNAJC10_uc002uoy.1_Intron|DNAJC10_uc002uoz.1_Intron|DNAJC10_uc010fro.1_Intron	NM_018981	NP_061854			DnaJ (Hsp40) homolog, subfamily C, member 10						apoptosis in response to endoplasmic reticulum stress|cell redox homeostasis|ER-associated protein catabolic process|glycerol ether metabolic process|negative regulation of protein phosphorylation|protein folding|response to endoplasmic reticulum stress	endoplasmic reticulum chaperone complex|endoplasmic reticulum lumen|extracellular region	ATPase activator activity|ATPase binding|chaperone binding|electron carrier activity|heat shock protein binding|misfolded protein binding|protein disulfide oxidoreductase activity|unfolded protein binding			ovary(1)|large_intestine(1)|breast(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.0942)|Epithelial(96;0.209)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	184058577	184058577	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:184058577delT								NUP35 (32170 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	185325502	185325502	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:185325502delC								None (None upstream) : ZNF804A (137591 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	185910208	185910208	+	IGR	DEL	A	-	-	rs75697840		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:185910208delA								ZNF804A (105996 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	186603605	186603606	+	5'Flank	INS	-	G	G	rs145859598	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:186603605_186603606insG	uc002upi.3	-											Homo sapiens cDNA clone IMAGE:5271897.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	186659894	186659894	+	RNA	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:186659894delA	uc002upm.2	+	1		c.550delA								Homo sapiens cDNA FLJ44048 fis, clone TESTI4030669.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	187043539	187043539	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187043539delA								None (None upstream) : ZC3H15 (307346 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	187163446	187163446	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187163446delA								None (None upstream) : ZC3H15 (187439 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	187390713	187390714	+	IGR	DEL	TT	-	-	rs111281617		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187390713_187390714delTT								ZC3H15 (16628 upstream) : ITGAV (64076 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	187689007	187689008	+	IGR	INS	-	AAA	AAA	rs149248856	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187689007_187689008insAAA								FAM171B (58323 upstream) : ZSWIM2 (3199 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	187897723	187897724	+	IGR	DEL	AG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187897723_187897724delAG								ZSWIM2 (183826 upstream) : CALCRL (310127 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	188164453	188164453	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:188164453delA								ZSWIM2 (450556 upstream) : CALCRL (43398 downstream)																																			---	---	---	---
CALCRL	10203	broad.mit.edu	37	2	188247707	188247707	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:188247707delT	uc002upv.3	-						CALCRL_uc010frt.2_Intron	NM_005795	NP_005786			calcitonin receptor-like precursor							integral to plasma membrane				lung(3)|ovary(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.0554)|Epithelial(96;0.227)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	190138735	190138735	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190138735delA								COL5A2 (94130 upstream) : WDR75 (167424 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	190349689	190349689	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190349689delT								WDR75 (9425 upstream) : SLC40A1 (75629 downstream)																																			---	---	---	---
SLC40A1	30061	broad.mit.edu	37	2	190448547	190448552	+	5'Flank	DEL	ACATAT	-	-	rs71946330	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190448547_190448552delACATAT	uc002uqr.1	-						SLC40A1_uc002uqs.1_5'Flank					Synthetic construct DNA, clone: pF1KB8672, Homo sapiens SLC40A1 gene for solute carrier family 40 (iron-regulated transporter), member 1, without stop codon, in Flexi system.						anatomical structure morphogenesis|cellular iron ion homeostasis	cytoplasm|integral to plasma membrane	iron ion transmembrane transporter activity|protein binding			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.000917)|Epithelial(96;0.014)|all cancers(119;0.0491)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	191582534	191582535	+	IGR	INS	-	AAC	AAC	rs138472798	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191582534_191582535insAAC								NAB1 (25043 upstream) : GLS (163012 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	191696384	191696385	+	IGR	INS	-	AAAAAAAA	AAAAAAAA	rs116702729	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191696384_191696385insAAAAAAAA								NAB1 (138893 upstream) : GLS (49162 downstream)																																			---	---	---	---
STAT4	6775	broad.mit.edu	37	2	192035977	192035977	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:192035977delT	uc010zgm.1	-						STAT4_uc010zgn.1_Intron|STAT4_uc010zgo.1_Intron					Homo sapiens cDNA FLJ60872 complete cds, moderately similar to Signal transducer and activator of transcription 4.						JAK-STAT cascade	cytoplasm|nucleus	calcium ion binding|protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			breast(3)|skin(2)|lung(1)|ovary(1)|prostate(1)|pancreas(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.00854)|Epithelial(96;0.0864)|all cancers(119;0.204)															---	---	---	---
TMEFF2	23671	broad.mit.edu	37	2	192880805	192880805	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:192880805delA	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	192932083	192932083	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:192932083delG	uc002utc.2	-							NM_016192	NP_057276			transmembrane protein with EGF-like and two							extracellular region|integral to membrane				lung(2)|pancreas(1)|breast(1)|skin(1)	5			OV - Ovarian serous cystadenocarcinoma(117;0.0835)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	195250167	195250168	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:195250167_195250168insT	uc002utf.1	+											Homo sapiens, clone IMAGE:5242593, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	195591971	195591971	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:195591971delA								None (None upstream) : SLC39A10 (929561 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	196060176	196060176	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196060176delA								None (None upstream) : SLC39A10 (461356 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	196949633	196949633	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196949633delT								DNAH7 (16097 upstream) : STK17B (48675 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	196966793	196966794	+	IGR	DEL	CA	-	-	rs140754739		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196966793_196966794delCA								DNAH7 (33257 upstream) : STK17B (31514 downstream)																																			---	---	---	---
HECW2	57520	broad.mit.edu	37	2	197249650	197249650	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197249650delT	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																		---	---	---	---
HECW2	57520	broad.mit.edu	37	2	197370262	197370262	+	Intron	DEL	A	-	-	rs75239387		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197370262delA	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																		---	---	---	---
HSPD1	3329	broad.mit.edu	37	2	198359954	198359954	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198359954delA	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	199532452	199532454	+	IGR	DEL	AAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:199532452_199532454delAAA								PLCL1 (517846 upstream) : SATB2 (601770 downstream)																																			---	---	---	---
SATB2	23314	broad.mit.edu	37	2	200255485	200255485	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:200255485delT	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																		---	---	---	---
SATB2	23314	broad.mit.edu	37	2	200301640	200301640	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:200301640delA	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																		---	---	---	---
FLJ32063	150538	broad.mit.edu	37	2	200340075	200340075	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:200340075delA	uc002uve.1	+											Homo sapiens cDNA FLJ32063 fis, clone OCBBF1000067.												0																		---	---	---	---
C2orf60	129450	broad.mit.edu	37	2	200800573	200800573	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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																		---	---	---	---
SPATS2L	26010	broad.mit.edu	37	2	201192584	201192585	+	Intron	DEL	CA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201192584_201192585delCA	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	201487717	201487717	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201487717delT	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)													---	---	---	---
ALS2CR11	151254	broad.mit.edu	37	2	202444406	202444406	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202444406delT	uc002uye.2	-						ALS2CR11_uc002uyf.2_Intron|ALS2CR11_uc010fti.2_Intron	NM_152525	NP_689738			amyotrophic lateral sclerosis 2 (juvenile)											large_intestine(1)|ovary(1)|skin(1)	3																		---	---	---	---
NOP58	51602	broad.mit.edu	37	2	203149027	203149027	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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																		---	---	---	---
NOP58	51602	broad.mit.edu	37	2	203155725	203155725	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203155725delT	uc002uzb.2	+						SNORD11B_uc010ftq.1_5'Flank|SNORD11_uc002uzd.1_5'Flank	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																		---	---	---	---
ALS2CR8	79800	broad.mit.edu	37	2	203797371	203797373	+	Intron	DEL	GCA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203797371_203797373delGCA	uc002uzo.2	+						ALS2CR8_uc002uzn.2_Intron|ALS2CR8_uc002uzm.2_Intron|ALS2CR8_uc010zhy.1_Intron|ALS2CR8_uc010zhz.1_Intron|ALS2CR8_uc010ftu.1_Intron|ALS2CR8_uc010zia.1_Intron|ALS2CR8_uc010zib.1_Intron|ALS2CR8_uc010zic.1_Intron|ALS2CR8_uc002uzp.2_Intron	NM_001104586	NP_001098056			amyotrophic lateral sclerosis 2 (juvenile)											large_intestine(1)|ovary(1)	2																		---	---	---	---
NBEAL1	65065	broad.mit.edu	37	2	203912633	203912634	+	Intron	DEL	TT	-	-	rs111954808		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203912633_203912634delTT	uc002uzt.3	+						NBEAL1_uc002uzq.3_Intron|NBEAL1_uc010zid.1_Intron|NBEAL1_uc010zie.1_Intron	NM_001114132	NP_001107604			neurobeachin-like 1 isoform 3								binding			ovary(1)|skin(1)	2																		---	---	---	---
ABI2	10152	broad.mit.edu	37	2	204292195	204292196	+	3'UTR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204292195_204292196delTT	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																		---	---	---	---
RAPH1	65059	broad.mit.edu	37	2	204346740	204346741	+	Intron	INS	-	AC	AC	rs9808515	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204346740_204346741insAC	uc002vad.2	-						RAPH1_uc002vae.2_Intron|RAPH1_uc002vaf.2_Intron	NM_213589	NP_998754			Ras association and pleckstrin homology domains						cell-matrix adhesion|signal transduction	cytoplasm|cytoskeleton|filopodium|lamellipodium|nucleus|plasma membrane				ovary(3)|breast(3)|central_nervous_system(2)|lung(1)|skin(1)	10																		---	---	---	---
PARD3B	117583	broad.mit.edu	37	2	205580207	205580208	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:205580207_205580208insT	uc002var.1	+						PARD3B_uc010fub.1_Intron|PARD3B_uc002vao.1_Intron|PARD3B_uc002vap.1_Intron|PARD3B_uc002vaq.1_Intron	NM_152526	NP_689739			par-3 partitioning defective 3 homolog B isoform						cell cycle|cell division	endomembrane system|tight junction				skin(2)|ovary(1)|breast(1)	4		all_cancers(1;2.88e-06)|all_epithelial(1;3.23e-06)		Epithelial(149;0.0739)														---	---	---	---
PARD3B	117583	broad.mit.edu	37	2	205949433	205949433	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:205949433delT	uc002var.1	+						PARD3B_uc010fub.1_Intron|PARD3B_uc002vao.1_Intron|PARD3B_uc002vap.1_Intron|PARD3B_uc002vaq.1_Intron	NM_152526	NP_689739			par-3 partitioning defective 3 homolog B isoform						cell cycle|cell division	endomembrane system|tight junction				skin(2)|ovary(1)|breast(1)	4		all_cancers(1;2.88e-06)|all_epithelial(1;3.23e-06)		Epithelial(149;0.0739)														---	---	---	---
PARD3B	117583	broad.mit.edu	37	2	205983921	205983921	+	Intron	DEL	T	-	-	rs16836973	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:205983921delT	uc002var.1	+						PARD3B_uc010fub.1_Intron|PARD3B_uc002vao.1_Intron|PARD3B_uc002vap.1_Intron|PARD3B_uc002vaq.1_Intron	NM_152526	NP_689739			par-3 partitioning defective 3 homolog B isoform						cell cycle|cell division	endomembrane system|tight junction				skin(2)|ovary(1)|breast(1)	4		all_cancers(1;2.88e-06)|all_epithelial(1;3.23e-06)		Epithelial(149;0.0739)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	207087490	207087490	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207087490delT								GPR1 (4719 upstream) : ZDBF2 (52033 downstream)																																			---	---	---	---
KLF7	8609	broad.mit.edu	37	2	208030440	208030440	+	5'UTR	DEL	A	-	-	rs71412410		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208030440delA	uc002vbz.1	-	1					KLF7_uc002vca.1_Intron	NM_003709	NP_003700			Kruppel-like factor 7 (ubiquitous)						regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|zinc ion binding			central_nervous_system(1)|skin(1)	2				LUSC - Lung squamous cell carcinoma(261;0.0856)|Lung(261;0.166)|Epithelial(149;0.173)														---	---	---	---
MIR1302-4	100302130	broad.mit.edu	37	2	208134663	208134663	+	5'Flank	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208134663delA	hsa-mir-1302-4|MI0006365	-																							0																		---	---	---	---
PLEKHM3	389072	broad.mit.edu	37	2	208695402	208695419	+	Intron	DEL	AAGAAGGACACTTCTTCT	-	-	rs113207130	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208695402_208695419delAAGAAGGACACTTCTTCT	uc002vcl.2	-							NM_001080475	NP_001073944			pleckstrin homology domain containing, family M,						intracellular signal transduction		metal ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	208904831	208904832	+	IGR	INS	-	A	A	rs13422649	byFrequency;by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208904831_208904832insA								PLEKHM3 (14547 upstream) : CRYGD (81500 downstream)																																	OREG0015168	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
C2orf80	389073	broad.mit.edu	37	2	209047928	209047928	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:209047928delT	uc002vcr.2	-							NM_001099334	NP_001092804			hypothetical protein LOC389073											skin(1)	1																		---	---	---	---
PTH2R	5746	broad.mit.edu	37	2	209502908	209502908	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:209502908delT	uc010fuo.1	+											Homo sapiens cDNA FLJ60238 complete cds, highly similar to Parathyroid hormone receptor precursor.							integral to plasma membrane	parathyroid hormone receptor activity			ovary(1)|breast(1)|skin(1)	3				Epithelial(149;0.0684)|Lung(261;0.0785)|LUSC - Lung squamous cell carcinoma(261;0.0836)														---	---	---	---
MAP2	4133	broad.mit.edu	37	2	210307941	210307943	+	Intron	DEL	TTT	-	-	rs143329860		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210307941_210307943delTTT	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	210399251	210399251	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210399251delA	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	210550581	210550581	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210550581delA	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)													---	---	---	---
ERBB4	2066	broad.mit.edu	37	2	212378849	212378849	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:212378849delC	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)			---	---	---	---
IKZF2	22807	broad.mit.edu	37	2	213933637	213933642	+	Intron	DEL	ACACAC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:213933637_213933642delACACAC	uc002vem.2	-						IKZF2_uc010fuu.2_Intron|IKZF2_uc002vej.2_Intron|IKZF2_uc002vek.2_Intron|IKZF2_uc010fuv.2_Intron|IKZF2_uc002vel.2_Intron|IKZF2_uc010fuw.2_Intron|IKZF2_uc010fux.2_Intron|IKZF2_uc010fuy.2_Intron|IKZF2_uc002ven.2_Intron	NM_016260	NP_057344			helios isoform 1						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)														---	---	---	---
SPAG16	79582	broad.mit.edu	37	2	214967635	214967635	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:214967635delA	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)														---	---	---	---
ABCA12	26154	broad.mit.edu	37	2	215811601	215811602	+	Intron	INS	-	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215811601_215811602insC	uc002vew.2	-						ABCA12_uc002vev.2_Intron|ABCA12_uc010zjn.1_Intron	NM_173076	NP_775099			ATP-binding cassette, sub-family A, member 12						cellular homeostasis|lipid transport	integral to membrane	ATP binding|ATPase activity			ovary(6)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	11		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	216581032	216581033	+	Intron	DEL	AT	-	-	rs113603309		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216581032_216581033delAT	uc002vfm.1	-						uc002vfn.1_Intron					Homo sapiens cDNA FLJ34546 fis, clone HLUNG2008959.																														---	---	---	---
MARCH4	57574	broad.mit.edu	37	2	217173140	217173140	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:217173140delA	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	217175971	217175971	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:217175971delT	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)														---	---	---	---
DIRC3	729582	broad.mit.edu	37	2	218508105	218508105	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:218508105delA	uc002vgo.2	-							NR_026597				Homo sapiens cDNA FLJ14199 fis, clone NT2RP3002713.												0																		---	---	---	---
PNKD	25953	broad.mit.edu	37	2	219141364	219141365	+	Intron	INS	-	C	C	rs146501309	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219141364_219141365insC	uc002vhn.2	+						TMBIM1_uc002vhp.1_Intron|TMBIM1_uc010zjz.1_Intron|TMBIM1_uc010zka.1_Intron|TMBIM1_uc002vho.1_Intron	NM_015488	NP_056303			myofibrillogenesis regulator 1 isoform 1							membrane|mitochondrion|nucleus	hydroxyacylglutathione hydrolase activity|zinc ion binding				0		Renal(207;0.0474)		Epithelial(149;7.33e-07)|all cancers(144;0.000133)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	219237777	219237777	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219237777delT								C2orf62 (4961 upstream) : SLC11A1 (8975 downstream)																																			---	---	---	---
VIL1	7429	broad.mit.edu	37	2	219306117	219306118	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219306117_219306118insA	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)														---	---	---	---
VIL1	7429	broad.mit.edu	37	2	219309737	219309737	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219309737delG	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	219775359	219775361	+	Intron	DEL	GAA	-	-	rs78576602		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219775359_219775361delGAA	uc002vje.1	-											Homo sapiens, clone IMAGE:5191738, mRNA.																														---	---	---	---
DNPEP	23549	broad.mit.edu	37	2	220236209	220236209	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220236209delT	uc010zlf.1	-							NM_012100				aspartyl aminopeptidase						peptide metabolic process|proteolysis	cytoplasm	aminopeptidase activity|metallopeptidase activity|protein binding|zinc ion binding				0		Renal(207;0.0474)		Epithelial(149;1.09e-06)|all cancers(144;0.000179)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)	L-Glutamic Acid(DB00142)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	220441437	220441438	+	IGR	DEL	GT	-	-	rs33923026		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220441437_220441438delGT								INHA (1010 upstream) : STK11IP (21158 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	220945776	220945791	+	IGR	DEL	GTGTGTGTGTGTGTGT	-	-	rs72215816		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220945776_220945791delGTGTGTGTGTGTGTGT								SLC4A3 (439075 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	221543218	221543218	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:221543218delA								None (None upstream) : EPHA4 (739531 downstream)																																			---	---	---	---
EPHA4	2043	broad.mit.edu	37	2	222379109	222379110	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:222379109_222379110delTT	uc002vmq.2	-						EPHA4_uc002vmr.2_Intron|EPHA4_uc010zlm.1_Intron|EPHA4_uc010zln.1_Intron	NM_004438	NP_004429			ephrin receptor EphA4 precursor							integral to plasma membrane	ATP binding|ephrin receptor activity			lung(6)|large_intestine(2)|central_nervous_system(2)|urinary_tract(1)|skin(1)	12		Renal(207;0.0183)		Epithelial(121;5.38e-09)|all cancers(144;2.47e-06)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(261;0.0154)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	222728538	222728538	+	IGR	DEL	A	-	-	rs76106221		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:222728538delA								EPHA4 (289616 upstream) : PAX3 (336069 downstream)																																			---	---	---	---
PAX3	5077	broad.mit.edu	37	2	223094895	223094895	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223094895delA	uc010fwo.2	-						PAX3_uc002vmt.1_Intron|PAX3_uc002vmy.1_Intron|PAX3_uc002vmv.1_Intron|PAX3_uc002vmw.1_Intron|PAX3_uc002vmx.1_Intron	NM_181457	NP_852122			paired box 3 isoform PAX3						apoptosis|organ morphogenesis|positive regulation of transcription from RNA polymerase II promoter|sensory perception of sound|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		PAX3/FOXO1(749)|PAX3/NCOA1(8)|PAX3/NCOA2(4)	soft_tissue(761)|ovary(4)|skin(1)	766		Renal(207;0.0183)		Epithelial(121;4.13e-10)|all cancers(144;1.85e-07)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)				T	FOXO1A|NCOA1	alveolar rhabdomyosarcoma		Waardenburg syndrome; craniofacial-deafness-hand syndrome						---	---	---	---
CCDC140	151278	broad.mit.edu	37	2	223167763	223167763	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223167763delT	uc002vnb.1	+							NM_153038	NP_694583			coiled-coil domain containing 140												0		Renal(207;0.0376)		Epithelial(121;4.03e-10)|all cancers(144;1.8e-07)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	223431205	223431205	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223431205delA								SGPP2 (7589 upstream) : FARSB (4957 downstream)																																			---	---	---	---
ACSL3	2181	broad.mit.edu	37	2	223799146	223799146	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223799146delA	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	223817653	223817653	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223817653delA								ACSL3 (8299 upstream) : KCNE4 (99209 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	224156166	224156166	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:224156166delT								KCNE4 (235813 upstream) : SCG2 (305494 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	224493133	224493133	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:224493133delT								SCG2 (26012 upstream) : AP1S3 (126915 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	224534795	224534795	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:224534795delT								SCG2 (67674 upstream) : AP1S3 (85253 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	225025674	225025674	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225025674delG								SERPINE2 (121638 upstream) : FAM124B (217742 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	225227924	225227925	+	IGR	INS	-	AC	AC			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225227924_225227925insAC								SERPINE2 (323888 upstream) : FAM124B (15491 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	225326146	225326147	+	IGR	INS	-	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225326146_225326147insC								FAM124B (59435 upstream) : CUL3 (8722 downstream)																																			---	---	---	---
DOCK10	55619	broad.mit.edu	37	2	225806093	225806093	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225806093delT	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	226919982	226919983	+	IGR	INS	-	A	A	rs57237355		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:226919982_226919983insA								KIAA1486 (324511 upstream) : IRS1 (676051 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	227311677	227311677	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:227311677delA								KIAA1486 (716206 upstream) : IRS1 (284357 downstream)																																			---	---	---	---
IRS1	3667	broad.mit.edu	37	2	227631736	227631736	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:227631736delA	uc002voh.3	-							NM_005544	NP_005535			insulin receptor substrate 1						fibroblast growth factor receptor signaling pathway|glucose homeostasis|insulin receptor signaling pathway|negative regulation of insulin receptor signaling pathway|negative regulation of insulin secretion|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol-mediated signaling|positive regulation of fatty acid beta-oxidation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of insulin receptor signaling pathway|positive regulation of phosphatidylinositol 3-kinase activity	caveola|cytosol|insulin receptor complex|microsome|nucleus	insulin receptor binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase binding|protein kinase C binding|SH2 domain binding|transmembrane receptor protein tyrosine kinase adaptor activity			lung(5)|central_nervous_system(4)|ovary(2)|pancreas(1)	12		Renal(207;0.023)|all_lung(227;0.0994)|all_hematologic(139;0.118)|Esophageal squamous(248;0.23)		Epithelial(121;3.03e-11)|all cancers(144;2.42e-08)|Lung(261;0.00712)|LUSC - Lung squamous cell carcinoma(224;0.0137)														---	---	---	---
IRS1	3667	broad.mit.edu	37	2	227646971	227646972	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:227646971_227646972insT	uc002voh.3	-							NM_005544	NP_005535			insulin receptor substrate 1						fibroblast growth factor receptor signaling pathway|glucose homeostasis|insulin receptor signaling pathway|negative regulation of insulin receptor signaling pathway|negative regulation of insulin secretion|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol-mediated signaling|positive regulation of fatty acid beta-oxidation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of insulin receptor signaling pathway|positive regulation of phosphatidylinositol 3-kinase activity	caveola|cytosol|insulin receptor complex|microsome|nucleus	insulin receptor binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase binding|protein kinase C binding|SH2 domain binding|transmembrane receptor protein tyrosine kinase adaptor activity			lung(5)|central_nervous_system(4)|ovary(2)|pancreas(1)	12		Renal(207;0.023)|all_lung(227;0.0994)|all_hematologic(139;0.118)|Esophageal squamous(248;0.23)		Epithelial(121;3.03e-11)|all cancers(144;2.42e-08)|Lung(261;0.00712)|LUSC - Lung squamous cell carcinoma(224;0.0137)														---	---	---	---
COL4A3	1285	broad.mit.edu	37	2	228120430	228120430	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228120430delT	uc002vom.1	+						COL4A3_uc002von.1_Intron|COL4A3_uc002voo.1_Intron|COL4A3_uc002vop.1_Intron|uc002voq.1_Intron|uc002vor.1_Intron	NM_000091	NP_000082			alpha 3 type IV collagen isoform 1 precursor						activation of caspase activity|axon guidance|blood circulation|cell adhesion|cell proliferation|cell surface receptor linked signaling pathway|glomerular basement membrane development|induction of apoptosis|negative regulation of angiogenesis|negative regulation of cell proliferation|sensory perception of sound	collagen type IV	extracellular matrix structural constituent|integrin binding|metalloendopeptidase inhibitor activity			skin(2)|ovary(1)	3		all_lung(227;0.00101)|Lung NSC(271;0.00278)|Renal(207;0.0112)|Ovarian(221;0.0129)|all_hematologic(139;0.211)|Esophageal squamous(248;0.247)		Epithelial(121;1.17e-46)|all cancers(144;6.87e-42)|Lung(261;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0187)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	228330717	228330717	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228330717delC								TM4SF20 (86695 upstream) : AGFG1 (6171 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	228636767	228636767	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228636767delA								SLC19A3 (54022 upstream) : CCL20 (41791 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	229638277	229638278	+	IGR	INS	-	G	G	rs143466491	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:229638277_229638278insG								SPHKAP (591916 upstream) : PID1 (250412 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	229762565	229762565	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:229762565delT								SPHKAP (716204 upstream) : PID1 (126125 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	230204834	230204834	+	IGR	DEL	G	-	-	rs151212272		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230204834delG								PID1 (68777 upstream) : DNER (17512 downstream)																																			---	---	---	---
DNER	92737	broad.mit.edu	37	2	230574195	230574196	+	Intron	INS	-	TG	TG	rs143241138	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230574195_230574196insTG	uc002vpv.2	-							NM_139072	NP_620711			delta-notch-like EGF repeat-containing						central nervous system development|endocytosis|neuron migration|Notch signaling pathway|synapse assembly	dendrite|early endosome|integral to membrane|plasma membrane	calcium ion binding|clathrin binding|transmembrane receptor activity			lung(5)|ovary(2)|skin(1)	8		all_lung(227;0.00413)|Renal(207;0.0113)|Lung NSC(271;0.0211)|all_hematologic(139;0.105)|Acute lymphoblastic leukemia(138;0.175)		Epithelial(121;1.4e-11)|all cancers(144;7.7e-09)|LUSC - Lung squamous cell carcinoma(224;0.034)|Lung(119;0.0375)														---	---	---	---
TRIP12	9320	broad.mit.edu	37	2	230652431	230652431	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230652431delA	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	230918496	230918496	+	Intron	DEL	A	-	-	rs5028780	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230918496delA	uc002vqd.1	-						FBXO36_uc010fxi.1_Intron|SLC16A14_uc002vqe.2_Intron|SLC16A14_uc002vqf.2_Intron	NM_152527	NP_689740			solute carrier family 16 (monocarboxylic acid							integral to membrane|plasma membrane	symporter activity			ovary(4)|skin(2)	6		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.149)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;7.31e-13)|all cancers(144;5.1e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00948)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	231521345	231521345	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231521345delA								SP100 (111028 upstream) : CAB39 (56212 downstream)																																			---	---	---	---
CAB39	51719	broad.mit.edu	37	2	231674959	231674959	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231674959delT	uc002vqx.2	+						CAB39_uc010fxr.2_Intron|CAB39_uc010fxq.2_Intron	NM_016289	NP_057373			calcium binding protein 39						cell cycle arrest|insulin receptor signaling pathway|regulation of fatty acid oxidation	cytosol	kinase binding			central_nervous_system(1)	1		all_lung(227;4.63e-07)|all_hematologic(139;1.83e-06)|Lung NSC(271;2.11e-05)|Acute lymphoblastic leukemia(138;5.51e-05)|Hepatocellular(293;0.0207)|Lung SC(224;0.187)		all cancers(144;1.64e-12)|Epithelial(121;5.29e-11)|LUSC - Lung squamous cell carcinoma(224;0.0154)|Lung(119;0.0177)|COAD - Colon adenocarcinoma(134;0.226)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	231845287	231845287	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231845287delA								GPR55 (19596 upstream) : SPATA3 (15552 downstream)																																			---	---	---	---
SPATA3	130560	broad.mit.edu	37	2	231885824	231885824	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231885824delT	uc002vrk.2	+							NM_139073				testis and spermatogenesis cell apoptosis						apoptosis|spermatogenesis						0																		---	---	---	---
PDE6D	5147	broad.mit.edu	37	2	232604348	232604348	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232604348delT	uc002vse.1	-						PDE6D_uc002vsf.1_Intron	NM_002601	NP_002592			phosphodiesterase 6D						regulation of GTP catabolic process|response to stimulus|visual perception		3',5'-cyclic-nucleotide phosphodiesterase activity|GTPase inhibitor activity|protein binding				0		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.142)		Epithelial(121;2.19e-12)|BRCA - Breast invasive adenocarcinoma(100;0.00145)|LUSC - Lung squamous cell carcinoma(224;0.0125)|Lung(119;0.0154)														---	---	---	---
DIS3L2	129563	broad.mit.edu	37	2	232865580	232865580	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232865580delT	uc010fxz.2	+						DIS3L2_uc002vsm.3_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)														---	---	---	---
DIS3L2	129563	broad.mit.edu	37	2	232984717	232984717	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232984717delT	uc010fxz.2	+						DIS3L2_uc002vsm.3_Intron|DIS3L2_uc002vsn.1_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)														---	---	---	---
NGEF	25791	broad.mit.edu	37	2	233759235	233759235	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233759235delG	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)														---	---	---	---
UGT1A8	54576	broad.mit.edu	37	2	234551534	234551535	+	Intron	DEL	CT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234551534_234551535delCT	uc002vup.2	+						UGT1A8_uc010zmv.1_Intron|UGT1A10_uc002vuq.3_Intron|UGT1A10_uc002vur.2_Intron	NM_019076	NP_061949			UDP glycosyltransferase 1 family, polypeptide A8						drug metabolic process|fatty acid metabolic process|flavone metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	enzyme inhibitor activity|fatty acid binding|glucuronosyltransferase activity|protein heterodimerization activity|protein homodimerization activity|steroid binding			ovary(2)	2		Breast(86;0.000766)|all_lung(227;0.00271)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0334)|Lung NSC(271;0.0461)|Lung SC(224;0.128)		Epithelial(121;2.56e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000482)|Lung(119;0.00404)|LUSC - Lung squamous cell carcinoma(224;0.008)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	235453538	235453541	+	IGR	DEL	GAGA	-	-	rs66518389		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:235453538_235453541delGAGA								ARL4C (47845 upstream) : SH3BP4 (407087 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	235560980	235560980	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:235560980delT								ARL4C (155287 upstream) : SH3BP4 (299648 downstream)																																			---	---	---	---
SH3BP4	23677	broad.mit.edu	37	2	235938764	235938764	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:235938764delT	uc002vvp.2	+						SH3BP4_uc010fym.2_Intron|SH3BP4_uc002vvq.2_Intron	NM_014521	NP_055336			SH3-domain binding protein 4						endocytosis	clathrin-coated vesicle|coated pit|nucleus	protein binding			skin(3)|ovary(1)	4		Breast(86;0.000332)|Renal(207;0.00339)|all_lung(227;0.00458)|all_hematologic(139;0.0296)|Lung NSC(271;0.0419)		Epithelial(121;7.66e-20)|BRCA - Breast invasive adenocarcinoma(100;0.000402)|Lung(119;0.00299)|LUSC - Lung squamous cell carcinoma(224;0.00645)|GBM - Glioblastoma multiforme(43;0.237)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	236116019	236116019	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236116019delC								SH3BP4 (151663 upstream) : AGAP1 (286717 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	236225477	236225477	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236225477delA								SH3BP4 (261121 upstream) : AGAP1 (177259 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	236247328	236247328	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236247328delT								SH3BP4 (282972 upstream) : AGAP1 (155408 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	237813108	237813108	+	IGR	DEL	A	-	-	rs111828277		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:237813108delA								CXCR7 (322116 upstream) : COPS8 (180976 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	237966508	237966509	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:237966508_237966509delAA								CXCR7 (475516 upstream) : COPS8 (27575 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	238159749	238159749	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238159749delG								COPS8 (152262 upstream) : COL6A3 (72906 downstream)																																			---	---	---	---
SCLY	51540	broad.mit.edu	37	2	238907579	238907579	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238907579delA	uc002vxm.3	+						UBE2F_uc010znn.1_Intron|UBE2F_uc002vxk.2_Intron|UBE2F_uc002vxl.2_Intron|UBE2F_uc010zno.1_Intron|UBE2F_uc010znp.1_Intron	NM_016510	NP_057594			selenocysteine lyase						cellular amino acid metabolic process	cytosol	pyridoxal phosphate binding|selenocysteine lyase activity|transferase activity			ovary(2)	2		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;1.37e-23)|OV - Ovarian serous cystadenocarcinoma(60;4.6e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;8.25e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000128)|Lung(119;0.0118)|LUSC - Lung squamous cell carcinoma(224;0.0285)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	239320787	239320788	+	IGR	INS	-	GTGTGTGTGT	GTGTGTGTGT	rs142200635	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239320787_239320788insGTGTGTGTGT								TRAF3IP1 (11248 upstream) : ASB1 (14838 downstream)																																			---	---	---	---
HDAC4	9759	broad.mit.edu	37	2	240054408	240054408	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240054408delA	uc002vyk.3	-						HDAC4_uc010fyz.1_Intron|HDAC4_uc010zoa.1_Intron|HDAC4_uc010fza.2_Intron|HDAC4_uc010fyy.2_Intron|HDAC4_uc010znz.1_Intron|HDAC4_uc010fzb.1_Intron	NM_006037	NP_006028			histone deacetylase 4						B cell differentiation|cardiac muscle hypertrophy in response to stress|chromatin remodeling|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of glycolysis|negative regulation of myotube differentiation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|nervous system development|peptidyl-lysine deacetylation|positive regulation of cell proliferation|positive regulation of protein sumoylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of protein binding|response to denervation involved in regulation of muscle adaptation|response to interleukin-1|transcription, DNA-dependent	histone deacetylase complex|transcriptional repressor complex	activating transcription factor binding|histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|potassium ion binding|repressing transcription factor binding|zinc ion binding			breast(3)|skin(2)|ovary(1)	6		all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159)		Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	240550436	240550436	+	IGR	DEL	G	-	-	rs66878675		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240550436delG								HDAC4 (227090 upstream) : NDUFA10 (349722 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	240850147	240850147	+	IGR	DEL	G	-	-	rs144628561		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240850147delG								HDAC4 (526801 upstream) : NDUFA10 (50011 downstream)																																			---	---	---	---
MYEOV2	150678	broad.mit.edu	37	2	241066780	241066781	+	Intron	DEL	TC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241066780_241066781delTC	uc002vyu.1	-							NM_138336	NP_612209			hypothetical protein LOC150678 isoform 1												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)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	241087637	241087638	+	IGR	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241087637_241087638delTG								OTOS (7564 upstream) : GPC1 (287477 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	241113820	241113821	+	IGR	DEL	GC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241113820_241113821delGC								OTOS (33747 upstream) : GPC1 (261294 downstream)																																			---	---	---	---
KIF1A	547	broad.mit.edu	37	2	241690222	241690223	+	Intron	INS	-	C	C	rs147825071	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241690222_241690223insC	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)														---	---	---	---
SNED1	25992	broad.mit.edu	37	2	242002194	242002195	+	Intron	DEL	CT	-	-	rs145725032	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242002194_242002195delCT	uc002wah.1	+						SNED1_uc002wai.1_5'Flank|SNED1_uc002waj.1_5'Flank|SNED1_uc002wak.2_5'Flank	NM_001080437	NP_001073906			6720455I24Rik homolog precursor						cell-matrix adhesion	extracellular region	calcium ion binding			breast(1)|central_nervous_system(1)	2		all_cancers(19;7.48e-31)|all_epithelial(40;1.35e-12)|Breast(86;0.000148)|Renal(207;0.00528)|Ovarian(221;0.104)|Esophageal squamous(248;0.131)|all_lung(227;0.17)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;6.46e-32)|all cancers(36;6.23e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.1e-14)|Kidney(56;6.35e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.98e-08)|BRCA - Breast invasive adenocarcinoma(100;3.66e-06)|Lung(119;0.00072)|LUSC - Lung squamous cell carcinoma(224;0.00553)|Colorectal(34;0.0162)|COAD - Colon adenocarcinoma(134;0.109)														---	---	---	---
FARP2	9855	broad.mit.edu	37	2	242392358	242392360	+	Intron	DEL	AAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242392358_242392360delAAA	uc002wbi.1	+						FARP2_uc010zoq.1_Intron|FARP2_uc010zor.1_Intron	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)														---	---	---	---
FARP2	9855	broad.mit.edu	37	2	242417690	242417690	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242417690delG	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	243010760	243010761	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:243010760_243010761delTT								C2orf85 (195278 upstream) : LOC728323 (20083 downstream)																																			---	---	---	---
CNTN6	27255	broad.mit.edu	37	3	1445212	1445212	+	3'UTR	DEL	A	-	-	rs74788015		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:1445212delA	uc003boz.2	+	23					CNTN6_uc011asj.1_3'UTR|CNTN6_uc003bpa.2_3'UTR	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)														---	---	---	---
CNTN4	152330	broad.mit.edu	37	3	2662844	2662845	+	Intron	INS	-	G	G	rs139792809	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:2662844_2662845insG	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	2878603	2878605	+	Intron	DEL	AAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:2878603_2878605delAAA	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)														---	---	---	---
TRNT1	51095	broad.mit.edu	37	3	3183025	3183026	+	Intron	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:3183025_3183026delAC	uc003bpp.3	+						TRNT1_uc010hbv.2_Intron|TRNT1_uc003bpm.2_Intron	NM_182916	NP_886552			tRNA nucleotidyl transferase, CCA-adding, 1						protein targeting to mitochondrion|tRNA 3'-end processing	mitochondrion	ATP binding|tRNA adenylyltransferase activity|tRNA binding				0				Epithelial(13;0.00226)|OV - Ovarian serous cystadenocarcinoma(96;0.00592)|all cancers(10;0.011)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	3259471	3259472	+	IGR	DEL	CA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:3259471_3259472delCA								CRBN (38081 upstream) : SUMF1 (563564 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	3503220	3503220	+	IGR	DEL	T	-	-	rs36080529		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:3503220delT								CRBN (281830 upstream) : SUMF1 (319816 downstream)																																			---	---	---	---
SUMF1	285362	broad.mit.edu	37	3	4341318	4341318	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:4341318delC	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	4342563	4342564	+	Intron	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:4342563_4342564delAC	uc003bps.1	-						SETMAR_uc003bpw.3_5'Flank|SETMAR_uc011asp.1_5'Flank|SETMAR_uc003bpy.3_5'Flank|SETMAR_uc011asq.1_5'Flank|SETMAR_uc011asr.1_5'Flank|SETMAR_uc010hbx.2_5'Flank	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)														---	---	---	---
ITPR1	3708	broad.mit.edu	37	3	4669682	4669682	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:4669682delT	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	4710159	4710159	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:4710159delT	uc003bqa.2	+						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	4787922	4787922	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:4787922delC	uc003bqa.2	+						ITPR1_uc010hca.1_Intron|ITPR1_uc011asu.1_Intron|ITPR1_uc003bqc.2_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	5073818	5073818	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:5073818delA								BHLHE40 (46955 upstream) : ARL8B (90112 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	5079606	5079606	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:5079606delA								BHLHE40 (52743 upstream) : ARL8B (84324 downstream)																																			---	---	---	---
ARL8B	55207	broad.mit.edu	37	3	5212424	5212424	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:5212424delT	uc003bqg.2	+						ARL8B_uc011asx.1_Intron|ARL8B_uc011asy.1_Intron	NM_018184	NP_060654			ADP-ribosylation factor-like 10C						cell cycle|cell division|chromosome segregation|small GTPase mediated signal transduction	late endosome membrane|lysosomal membrane|midbody|spindle midzone	alpha-tubulin binding|beta-tubulin binding|GDP binding|GTP binding|GTPase activity				0				OV - Ovarian serous cystadenocarcinoma(96;0.0717)|Epithelial(13;0.0777)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	5620523	5620523	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:5620523delT								EDEM1 (358874 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	5925091	5925091	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:5925091delA								EDEM1 (663442 upstream) : GRM7 (977711 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	6076492	6076492	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:6076492delT								EDEM1 (814843 upstream) : GRM7 (826310 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	6520599	6520601	+	IGR	DEL	TTT	-	-	rs34305092		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:6520599_6520601delTTT								None (None upstream) : GRM7 (382201 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	6646198	6646198	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:6646198delT	uc003bqj.1	+											Homo sapiens clone P1 NTera2D1 teratocarcinoma mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	8478101	8478103	+	Intron	DEL	AAC	-	-	rs2324623	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:8478101_8478103delAAC	uc003bqp.2	-											Homo sapiens cDNA FLJ42094 fis, clone TESOP2002489.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	8875651	8875651	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:8875651delG								OXTR (64351 upstream) : RAD18 (45910 downstream)																																			---	---	---	---
SRGAP3	9901	broad.mit.edu	37	3	9139089	9139089	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9139089delA	uc003brf.1	-						SRGAP3_uc003brg.1_Intron|SRGAP3_uc003bri.1_Intron|SRGAP3_uc003brk.2_Intron	NM_014850	NP_055665			SLIT-ROBO Rho GTPase activating protein 3						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding		SRGAP3/RAF1(4)	central_nervous_system(4)|skin(3)|urinary_tract(1)|breast(1)	9				OV - Ovarian serous cystadenocarcinoma(96;0.0563)				T	RAF1	pilocytic astrocytoma								---	---	---	---
Unknown	0	broad.mit.edu	37	3	9300971	9300971	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9300971delT								SRGAP3 (9660 upstream) : LOC440944 (90403 downstream)																																			---	---	---	---
LOC440944	440944	broad.mit.edu	37	3	9432957	9432959	+	Intron	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9432957_9432959delTTT	uc003brm.2	-						LOC440944_uc003brq.2_Intron|LOC440944_uc003brp.2_Intron|LOC440944_uc003brr.3_RNA					Homo sapiens hypothetical gene supported by AK128398, mRNA (cDNA clone IMAGE:5266032).											breast(1)	1																		---	---	---	---
SETD5	55209	broad.mit.edu	37	3	9516725	9516725	+	Intron	DEL	T	-	-	rs113358265		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9516725delT	uc003brt.2	+						SETD5_uc003bru.2_Intron|SETD5_uc003brv.2_Intron|SETD5_uc010hck.2_Intron|SETD5_uc003brx.2_Intron	NM_001080517	NP_001073986			SET domain containing 5											ovary(2)	2	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.112)														---	---	---	---
OGG1	4968	broad.mit.edu	37	3	9797996	9797996	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9797996delA	uc003bsi.2	+						OGG1_uc003bsh.2_Intron|OGG1_uc003bsj.2_Intron|OGG1_uc003bsk.2_Intron|OGG1_uc003bsl.2_Intron|OGG1_uc003bsm.2_Intron|OGG1_uc003bsn.2_Intron|OGG1_uc003bso.2_Intron|OGG1_uc003bsp.1_Intron|OGG1_uc010hcm.1_Intron|OGG1_uc003bsq.1_Intron|OGG1_uc003bsr.1_Intron	NM_002542	NP_002533			8-oxoguanine DNA-glycosylase 1 isoform 1a						depurination|nucleotide-excision repair|regulation of protein import into nucleus, translocation|regulation of transcription, DNA-dependent|response to oxidative stress|response to radiation	mitochondrion|nuclear matrix|nuclear speck	damaged DNA binding|endonuclease activity|oxidized purine base lesion DNA N-glycosylase activity|protein binding				0	Medulloblastoma(99;0.227)												BER_DNA_glycosylases					---	---	---	---
FANCD2	2177	broad.mit.edu	37	3	10081107	10081107	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10081107delT	uc003buw.2	+						FANCD2_uc003bux.1_Intron|FANCD2_uc003buy.1_Intron|FANCD2_uc003buv.2_Intron	NM_033084	NP_149075			Fanconi anemia complementation group D2 isoform						DNA repair|response to gamma radiation	nucleoplasm	protein binding|protein binding			central_nervous_system(2)|ovary(1)|skin(1)	4				OV - Ovarian serous cystadenocarcinoma(96;0.148)				D|Mis|N|F			AML|leukemia		Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				---	---	---	---
FANCD2	2177	broad.mit.edu	37	3	10110318	10110318	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10110318delA	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				---	---	---	---
FANCD2	2177	broad.mit.edu	37	3	10128180	10128180	+	Intron	DEL	T	-	-	rs80125759		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10128180delT	uc003buw.2	+						FANCD2_uc003bux.1_Intron|FANCD2_uc003buy.1_Intron|FANCD2_uc010hcw.1_Intron|C3orf24_uc003buz.2_Intron	NM_033084	NP_149075			Fanconi anemia complementation group D2 isoform						DNA repair|response to gamma radiation	nucleoplasm	protein binding|protein binding			central_nervous_system(2)|ovary(1)|skin(1)	4				OV - Ovarian serous cystadenocarcinoma(96;0.148)				D|Mis|N|F			AML|leukemia		Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				---	---	---	---
VHL	7428	broad.mit.edu	37	3	10184982	10184982	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10184982delT	uc003bvc.2	+						VHL_uc003bvd.2_Intron	NM_000551	NP_000542			von Hippel-Lindau tumor suppressor isoform 1						anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding			kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1)	1346				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)			1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				---	---	---	---
ATP2B2	491	broad.mit.edu	37	3	10427117	10427118	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10427117_10427118delAA	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																		---	---	---	---
SLC6A11	6538	broad.mit.edu	37	3	10919922	10919922	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10919922delC	uc003bvz.2	+							NM_014229	NP_055044			solute carrier family 6 (neurotransmitter						neurotransmitter secretion	integral to plasma membrane	gamma-aminobutyric acid:sodium symporter activity|neurotransmitter:sodium symporter activity			skin(3)|ovary(1)	4				OV - Ovarian serous cystadenocarcinoma(96;0.229)														---	---	---	---
HRH1	3269	broad.mit.edu	37	3	11257591	11257591	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:11257591delT	uc010hdr.2	+						HRH1_uc010hds.2_Intron	NM_001098213	NP_001091683			histamine receptor H1						activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|inflammatory response	cytoplasm|integral to plasma membrane|nucleus	histamine receptor activity			large_intestine(1)|ovary(1)	2					Aceprometazine(DB01615)|Astemizole(DB00637)|Azatadine(DB00719)|Azelastine(DB00972)|Benzquinamide(DB00767)|Bepotastine(DB04890)|Bromodiphenhydramine(DB01237)|Brompheniramine(DB00835)|Buclizine(DB00354)|Carbinoxamine(DB00748)|Cetirizine(DB00341)|Chlophedianol(DB04837)|Chlorpheniramine(DB01114)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clemastine(DB00283)|Clozapine(DB00363)|Cyclizine(DB01176)|Cyproheptadine(DB00434)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexbrompheniramine(DB00405)|Dimenhydrinate(DB00985)|Diphenhydramine(DB01075)|Diphenylpyraline(DB01146)|Doxepin(DB01142)|Doxylamine(DB00366)|Emedastine(DB01084)|Epinastine(DB00751)|Fexofenadine(DB00950)|Flunarizine(DB04841)|Histamine Phosphate(DB00667)|Hydroxyzine(DB00557)|Ketotifen(DB00920)|Levocabastine(DB01106)|Loratadine(DB00455)|Maprotiline(DB00934)|Meclizine(DB00737)|Mequitazine(DB01071)|Methdilazine(DB00902)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Mirtazapine(DB00370)|Nedocromil(DB00716)|Olanzapine(DB00334)|Olopatadine(DB00768)|Orphenadrine(DB01173)|Pemirolast(DB00885)|Phenindamine(DB01619)|Pheniramine(DB01620)|Prochlorperazine(DB00433)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Risperidone(DB00734)|Terfenadine(DB00342)|Thiethylperazine(DB00372)|Trazodone(DB00656)|Trimeprazine(DB01246)|Tripelennamine(DB00792)|Triprolidine(DB00427)|Ziprasidone(DB00246)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	12038921	12038922	+	IGR	DEL	TT	-	-	rs75728038		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12038921_12038922delTT								C3orf31 (150569 upstream) : SYN2 (6940 downstream)																																			---	---	---	---
IQSEC1	9922	broad.mit.edu	37	3	12986733	12986733	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12986733delG	uc003bxt.2	-						IQSEC1_uc003bxu.3_Intron|IQSEC1_uc011auw.1_Intron	NM_014869	NP_055684			IQ motif and Sec7 domain 1 isoform b						regulation of ARF protein signal transduction	cytoplasm|nucleus	ARF guanyl-nucleotide exchange factor activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	13134724	13134724	+	IGR	DEL	A	-	-	rs35347959		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:13134724delA								IQSEC1 (20107 upstream) : NUP210 (223013 downstream)																																			---	---	---	---
NUP210	23225	broad.mit.edu	37	3	13367111	13367111	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:13367111delA	uc003bxv.1	-							NM_024923	NP_079199			nucleoporin 210 precursor						carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	endoplasmic reticulum membrane|nuclear membrane|nuclear pore				ovary(3)|large_intestine(3)|skin(3)|pancreas(1)|liver(1)	11	all_neural(104;0.187)																	---	---	---	---
FBLN2	2199	broad.mit.edu	37	3	13570826	13570829	+	5'Flank	DEL	TCCG	-	-	rs2655231	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:13570826_13570829delTCCG	uc011auz.1	+							NM_001998	NP_001989			fibulin 2 isoform b precursor							proteinaceous extracellular matrix	calcium ion binding|extracellular matrix structural constituent			ovary(1)	1			UCEC - Uterine corpus endometrioid carcinoma (1;0.00416)															---	---	---	---
LSM3	27258	broad.mit.edu	37	3	14237449	14237450	+	Intron	INS	-	T	T	rs67496933		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14237449_14237450insT	uc003byn.2	+						uc003byo.1_5'Flank	NM_014463	NP_055278			Lsm3 protein						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay	catalytic step 2 spliceosome|cytosol	protein binding|RNA binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	14640004	14640004	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14640004delT								GRIP2 (56416 upstream) : C3orf19 (53249 downstream)																																			---	---	---	---
ZFYVE20	64145	broad.mit.edu	37	3	15112338	15112339	+	3'UTR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15112338_15112339insT	uc003bzm.1	-	14					ZFYVE20_uc010hek.1_3'UTR	NM_022340	NP_071735			FYVE-finger-containing Rab5 effector protein						blood coagulation|endosome transport|protein transport	early endosome membrane|plasma membrane	protein binding|zinc ion binding			skin(2)	2																		---	---	---	---
CAPN7	23473	broad.mit.edu	37	3	15282164	15282164	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15282164delA	uc003bzn.2	+							NM_014296	NP_055111			calpain 7						proteolysis	nucleus	calcium-dependent cysteine-type endopeptidase activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	15930618	15930619	+	IGR	DEL	TC	-	-	rs145982723		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15930618_15930619delTC								MIR563 (15262 upstream) : GALNTL2 (4950 downstream)																																			---	---	---	---
GALNTL2	117248	broad.mit.edu	37	3	16002237	16002238	+	Intron	DEL	TC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:16002237_16002238delTC	uc003caq.3	+							NM_054110	NP_473451			UDP-N-acetyl-alpha-D-galactosamine:polypeptide							Golgi membrane|integral to membrane|transport vesicle	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			breast(1)	1																		---	---	---	---
GALNTL2	117248	broad.mit.edu	37	3	16174154	16174154	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:16174154delA	uc003caq.3	+							NM_054110	NP_473451			UDP-N-acetyl-alpha-D-galactosamine:polypeptide							Golgi membrane|integral to membrane|transport vesicle	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			breast(1)	1																		---	---	---	---
GALNTL2	117248	broad.mit.edu	37	3	16192519	16192520	+	Intron	DEL	CT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:16192519_16192520delCT	uc003caq.3	+							NM_054110	NP_473451			UDP-N-acetyl-alpha-D-galactosamine:polypeptide							Golgi membrane|integral to membrane|transport vesicle	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			breast(1)	1																		---	---	---	---
GALNTL2	117248	broad.mit.edu	37	3	16209341	16209341	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:16209341delA	uc003caq.3	+							NM_054110	NP_473451			UDP-N-acetyl-alpha-D-galactosamine:polypeptide							Golgi membrane|integral to membrane|transport vesicle	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			breast(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	16667898	16667899	+	IGR	DEL	AA	-	-	rs36001672		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:16667898_16667899delAA								DAZL (20892 upstream) : PLCL2 (176260 downstream)																																			---	---	---	---
PLCL2	23228	broad.mit.edu	37	3	17050785	17050786	+	Intron	DEL	AT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:17050785_17050786delAT	uc011awc.1	+						PLCL2_uc010het.1_Intron|PLCL2_uc011awd.1_Intron	NM_001144382	NP_001137854			phospholipase C-like 2 isoform 1						intracellular signal transduction|lipid metabolic process	cytoplasm	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			skin(2)|ovary(1)|lung(1)	4																		---	---	---	---
TBC1D5	9779	broad.mit.edu	37	3	17533934	17533934	+	Intron	DEL	T	-	-	rs35021712		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:17533934delT	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	18805219	18805220	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:18805219_18805220delTT								SATB1 (324967 upstream) : KCNH8 (384797 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	19011189	19011190	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:19011189_19011190delAA								SATB1 (530937 upstream) : KCNH8 (178827 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	19785222	19785222	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:19785222delT								KCNH8 (208087 upstream) : EFHB (135746 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	19810045	19810046	+	IGR	DEL	GA	-	-	rs60340159		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:19810045_19810046delGA								KCNH8 (232910 upstream) : EFHB (110922 downstream)																																			---	---	---	---
EFHB	151651	broad.mit.edu	37	3	19940096	19940096	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:19940096delA	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	20751150	20751150	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:20751150delA								SGOL1 (523467 upstream) : VENTXP7 (696068 downstream)																																			---	---	---	---
ZNF385D	79750	broad.mit.edu	37	3	22172482	22172482	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:22172482delA	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	23226343	23226343	+	IGR	DEL	C	-	-	rs76978067		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:23226343delC								ZNF385D (812220 upstream) : UBE2E2 (18310 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	24795306	24795306	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:24795306delT								THRB (258853 upstream) : RARB (420517 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	24997966	24997966	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:24997966delT								THRB (461513 upstream) : RARB (217857 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	25039984	25039985	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:25039984_25039985delAA								THRB (503531 upstream) : RARB (175838 downstream)																																			---	---	---	---
NGLY1	55768	broad.mit.edu	37	3	25826714	25826714	+	5'Flank	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:25826714delT	uc003cdl.2	-						NGLY1_uc010hfg.2_5'Flank|NGLY1_uc003cdm.2_5'Flank|NGLY1_uc011awo.1_Intron	NM_018297	NP_060767			N-glycanase 1 isoform 1						glycoprotein catabolic process	cytoplasm	metal ion binding|peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity|protein binding			breast(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	25855250	25855252	+	IGR	DEL	TTT	-	-	rs35218360		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:25855250_25855252delTTT								OXSM (19226 upstream) : LRRC3B (809048 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	27997386	27997387	+	IGR	INS	-	CCTTC	CCTTC			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27997386_27997387insCCTTC								EOMES (233180 upstream) : CMC1 (285737 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	28910418	28910418	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:28910418delT								ZCWPW2 (343788 upstream) : RBMS3 (412525 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	29275884	29275887	+	IGR	DEL	AAAA	-	-	rs75288130		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:29275884_29275887delAAAA								ZCWPW2 (709254 upstream) : RBMS3 (47056 downstream)																																			---	---	---	---
RBMS3	27303	broad.mit.edu	37	3	29542329	29542330	+	Intron	INS	-	TG	TG	rs151036945	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:29542329_29542330insTG	uc003cel.2	+						RBMS3_uc003cek.2_Intron|RBMS3_uc010hfq.2_Intron|RBMS3_uc003cem.2_Intron|RBMS3_uc010hfr.2_Intron	NM_001003793	NP_001003793			RNA binding motif, single stranded interacting							cytoplasm	nucleotide binding|RNA binding			central_nervous_system(1)	1		Ovarian(412;0.0956)																---	---	---	---
RBMS3	27303	broad.mit.edu	37	3	30045474	30045474	+	3'UTR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:30045474delT	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)																---	---	---	---
GADL1	339896	broad.mit.edu	37	3	30795986	30795987	+	Intron	INS	-	T	T	rs139870562	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:30795986_30795987insT	uc003cep.2	-							NM_207359	NP_997242			glutamate decarboxylase-like 1						carboxylic acid metabolic process		carboxy-lyase activity|pyridoxal phosphate binding				0					Pyridoxal Phosphate(DB00114)													---	---	---	---
OSBPL10	114884	broad.mit.edu	37	3	31703885	31703885	+	Intron	DEL	A	-	-	rs35980971		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:31703885delA	uc003cev.2	-						OSBPL10_uc003ceu.1_3'UTR|OSBPL10_uc011axf.1_Intron	NM_017784	NP_060254			oxysterol-binding protein-like protein 10						lipid transport		lipid binding			skin(1)	1				STAD - Stomach adenocarcinoma(1;0.00406)														---	---	---	---
OSBPL10	114884	broad.mit.edu	37	3	31710397	31710397	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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)														---	---	---	---
OSBPL10	114884	broad.mit.edu	37	3	31730611	31730611	+	Intron	DEL	A	-	-	rs34009655		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:31730611delA	uc003cev.2	-						OSBPL10_uc003ceu.1_Intron|OSBPL10_uc011axf.1_Intron	NM_017784	NP_060254			oxysterol-binding protein-like protein 10						lipid transport		lipid binding			skin(1)	1				STAD - Stomach adenocarcinoma(1;0.00406)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	32234227	32234227	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32234227delA								GPD1L (24031 upstream) : CMTM8 (45944 downstream)																																			---	---	---	---
CMTM7	112616	broad.mit.edu	37	3	32493537	32493537	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32493537delT	uc003cey.1	+						CMTM7_uc003cez.1_Intron	NM_138410	NP_612419			CKLF-like MARVEL transmembrane domain containing						chemotaxis	extracellular space|integral to membrane	cytokine activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	32722360	32722362	+	IGR	DEL	ATT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32722360_32722362delATT								DYNC1LI1 (110010 upstream) : CNOT10 (4336 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	32849762	32849762	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32849762delA								CNOT10 (34408 upstream) : TRIM71 (9748 downstream)																																			---	---	---	---
CLASP2	23122	broad.mit.edu	37	3	33678869	33678869	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33678869delA	uc003cfu.2	-						CLASP2_uc003cft.2_Intron|CLASP2_uc010hgb.2_Intron|CLASP2_uc003cfv.2_Intron|CLASP2_uc011axu.1_Intron|CLASP2_uc003cfw.2_Intron	NM_015097	NP_055912			CLIP-associating protein 2											ovary(3)|central_nervous_system(1)	4																		---	---	---	---
ARPP21	10777	broad.mit.edu	37	3	35723675	35723675	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:35723675delT	uc003cgb.2	+						ARPP21_uc003cga.2_Intron|ARPP21_uc011axy.1_Intron|ARPP21_uc003cfz.2_Intron|ARPP21_uc003cgc.2_Intron|ARPP21_uc003cgd.2_Intron|ARPP21_uc011axx.1_Intron|ARPP21_uc003cge.2_Intron	NM_016300	NP_057384			cyclic AMP-regulated phosphoprotein, 21 kD							cytoplasm	nucleic acid binding			ovary(2)|skin(1)	3																		---	---	---	---
ARPP21	10777	broad.mit.edu	37	3	35748755	35748755	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:35748755delA	uc003cgb.2	+						ARPP21_uc003cga.2_Intron|ARPP21_uc011axy.1_Intron|ARPP21_uc003cgf.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	35911697	35911698	+	IGR	DEL	TT	-	-	rs72270962		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:35911697_35911698delTT								ARPP21 (75710 upstream) : STAC (510399 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	36980451	36980452	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:36980451_36980452delAA								TRANK1 (78040 upstream) : EPM2AIP1 (46906 downstream)																																			---	---	---	---
ITGA9	3680	broad.mit.edu	37	3	37687053	37687054	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37687053_37687054insA	uc003chd.2	+							NM_002207	NP_002198			integrin, alpha 9 precursor						axon guidance|cell adhesion|integrin-mediated signaling pathway	integrin complex	receptor activity			breast(3)|pancreas(1)|lung(1)|skin(1)	6				KIRC - Kidney renal clear cell carcinoma(284;0.165)|Kidney(284;0.197)														---	---	---	---
CTDSPL	10217	broad.mit.edu	37	3	37940667	37940667	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37940667delG	uc003chg.2	+						CTDSPL_uc003chh.2_Intron	NM_001008392	NP_001008393			small CTD phosphatase 3 isoform 1							nucleus	metal ion binding|phosphoprotein phosphatase activity				0		Melanoma(1037;0.0122)		KIRC - Kidney renal clear cell carcinoma(284;0.0729)|Kidney(284;0.0902)														---	---	---	---
CTDSPL	10217	broad.mit.edu	37	3	37963730	37963730	+	Intron	DEL	A	-	-	rs77932154		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37963730delA	uc003chg.2	+						CTDSPL_uc003chh.2_Intron	NM_001008392	NP_001008393			small CTD phosphatase 3 isoform 1							nucleus	metal ion binding|phosphoprotein phosphatase activity				0		Melanoma(1037;0.0122)		KIRC - Kidney renal clear cell carcinoma(284;0.0729)|Kidney(284;0.0902)														---	---	---	---
EXOG	9941	broad.mit.edu	37	3	38539074	38539074	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38539074delT	uc003cih.2	+						EXOG_uc010hhg.2_Intron|EXOG_uc011ayq.1_Intron|EXOG_uc003cij.2_Intron|EXOG_uc010hhd.2_Intron|EXOG_uc010hhe.2_Intron|EXOG_uc003cik.2_Intron|EXOG_uc010hhf.2_Intron|EXOG_uc003cii.2_Intron	NM_005107	NP_005098			endo/exonuclease (5'-3'), endonuclease G-like							mitochondrial inner membrane	endonuclease activity|metal ion binding|nucleic acid binding				0																		---	---	---	---
SCN5A	6331	broad.mit.edu	37	3	38627658	38627659	+	Intron	INS	-	C	C	rs144923222	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38627658_38627659insC	uc003cio.2	-						SCN5A_uc003cin.2_Intron|SCN5A_uc003cil.3_Intron|SCN5A_uc010hhi.2_Intron|SCN5A_uc010hhk.2_Intron|SCN5A_uc011ayr.1_Intron|SCN5A_uc010hhj.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)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	38711510	38711510	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38711510delA								SCN5A (20346 upstream) : SCN10A (27328 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	38720845	38720852	+	IGR	DEL	TAGGGGTC	-	-	rs113250970		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38720845_38720852delTAGGGGTC								SCN5A (29681 upstream) : SCN10A (17986 downstream)																																			---	---	---	---
SCN11A	11280	broad.mit.edu	37	3	38969843	38969844	+	Intron	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38969843_38969844delAC	uc011ays.1	-							NM_014139	NP_054858			sodium channel, voltage-gated, type XI, alpha						response to drug	voltage-gated sodium channel complex	voltage-gated sodium channel activity			skin(6)|ovary(1)|haematopoietic_and_lymphoid_tissue(1)|pancreas(1)	9				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)													---	---	---	---
MYRIP	25924	broad.mit.edu	37	3	40301475	40301477	+	3'UTR	DEL	AGC	-	-	rs10568656		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:40301475_40301477delAGC	uc003cka.2	+	17					MYRIP_uc010hhu.2_RNA|MYRIP_uc010hhv.2_3'UTR|MYRIP_uc010hhw.2_3'UTR|MYRIP_uc011ayz.1_3'UTR|uc003ckb.2_Intron	NM_015460	NP_056275			myosin VIIA and Rab interacting protein						intracellular protein transport		actin binding|zinc ion binding			ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	5				KIRC - Kidney renal clear cell carcinoma(284;0.174)|Kidney(284;0.206)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	40403166	40403166	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:40403166delG								EIF1B (49253 upstream) : ENTPD3 (25507 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	41183767	41183767	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41183767delA								ZNF621 (602724 upstream) : CTNNB1 (52634 downstream)																																			---	---	---	---
ULK4	54986	broad.mit.edu	37	3	41949941	41949941	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41949941delT	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)														---	---	---	---
HHATL	57467	broad.mit.edu	37	3	42746571	42746572	+	5'Flank	INS	-	TTGC	TTGC	rs112660480		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42746571_42746572insTTGC	uc003clx.2	-							NM_020707	NP_065758			hedgehog acyltransferase-like						negative regulation of N-terminal protein palmitoylation	endoplasmic reticulum membrane|integral to membrane|perinuclear region of cytoplasm				ovary(3)	3				KIRC - Kidney renal clear cell carcinoma(284;0.215)														---	---	---	---
CCDC13	152206	broad.mit.edu	37	3	42798875	42798875	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42798875delA	uc003cly.3	-						CCDC13_uc003clz.2_Intron|CCDC13_uc011azq.1_Intron	NM_144719	NP_653320			coiled-coil domain containing 13											ovary(1)	1																		---	---	---	---
CYP8B1	1582	broad.mit.edu	37	3	42901743	42901744	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42901743_42901744insA	uc010hif.2	-						CCBP2_uc003cmd.1_Intron|CCBP2_uc003cme.2_Intron|CCBP2_uc003cmf.2_Intron|CCBP2_uc003cmg.2_Intron	NM_004391	NP_004382			cytochrome P450, family 8, subfamily B,						bile acid biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	7alpha-hydroxycholest-4-en-3-one 12alpha-hydroxylase activity|electron carrier activity|heme binding|oxygen binding|sterol 12-alpha-hydroxylase activity			ovary(2)	2				KIRC - Kidney renal clear cell carcinoma(284;0.213)|Kidney(284;0.249)														---	---	---	---
C3orf39	84892	broad.mit.edu	37	3	43127256	43127256	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:43127256delA	uc003cmq.1	-						C3orf39_uc003cmr.1_Intron	NM_032806	NP_116195			glycosyltransferase precursor							extracellular region	transferase activity, transferring glycosyl groups			ovary(1)|skin(1)	2				KIRC - Kidney renal clear cell carcinoma(284;0.0571)|Kidney(284;0.0718)														---	---	---	---
KIF15	56992	broad.mit.edu	37	3	44890183	44890183	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44890183delT	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	44979484	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44979483_44979484delTT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	45228581	45228581	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45228581delG								CDCP1 (40667 upstream) : TMEM158 (37376 downstream)																																			---	---	---	---
CCR2	729230	broad.mit.edu	37	3	46393933	46393935	+	5'Flank	DEL	ACA	-	-	rs35424113		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46393933_46393935delACA	uc003cpn.3	+						CCR2_uc003cpm.3_5'Flank	NM_001123041	NP_001116513			chemokine (C-C motif) receptor 2 isoform A						astrocyte cell migration|blood vessel remodeling|cellular defense response|chemokine-mediated signaling pathway|dendritic cell chemotaxis|elevation of cytosolic calcium ion concentration|immune response|inflammatory response|interspecies interaction between organisms|JAK-STAT cascade|monocyte extravasation|negative regulation of adenylate cyclase activity|negative regulation of angiogenesis|negative regulation of eosinophil degranulation|negative regulation of type 2 immune response|positive regulation of alpha-beta T cell proliferation|positive regulation of immune complex clearance by monocytes and macrophages|positive regulation of inflammatory response|positive regulation of interferon-gamma production|positive regulation of interleukin-2 production|positive regulation of monocyte chemotaxis|positive regulation of T cell chemotaxis|positive regulation of T cell extravasation|positive regulation of T-helper 1 type immune response|positive regulation of tumor necrosis factor biosynthetic process|regulation of vascular endothelial growth factor production|T-helper 17 cell chemotaxis	cytosol|dendrite|integral to plasma membrane|perikaryon|perinuclear region of cytoplasm|soluble fraction	C-C chemokine receptor activity|CCR2 chemokine receptor binding|protein homodimerization activity			lung(1)|breast(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.00114)|KIRC - Kidney renal clear cell carcinoma(197;0.0174)|Kidney(197;0.0206)														---	---	---	---
CCR2	729230	broad.mit.edu	37	3	46401710	46401710	+	3'UTR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46401710delG	uc003cpn.3	+	3						NM_001123041	NP_001116513			chemokine (C-C motif) receptor 2 isoform A						astrocyte cell migration|blood vessel remodeling|cellular defense response|chemokine-mediated signaling pathway|dendritic cell chemotaxis|elevation of cytosolic calcium ion concentration|immune response|inflammatory response|interspecies interaction between organisms|JAK-STAT cascade|monocyte extravasation|negative regulation of adenylate cyclase activity|negative regulation of angiogenesis|negative regulation of eosinophil degranulation|negative regulation of type 2 immune response|positive regulation of alpha-beta T cell proliferation|positive regulation of immune complex clearance by monocytes and macrophages|positive regulation of inflammatory response|positive regulation of interferon-gamma production|positive regulation of interleukin-2 production|positive regulation of monocyte chemotaxis|positive regulation of T cell chemotaxis|positive regulation of T cell extravasation|positive regulation of T-helper 1 type immune response|positive regulation of tumor necrosis factor biosynthetic process|regulation of vascular endothelial growth factor production|T-helper 17 cell chemotaxis	cytosol|dendrite|integral to plasma membrane|perikaryon|perinuclear region of cytoplasm|soluble fraction	C-C chemokine receptor activity|CCR2 chemokine receptor binding|protein homodimerization activity			lung(1)|breast(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.00114)|KIRC - Kidney renal clear cell carcinoma(197;0.0174)|Kidney(197;0.0206)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	46463382	46463391	+	IGR	DEL	TACAGGTTTC	-	-	rs78991305		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46463382_46463391delTACAGGTTTC								CCRL2 (12369 upstream) : LTF (14106 downstream)																																			---	---	---	---
LTF	4057	broad.mit.edu	37	3	46507404	46507407	+	5'Flank	DEL	ATAT	-	-	rs139025294		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46507404_46507407delATAT	uc003cpq.2	-						LTF_uc003fzr.2_5'Flank|LTF_uc010hjh.2_5'Flank|LTF_uc003cpr.2_Intron	NM_002343	NP_002334			lactotransferrin precursor						cellular iron ion homeostasis|defense response to bacterium|humoral immune response|iron ion transport	extracellular region|stored secretory granule	ferric iron binding|heparin binding|protein binding|serine-type endopeptidase activity			central_nervous_system(2)|ovary(1)|lung(1)	4				all cancers(1;7.55e-14)|GBM - Glioblastoma multiforme(1;2.1e-09)|Epithelial(1;9.25e-07)|Colorectal(1;3.81e-05)|BRCA - Breast invasive adenocarcinoma(193;0.00129)|COAD - Colon adenocarcinoma(1;0.00308)|KIRC - Kidney renal clear cell carcinoma(197;0.0205)|Kidney(197;0.0242)|OV - Ovarian serous cystadenocarcinoma(275;0.089)	Pefloxacin(DB00487)													---	---	---	---
LRRC2	79442	broad.mit.edu	37	3	46560368	46560368	+	3'UTR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46560368delT	uc010hji.2	-	9					LRRC2_uc003cpu.3_3'UTR	NM_024512	NP_078788			leucine rich repeat containing 2											ovary(1)	1		Ovarian(412;0.0563)		OV - Ovarian serous cystadenocarcinoma(275;6.37e-05)|BRCA - Breast invasive adenocarcinoma(193;0.00133)|KIRC - Kidney renal clear cell carcinoma(197;0.0214)|Kidney(197;0.0254)														---	---	---	---
NBEAL2	23218	broad.mit.edu	37	3	47048247	47048247	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47048247delT	uc003cqp.2	+						NBEAL2_uc010hjm.1_Intron|NBEAL2_uc010hjn.1_Intron|NBEAL2_uc010hjo.1_Intron	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)														---	---	---	---
SETD2	29072	broad.mit.edu	37	3	47155171	47155172	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47155171_47155172insA	uc003cqs.2	-						SETD2_uc003cqv.2_Intron	NM_014159	NP_054878			SET domain containing 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	DNA binding|histone-lysine N-methyltransferase activity|oxidoreductase activity|transition metal ion binding			kidney(24)|ovary(5)|skin(1)|central_nervous_system(1)|breast(1)	32		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)				N|F|S|Mis		clear cell renal carcinoma								---	---	---	---
KLHL18	23276	broad.mit.edu	37	3	47364585	47364585	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47364585delT	uc003crd.2	+						KLHL18_uc003crc.2_Intron|KLHL18_uc011bav.1_Intron	NM_025010	NP_079286			kelch-like 18												0		Acute lymphoblastic leukemia(5;0.164)		BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00645)|Kidney(197;0.00741)														---	---	---	---
PTPN23	25930	broad.mit.edu	37	3	47422858	47422858	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47422858delC	uc003crf.1	+						PTPN23_uc011baw.1_Intron|PTPN23_uc011bax.1_Intron|PTPN23_uc011bay.1_Intron	NM_015466	NP_056281			protein tyrosine phosphatase, non-receptor type						cilium morphogenesis	cilium|cytoplasmic membrane-bounded vesicle|microtubule basal body	protein tyrosine phosphatase activity			breast(1)|central_nervous_system(1)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(193;0.000271)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)														---	---	---	---
SCAP	22937	broad.mit.edu	37	3	47485974	47485974	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47485974delT	uc003crh.1	-						SCAP_uc011baz.1_Intron|SCAP_uc003crg.2_Intron	NM_012235	NP_036367			SREBF chaperone protein						cholesterol metabolic process|negative regulation of cholesterol biosynthetic process|positive regulation of low-density lipoprotein particle receptor biosynthetic process|positive regulation of transcription via sterol regulatory element binding involved in ER-nuclear sterol response pathway	endoplasmic reticulum membrane|ER to Golgi transport vesicle membrane|Golgi membrane|integral to membrane	unfolded protein binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000278)|KIRC - Kidney renal clear cell carcinoma(197;0.00592)|Kidney(197;0.00679)														---	---	---	---
C3orf75	54859	broad.mit.edu	37	3	47552509	47552509	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47552509delC	uc003crk.2	-						C3orf75_uc003crj.2_Intron|C3orf75_uc011bba.1_Intron|C3orf75_uc003crl.1_Intron	NM_001031703	NP_001026873			transmembrane protein 103												0																		---	---	---	---
MAP4	4134	broad.mit.edu	37	3	48073383	48073384	+	Intron	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48073383_48073384delAC	uc003csb.2	-						MAP4_uc003csc.3_Intron|MAP4_uc011bbf.1_Intron|MAP4_uc003csf.3_Intron|MAP4_uc003csg.2_Intron	NM_002375	NP_002366			microtubule-associated protein 4 isoform 1						negative regulation of microtubule depolymerization	cytoplasm|microtubule|microtubule associated complex	protein binding|structural molecule activity			ovary(2)|pancreas(1)	3				BRCA - Breast invasive adenocarcinoma(193;0.000721)|KIRC - Kidney renal clear cell carcinoma(197;0.00641)|Kidney(197;0.00736)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	48136912	48136913	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48136912_48136913insT								MAP4 (6143 upstream) : CDC25A (61755 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	48169270	48169270	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48169270delT								MAP4 (38501 upstream) : CDC25A (29398 downstream)																																			---	---	---	---
CCDC36	339834	broad.mit.edu	37	3	49289042	49289043	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49289042_49289043insT	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)														---	---	---	---
DAG1	1605	broad.mit.edu	37	3	49547840	49547840	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49547840delT	uc003cxc.3	+							NM_004393	NP_004384			dystroglycan 1 preproprotein						cytoskeletal anchoring at plasma membrane|interspecies interaction between organisms|microtubule anchoring|negative regulation of cell migration|negative regulation of MAPKKK cascade|negative regulation of protein kinase B signaling cascade	basement membrane|contractile ring|cytoplasm|cytoskeleton|dystrophin-associated glycoprotein complex|extracellular space|filopodium|integral to membrane|integral to membrane of membrane fraction|lamellipodium|nucleoplasm	actin binding|alpha-actinin binding|calcium ion binding|laminin-1 binding|receptor activity|structural constituent of muscle|tubulin binding|vinculin binding			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(193;5.13e-05)|Kidney(197;0.00241)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)														---	---	---	---
RNF123	63891	broad.mit.edu	37	3	49732703	49732704	+	Intron	DEL	TT	-	-	rs75428743		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49732703_49732704delTT	uc003cxh.2	+							NM_022064	NP_071347			ring finger protein 123							cytoplasm	ligase activity|protein binding|zinc ion binding			kidney(3)|ovary(1)|lung(1)|breast(1)|skin(1)	7				BRCA - Breast invasive adenocarcinoma(193;4.71e-05)|Kidney(197;0.00227)|KIRC - Kidney renal clear cell carcinoma(197;0.00255)														---	---	---	---
TRAIP	10293	broad.mit.edu	37	3	49888403	49888404	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49888403_49888404insT	uc003cxs.1	-						TRAIP_uc010hla.1_Intron|TRAIP_uc011bcx.1_Intron	NM_005879	NP_005870			TRAF interacting protein						cell proliferation|induction of apoptosis	perinuclear region of cytoplasm	protein binding|zinc ion binding			lung(4)|upper_aerodigestive_tract(1)|ovary(1)	6				BRCA - Breast invasive adenocarcinoma(193;4.71e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)														---	---	---	---
RBM6	10180	broad.mit.edu	37	3	49974824	49974824	+	5'Flank	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49974824delT	uc003cyc.2	+						RBM6_uc011bdh.1_5'Flank|RBM6_uc010hlc.1_5'Flank|RBM6_uc003cyd.2_5'Flank|RBM6_uc003cye.2_5'Flank|RBM6_uc011bdi.1_5'Flank|RBM6_uc010hld.1_5'Flank|RBM6_uc010hle.1_5'Flank|RBM6_uc010hlf.1_5'Flank	NM_005777	NP_005768			RNA binding motif protein 6						RNA processing	nucleus	DNA binding|nucleotide binding|RNA binding|zinc ion binding			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(193;6.81e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0084)|Kidney(197;0.00977)														---	---	---	---
RBM5	10181	broad.mit.edu	37	3	50143347	50143347	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50143347delT	uc003cyg.2	+						RBM5_uc011bdj.1_Intron|RBM5_uc011bdk.1_Intron	NM_005778	NP_005769			RNA binding motif protein 5						apoptosis|negative regulation of cell proliferation|positive regulation of apoptosis|regulation of alternative nuclear mRNA splicing, via spliceosome|spliceosome assembly	nucleoplasm|spliceosomal complex	DNA binding|mRNA binding|nucleotide binding|protein binding|zinc ion binding			lung(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000121)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)														---	---	---	---
RASSF1	11186	broad.mit.edu	37	3	50370065	50370065	+	Intron	DEL	A	-	-	rs28449453		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50370065delA	uc003dad.1	-						RASSF1_uc003daa.1_5'Flank|RASSF1_uc003dab.1_Intron|RASSF1_uc003dac.2_Intron|RASSF1_uc003dae.1_Intron|RASSF1_uc010hlk.1_Intron|RASSF1_uc003daf.1_Intron	NM_170714	NP_733832			Ras association domain family 1 isoform D						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	50574447	50574448	+	IGR	DEL	CA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50574447_50574448delCA								CACNA2D2 (33555 upstream) : C3orf18 (21015 downstream)																																			---	---	---	---
VPRBP	9730	broad.mit.edu	37	3	51477606	51477607	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51477606_51477607delAA	uc003dbe.1	-						VPRBP_uc003dbg.1_Intron	NM_014703	NP_055518			HIV-1 Vpr binding protein						interspecies interaction between organisms	cytoplasm|nucleus	protein binding			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.000272)|Kidney(197;0.000729)|KIRC - Kidney renal clear cell carcinoma(197;0.000875)														---	---	---	---
RAD54L2	23132	broad.mit.edu	37	3	51597073	51597073	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51597073delT	uc011bdt.1	+						RAD54L2_uc003dbh.2_Intron	NM_015106	NP_055921			RAD54-like 2							nucleus	ATP binding|DNA binding|helicase activity			ovary(3)	3				BRCA - Breast invasive adenocarcinoma(193;0.000102)|Kidney(197;0.000758)|KIRC - Kidney renal clear cell carcinoma(197;0.000896)														---	---	---	---
RAD54L2	23132	broad.mit.edu	37	3	51659882	51659882	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51659882delA	uc011bdt.1	+						RAD54L2_uc003dbh.2_Intron	NM_015106	NP_055921			RAD54-like 2							nucleus	ATP binding|DNA binding|helicase activity			ovary(3)	3				BRCA - Breast invasive adenocarcinoma(193;0.000102)|Kidney(197;0.000758)|KIRC - Kidney renal clear cell carcinoma(197;0.000896)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	51821576	51821576	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51821576delA								IQCF6 (8567 upstream) : IQCF1 (19153 downstream)																																			---	---	---	---
GPR62	118442	broad.mit.edu	37	3	51987402	51987403	+	5'Flank	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51987402_51987403delTT	uc003dca.3	+							NM_080865	NP_543141			G protein-coupled receptor 62							integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000534)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)														---	---	---	---
TWF2	11344	broad.mit.edu	37	3	52275895	52275896	+	5'Flank	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52275895_52275896delAA	uc003ddd.2	-						TWF2_uc010hmc.2_5'Flank	NM_007284	NP_009215			twinfilin-like protein							cytoskeleton|perinuclear region of cytoplasm	actin binding|ATP binding			stomach(1)|ovary(1)|lung(1)	3				BRCA - Breast invasive adenocarcinoma(193;2.43e-05)|Kidney(197;0.000539)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	53846944	53846945	+	IGR	INS	-	GAA	GAA	rs149026717	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53846944_53846945insGAA								CACNA1D (453 upstream) : CHDH (3443 downstream)																																			---	---	---	---
CHDH	55349	broad.mit.edu	37	3	53868480	53868480	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53868480delA	uc003dgz.2	-							NM_018397	NP_060867			choline dehydrogenase precursor						alcohol metabolic process		choline dehydrogenase activity|flavin adenine dinucleotide binding			ovary(1)|central_nervous_system(1)	2		Hepatocellular(537;0.152)		BRCA - Breast invasive adenocarcinoma(193;0.000158)|KIRC - Kidney renal clear cell carcinoma(284;0.00588)|Kidney(284;0.00673)|OV - Ovarian serous cystadenocarcinoma(275;0.118)	Choline(DB00122)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	54051930	54051931	+	IGR	INS	-	A	A	rs55721341		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:54051930_54051931insA								SELK (125941 upstream) : CACNA2D3 (104762 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	54144232	54144232	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:54144232delT								SELK (218243 upstream) : CACNA2D3 (12461 downstream)																																			---	---	---	---
CACNA2D3	55799	broad.mit.edu	37	3	54442480	54442481	+	Intron	INS	-	T	T	rs150433971	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:54442480_54442481insT	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	54680274	54680275	+	Intron	DEL	CT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:54680274_54680275delCT	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	54723749	54723750	+	Intron	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:54723749_54723750delAC	uc003dhf.2	+						CACNA2D3_uc011beu.1_Intron|CACNA2D3_uc003dhg.1_Intron|CACNA2D3_uc003dhh.1_Intron|CACNA2D3_uc010hmv.1_Intron	NM_018398	NP_060868			calcium channel, voltage-dependent, alpha							integral to membrane	calcium channel activity|metal ion binding|voltage-gated ion channel activity			large_intestine(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)														---	---	---	---
ERC2	26059	broad.mit.edu	37	3	55983403	55983403	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:55983403delG	uc003dhr.1	-						ERC2_uc003dhq.1_Intron|ERC2_uc003dht.1_Intron	NM_015576	NP_056391			cytomatrix protein p110							cell junction|cytoplasm|cytoskeleton|growth cone|presynaptic membrane|synaptosome	protein binding			ovary(2)	2				KIRC - Kidney renal clear cell carcinoma(284;0.0667)|Kidney(284;0.0873)|OV - Ovarian serous cystadenocarcinoma(275;0.219)														---	---	---	---
ERC2	26059	broad.mit.edu	37	3	56255930	56255931	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:56255930_56255931delAA	uc003dhr.1	-							NM_015576	NP_056391			cytomatrix protein p110							cell junction|cytoplasm|cytoskeleton|growth cone|presynaptic membrane|synaptosome	protein binding			ovary(2)	2				KIRC - Kidney renal clear cell carcinoma(284;0.0667)|Kidney(284;0.0873)|OV - Ovarian serous cystadenocarcinoma(275;0.219)														---	---	---	---
ERC2	26059	broad.mit.edu	37	3	56384580	56384581	+	Intron	INS	-	GA	GA	rs145371285	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:56384580_56384581insGA	uc003dhr.1	-							NM_015576	NP_056391			cytomatrix protein p110							cell junction|cytoplasm|cytoskeleton|growth cone|presynaptic membrane|synaptosome	protein binding			ovary(2)	2				KIRC - Kidney renal clear cell carcinoma(284;0.0667)|Kidney(284;0.0873)|OV - Ovarian serous cystadenocarcinoma(275;0.219)														---	---	---	---
C3orf63	23272	broad.mit.edu	37	3	56662794	56662794	+	Intron	DEL	T	-	-	rs35779948		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:56662794delT	uc003did.3	-						C3orf63_uc003dib.3_Intron|C3orf63_uc003dic.3_Intron|C3orf63_uc003die.3_Intron	NM_015224	NP_056039			retinoblastoma-associated protein 140 isoform b											ovary(3)|kidney(1)|central_nervous_system(1)	5				KIRC - Kidney renal clear cell carcinoma(284;0.0126)|Kidney(284;0.0147)														---	---	---	---
ARHGEF3	50650	broad.mit.edu	37	3	57010951	57010951	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57010951delA	uc003dih.2	-							NM_001128615	NP_001122087			Rho guanine nucleotide exchange factor 3 isoform						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|Rho protein signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0161)|Kidney(284;0.019)|OV - Ovarian serous cystadenocarcinoma(275;0.193)														---	---	---	---
ARHGEF3	50650	broad.mit.edu	37	3	57081405	57081405	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57081405delA	uc003dih.2	-							NM_001128615	NP_001122087			Rho guanine nucleotide exchange factor 3 isoform						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|Rho protein signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0161)|Kidney(284;0.019)|OV - Ovarian serous cystadenocarcinoma(275;0.193)														---	---	---	---
DNAH12	201625	broad.mit.edu	37	3	57439140	57439140	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57439140delA	uc003dit.2	-							NM_178504	NP_848599			dynein heavy chain domain 2 isoform 1						microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			pancreas(1)|skin(1)	2																		---	---	---	---
DNAH12	201625	broad.mit.edu	37	3	57494742	57494742	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57494742delT	uc003dit.2	-						DNAH12_uc003diu.2_Intron	NM_178504	NP_848599			dynein heavy chain domain 2 isoform 1						microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			pancreas(1)|skin(1)	2																		---	---	---	---
ARF4	378	broad.mit.edu	37	3	57579291	57579291	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57579291delA	uc003dix.3	-						ARF4_uc003diy.3_Intron|ARF4_uc010hnd.2_Intron|ARF4_uc003diz.3_Intron	NM_001660	NP_001651			ADP-ribosylation factor 4						protein transport|small GTPase mediated signal transduction|vesicle-mediated transport	Golgi apparatus	GTP binding|GTPase activity			upper_aerodigestive_tract(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0449)|Kidney(284;0.0561)														---	---	---	---
FAM116A	201627	broad.mit.edu	37	3	57680865	57680865	+	5'Flank	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57680865delA	uc003dja.2	-							NM_152678	NP_689891			hypothetical protein LOC201627											pancreas(1)	1				BRCA - Breast invasive adenocarcinoma(55;0.000621)|KIRC - Kidney renal clear cell carcinoma(284;0.0485)|Kidney(284;0.0607)														---	---	---	---
SLMAP	7871	broad.mit.edu	37	3	57850103	57850103	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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)														---	---	---	---
PXK	54899	broad.mit.edu	37	3	58316887	58316887	+	5'Flank	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58316887delT	uc003djz.1	+						PXK_uc003djx.1_5'Flank|PXK_uc003djy.1_5'Flank|PXK_uc003dka.1_5'Flank|PXK_uc003dkb.1_5'Flank|PXK_uc003dkc.1_5'Flank|PXK_uc011bfe.1_5'Flank|PXK_uc010hnj.1_5'Flank|PXK_uc003dkd.1_5'Flank	NM_017771	NP_060241			PX domain containing serine/threonine kinase						cell communication|inflammatory response|negative regulation of ATPase activity|negative regulation of ion transport|regulation of synaptic transmission	centrosome|cytoplasm|nucleus|plasma membrane	actin binding|ATP binding|phosphatidylinositol binding|phosphatidylinositol binding|protein C-terminus binding|protein kinase activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(55;0.000249)|KIRC - Kidney renal clear cell carcinoma(10;0.00346)|Kidney(10;0.00368)|OV - Ovarian serous cystadenocarcinoma(275;0.22)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	58536895	58536897	+	IGR	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58536895_58536897delTTT								ACOX2 (13966 upstream) : FAM107A (12950 downstream)																																			---	---	---	---
FHIT	2272	broad.mit.edu	37	3	59833002	59833002	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:59833002delT	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	59934562	59934562	+	Intron	DEL	T	-	-	rs113121652		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:59934562delT	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	60327329	60327329	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:60327329delT	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	60622183	60622184	+	Intron	INS	-	G	G	rs145899262	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:60622183_60622184insG	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	60927880	60927880	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:60927880delT	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	60928232	60928233	+	Intron	DEL	TC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:60928232_60928233delTC	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	61036922	61036925	+	Intron	DEL	TGTT	-	-	rs72332104		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:61036922_61036925delTGTT	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	61977157	61977157	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:61977157delG	uc003dlb.2	+						PTPRG_uc003dlc.2_Intron	NM_002841	NP_002832			protein tyrosine phosphatase, receptor type, G						transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	identical protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(5)|lung(2)	7				BRCA - Breast invasive adenocarcinoma(55;0.000376)|KIRC - Kidney renal clear cell carcinoma(10;0.0499)|Kidney(10;0.065)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	62374148	62374149	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:62374148_62374149delTT								FEZF2 (14958 upstream) : CADPS (9872 downstream)																																			---	---	---	---
CADPS	8618	broad.mit.edu	37	3	62422730	62422730	+	Intron	DEL	A	-	-	rs76046292		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:62422730delA	uc003dll.2	-						CADPS_uc003dlj.1_Intron|CADPS_uc003dlk.1_Intron|CADPS_uc003dlm.2_Intron|CADPS_uc003dln.2_Intron	NM_003716	NP_003707			Ca2+-dependent secretion activator isoform 1						exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|cytosol|synapse	lipid binding|metal ion binding			central_nervous_system(2)|ovary(1)	3		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)														---	---	---	---
SYNPR	132204	broad.mit.edu	37	3	63415722	63415723	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:63415722_63415723insT	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	63465134	63465135	+	Intron	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:63465134_63465135delAC	uc003dlq.2	+						SYNPR_uc003dlp.2_Intron|SYNPR_uc011bfk.1_Intron|SYNPR_uc011bfl.1_Intron|SYNPR_uc010hnt.2_Intron|SYNPR_uc011bfm.1_Intron	NM_144642	NP_653243			synaptoporin isoform 2							cell junction|integral to membrane|synaptic vesicle membrane|synaptosome	transporter activity				0				BRCA - Breast invasive adenocarcinoma(55;0.000918)|KIRC - Kidney renal clear cell carcinoma(15;0.0658)|Kidney(15;0.0904)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	63605962	63605965	+	IGR	DEL	TTTC	-	-	rs35315999		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:63605962_63605965delTTTC								SYNPR (3366 upstream) : SNTN (32379 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	63674948	63674948	+	IGR	DEL	A	-	-	rs34366272		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:63674948delA								SNTN (24067 upstream) : C3orf49 (130093 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	64696627	64696627	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:64696627delA	uc003dml.2	+											Homo sapiens cDNA FLJ25194 fis, clone REC04095.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	64847997	64848001	+	Intron	DEL	TTTTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:64847997_64848001delTTTTT	uc003dml.2	+											Homo sapiens cDNA FLJ25194 fis, clone REC04095.																														---	---	---	---
MAGI1	9223	broad.mit.edu	37	3	65367097	65367097	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:65367097delA	uc003dmn.2	-						MAGI1_uc003dmm.2_Intron|MAGI1_uc003dmo.2_Intron|MAGI1_uc003dmp.2_Intron|MAGI1_uc003dmq.1_5'Flank|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)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	66070473	66070473	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:66070473delA								MAGI1 (45964 upstream) : SLC25A26 (48812 downstream)																																			---	---	---	---
SLC25A26	115286	broad.mit.edu	37	3	66392349	66392349	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:66392349delT	uc011bfq.1	+						SLC25A26_uc011bfs.1_Intron|SLC25A26_uc011bft.1_Intron|SLC25A26_uc011bfr.1_Intron|SLC25A26_uc003dmt.2_Intron	NM_173471	NP_775742			solute carrier family 25, member 26 isoform a							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	66572890	66572890	+	IGR	DEL	A	-	-	rs72117070		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:66572890delA								LRIG1 (22045 upstream) : KBTBD8 (475837 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	66661317	66661321	+	IGR	DEL	TTTTG	-	-	rs71616230		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:66661317_66661321delTTTTG								LRIG1 (110472 upstream) : KBTBD8 (387406 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	67085366	67085367	+	IGR	DEL	CA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:67085366_67085367delCA								KBTBD8 (23736 upstream) : SUCLG2 (339778 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	67926673	67926674	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:67926673_67926674insT	uc003dnc.2	+											Homo sapiens mRNA; cDNA DKFZp686F1220 (from clone DKFZp686F1220).																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	67935335	67935337	+	Intron	DEL	TTC	-	-	rs11292334		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:67935335_67935337delTTC	uc003dnc.2	+											Homo sapiens mRNA; cDNA DKFZp686F1220 (from clone DKFZp686F1220).																														---	---	---	---
FAM19A4	151647	broad.mit.edu	37	3	68934196	68934197	+	Intron	INS	-	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:68934196_68934197insC	uc003dnh.1	-						FAM19A4_uc003dni.1_Intron	NM_182522	NP_872328			family with sequence similarity 19 (chemokine							extracellular region				skin(2)	2		Lung NSC(201;0.0198)		BRCA - Breast invasive adenocarcinoma(55;1.38e-05)|Epithelial(33;0.000124)|LUSC - Lung squamous cell carcinoma(21;0.0248)|KIRC - Kidney renal clear cell carcinoma(39;0.0729)|Kidney(39;0.0904)														---	---	---	---
FRMD4B	23150	broad.mit.edu	37	3	69261184	69261185	+	Intron	DEL	AA	-	-	rs113582561		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:69261184_69261185delAA	uc003dnv.2	-						FRMD4B_uc003dnw.2_Intron|FRMD4B_uc003dnx.1_Intron|FRMD4B_uc011bga.1_Intron	NM_015123	NP_055938			FERM domain containing 4B							cytoplasm|cytoskeleton	binding			ovary(3)|central_nervous_system(1)	4		Lung NSC(201;0.0138)|Prostate(884;0.11)		BRCA - Breast invasive adenocarcinoma(55;0.000201)|Epithelial(33;0.00141)|LUSC - Lung squamous cell carcinoma(21;0.00999)|Lung(16;0.0182)														---	---	---	---
FRMD4B	23150	broad.mit.edu	37	3	69262387	69262388	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:69262387_69262388insT	uc003dnv.2	-						FRMD4B_uc003dnw.2_Intron|FRMD4B_uc003dnx.1_Intron|FRMD4B_uc011bga.1_Intron	NM_015123	NP_055938			FERM domain containing 4B							cytoplasm|cytoskeleton	binding			ovary(3)|central_nervous_system(1)	4		Lung NSC(201;0.0138)|Prostate(884;0.11)		BRCA - Breast invasive adenocarcinoma(55;0.000201)|Epithelial(33;0.00141)|LUSC - Lung squamous cell carcinoma(21;0.00999)|Lung(16;0.0182)														---	---	---	---
MITF	4286	broad.mit.edu	37	3	70004983	70004983	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:70004983delA	uc003dnz.2	+						MITF_uc011bgb.1_Intron|MITF_uc003doa.2_Intron|MITF_uc003dob.2_Intron|MITF_uc003dod.2_Intron|MITF_uc003doe.2_Intron|MITF_uc003dof.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	70812574	70812574	+	IGR	DEL	A	-	-	rs112980102		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:70812574delA								MITF (795088 upstream) : FOXP1 (192163 downstream)																																			---	---	---	---
FOXP1	27086	broad.mit.edu	37	3	71119659	71119660	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:71119659_71119660insA	uc003dol.2	-						FOXP1_uc003dom.2_Intron|FOXP1_uc003don.2_Intron|FOXP1_uc003doo.2_Intron|FOXP1_uc003dop.2_Intron|FOXP1_uc003doq.1_Intron|FOXP1_uc003doj.2_Intron|FOXP1_uc003dok.2_Intron	NM_032682	NP_116071			forkhead box P1 isoform 1						cardiac muscle cell differentiation|embryo development|immunoglobulin V(D)J recombination|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of immunoglobulin production|positive regulation of mesenchymal cell proliferation|pre-B cell differentiation|regulation of sequence-specific DNA binding transcription factor activity|skeletal muscle tissue development|smooth muscle tissue development	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding			ovary(1)|lung(1)	2		Lung NSC(201;4.62e-05)|Prostate(10;0.0181)|Hepatocellular(537;0.186)|Myeloproliferative disorder(1037;0.209)		BRCA - Breast invasive adenocarcinoma(55;1.17e-05)|Epithelial(33;1.39e-05)|LUSC - Lung squamous cell carcinoma(21;2.35e-05)|Lung(16;4.26e-05)				T	PAX5	ALL								---	---	---	---
EIF4E3	317649	broad.mit.edu	37	3	71765390	71765391	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:71765390_71765391delTT	uc003dov.3	-						EIF4E3_uc011bgc.1_Intron|EIF4E3_uc003dox.2_Intron|EIF4E3_uc011bgd.1_Intron|EIF4E3_uc010hoc.2_Intron	NM_001134651	NP_001128123			eukaryotic translation initiation factor 4E						regulation of translation	cytoplasm|mRNA cap binding complex	translation initiation factor activity				0		Prostate(10;0.0166)		BRCA - Breast invasive adenocarcinoma(55;2.56e-05)|Epithelial(33;2.9e-05)|Lung(16;9.28e-05)|LUSC - Lung squamous cell carcinoma(21;0.00227)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	72033603	72033605	+	IGR	DEL	CTC	-	-	rs72155588		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:72033603_72033605delCTC								PROK2 (199246 upstream) : RYBP (390146 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	72047822	72047823	+	IGR	INS	-	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:72047822_72047823insG								PROK2 (213465 upstream) : RYBP (375928 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	72631180	72631180	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:72631180delA								RYBP (135406 upstream) : SHQ1 (167250 downstream)																																			---	---	---	---
SHQ1	55164	broad.mit.edu	37	3	72803536	72803538	+	Intron	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:72803536_72803538delTTT	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)														---	---	---	---
PPP4R2	151987	broad.mit.edu	37	3	73072341	73072342	+	Intron	INS	-	T	T	rs76445256		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:73072341_73072342insT	uc003dph.1	+						PPP4R2_uc003dpi.1_Intron	NM_174907	NP_777567			protein phosphatase 4, regulatory subunit 2						mRNA processing|protein modification process|regulation of double-strand break repair via homologous recombination|RNA splicing	centrosome|nucleus|protein phosphatase 4 complex	protein binding, bridging|protein phosphatase type 4 regulator activity			lung(1)	1		Prostate(10;0.0187)|Lung SC(41;0.236)		Epithelial(33;1.76e-07)|BRCA - Breast invasive adenocarcinoma(55;9.42e-05)|LUSC - Lung squamous cell carcinoma(21;0.00211)|Lung(16;0.00643)|KIRC - Kidney renal clear cell carcinoma(39;0.0164)|Kidney(39;0.0193)|OV - Ovarian serous cystadenocarcinoma(275;0.031)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	74670478	74670479	+	IGR	DEL	AA	-	-	rs71625988		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:74670478_74670479delAA								CNTN3 (100135 upstream) : FAM86D (800226 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	74929459	74929459	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:74929459delA								CNTN3 (359116 upstream) : FAM86D (541246 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	75007737	75007737	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:75007737delA								CNTN3 (437394 upstream) : FAM86D (462968 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	75991116	75991121	+	IGR	DEL	CTCTCT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:75991116_75991121delCTCTCT								ZNF717 (156446 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	76289816	76289816	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:76289816delC								ZNF717 (455146 upstream) : ROBO2 (799478 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	76372290	76372291	+	IGR	DEL	AC	-	-	rs72219531		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:76372290_76372291delAC								ZNF717 (537620 upstream) : ROBO2 (717003 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	76696935	76696935	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:76696935delA								ZNF717 (862265 upstream) : ROBO2 (392359 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	76750264	76750264	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:76750264delA								ZNF717 (915594 upstream) : ROBO2 (339030 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	76966897	76966897	+	IGR	DEL	A	-	-	rs33982913		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:76966897delA								None (None upstream) : ROBO2 (122397 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	77028788	77028788	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:77028788delT								None (None upstream) : ROBO2 (60506 downstream)																																			---	---	---	---
ROBO2	6092	broad.mit.edu	37	3	77094114	77094115	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:77094114_77094115insT	uc003dpy.3	+						ROBO2_uc003dpz.2_Intron|ROBO2_uc011bgj.1_Intron|ROBO2_uc011bgk.1_Intron	NM_002942	NP_002933			roundabout, axon guidance receptor, homolog 2						apoptosis involved in luteolysis|axon midline choice point recognition|cellular response to hormone stimulus|homophilic cell adhesion|metanephros development|negative regulation of negative chemotaxis|negative regulation of synaptogenesis|olfactory bulb interneuron development|positive regulation of axonogenesis|retinal ganglion cell axon guidance|ureteric bud development	axolemma|cell surface|integral to membrane	axon guidance receptor activity|identical protein binding			lung(5)|skin(3)|ovary(1)|large_intestine(1)|liver(1)	11				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)														---	---	---	---
ROBO2	6092	broad.mit.edu	37	3	77438912	77438912	+	Intron	DEL	A	-	-	rs4683976	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:77438912delA	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	78340084	78340084	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:78340084delT								ROBO2 (643423 upstream) : ROBO1 (306304 downstream)																																			---	---	---	---
ROBO1	6091	broad.mit.edu	37	3	79045866	79045867	+	Intron	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:79045866_79045867delAC	uc003dqe.2	-						ROBO1_uc003dqb.2_Intron|ROBO1_uc003dqc.2_Intron|ROBO1_uc003dqd.2_Intron	NM_002941	NP_002932			roundabout 1 isoform a						activation of caspase activity|axon midline choice point recognition|cell migration involved in sprouting angiogenesis|chemorepulsion involved in postnatal olfactory bulb interneuron migration|homophilic cell adhesion|negative regulation of chemokine-mediated signaling pathway|negative regulation of mammary gland epithelial cell proliferation|negative regulation of negative chemotaxis|positive regulation of axonogenesis|Roundabout signaling pathway	cell surface|cytoplasm|integral to plasma membrane	axon guidance receptor activity|identical protein binding|LRR domain binding			large_intestine(2)	2		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	80283199	80283199	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:80283199delA								ROBO1 (466140 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	80680004	80680005	+	IGR	INS	-	AC	AC	rs139111880	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:80680004_80680005insAC								ROBO1 (862945 upstream) : GBE1 (858845 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	81016539	81016539	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:81016539delT								None (None upstream) : GBE1 (522311 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	81210017	81210017	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:81210017delA								None (None upstream) : GBE1 (328833 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	81382993	81382995	+	IGR	DEL	TTG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:81382993_81382995delTTG								None (None upstream) : GBE1 (155855 downstream)																																			---	---	---	---
GBE1	2632	broad.mit.edu	37	3	81541630	81541630	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:81541630delA	uc003dqg.2	-							NM_000158	NP_000149			glucan (1,4-alpha-), branching enzyme 1						glucose metabolic process|glycogen biosynthetic process	cytosol	1,4-alpha-glucan branching enzyme activity|cation binding|hydrolase activity, hydrolyzing O-glycosyl compounds			ovary(3)	3		Lung NSC(201;0.0117)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0654)|Epithelial(33;0.00305)|LUSC - Lung squamous cell carcinoma(29;0.00646)|BRCA - Breast invasive adenocarcinoma(55;0.00813)|Lung(72;0.0129)|KIRC - Kidney renal clear cell carcinoma(39;0.212)|Kidney(39;0.247)										Glycogen_Storage_Disease_type_IV				---	---	---	---
GBE1	2632	broad.mit.edu	37	3	81541828	81541829	+	Intron	INS	-	TTCTCCCT	TTCTCCCT	rs149554537	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:81541828_81541829insTTCTCCCT	uc003dqg.2	-							NM_000158	NP_000149			glucan (1,4-alpha-), branching enzyme 1						glucose metabolic process|glycogen biosynthetic process	cytosol	1,4-alpha-glucan branching enzyme activity|cation binding|hydrolase activity, hydrolyzing O-glycosyl compounds			ovary(3)	3		Lung NSC(201;0.0117)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0654)|Epithelial(33;0.00305)|LUSC - Lung squamous cell carcinoma(29;0.00646)|BRCA - Breast invasive adenocarcinoma(55;0.00813)|Lung(72;0.0129)|KIRC - Kidney renal clear cell carcinoma(39;0.212)|Kidney(39;0.247)										Glycogen_Storage_Disease_type_IV				---	---	---	---
GBE1	2632	broad.mit.edu	37	3	81637723	81637723	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:81637723delA	uc003dqg.2	-						GBE1_uc011bgm.1_Intron	NM_000158	NP_000149			glucan (1,4-alpha-), branching enzyme 1						glucose metabolic process|glycogen biosynthetic process	cytosol	1,4-alpha-glucan branching enzyme activity|cation binding|hydrolase activity, hydrolyzing O-glycosyl compounds			ovary(3)	3		Lung NSC(201;0.0117)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0654)|Epithelial(33;0.00305)|LUSC - Lung squamous cell carcinoma(29;0.00646)|BRCA - Breast invasive adenocarcinoma(55;0.00813)|Lung(72;0.0129)|KIRC - Kidney renal clear cell carcinoma(39;0.212)|Kidney(39;0.247)										Glycogen_Storage_Disease_type_IV				---	---	---	---
Unknown	0	broad.mit.edu	37	3	82008037	82008038	+	IGR	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:82008037_82008038delTG								GBE1 (197087 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	82124903	82124903	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:82124903delT	uc003dqh.1	+											Homo sapiens cDNA clone IMAGE:5271111.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	82182440	82182440	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:82182440delA	uc003dqh.1	+											Homo sapiens cDNA clone IMAGE:5271111.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	82563051	82563051	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:82563051delT								GBE1 (752101 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	83871276	83871277	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:83871276_83871277delAA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	84047692	84047692	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:84047692delA								None (None upstream) : CADM2 (960441 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	84294614	84294615	+	IGR	INS	-	AAAT	AAAT	rs111812307		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:84294614_84294615insAAAT								None (None upstream) : CADM2 (713518 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	84324171	84324172	+	IGR	DEL	GT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:84324171_84324172delGT								None (None upstream) : CADM2 (683961 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	87059372	87059373	+	IGR	INS	-	TTT	TTT	rs139270862	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:87059372_87059373insTTT								VGLL3 (19115 upstream) : CHMP2B (217040 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	87543762	87543763	+	IGR	INS	-	AAGG	AAGG			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:87543762_87543763insAAGG								POU1F1 (218025 upstream) : HTR1F (487963 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	88997516	88997516	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:88997516delA								C3orf38 (790403 upstream) : EPHA3 (159158 downstream)																																			---	---	---	---
EPHA3	2042	broad.mit.edu	37	3	89460316	89460316	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:89460316delT	uc003dqy.2	+						EPHA3_uc010hon.1_Intron	NM_005233	NP_005224			ephrin receptor EphA3 isoform a precursor							extracellular region|integral to plasma membrane	ATP binding			lung(17)|ovary(7)|large_intestine(4)|central_nervous_system(2)|stomach(1)|skin(1)|pancreas(1)	33	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)											TSP Lung(6;0.00050)			---	---	---	---
Unknown	0	broad.mit.edu	37	3	90003397	90003397	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:90003397delT								EPHA3 (472115 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	90350978	90350978	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:90350978delT								EPHA3 (819696 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	94269006	94269006	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:94269006delA								NSUN3 (423376 upstream) : LOC255025 (388101 downstream)																																			---	---	---	---
EPHA6	285220	broad.mit.edu	37	3	97234787	97234792	+	Intron	DEL	AAAAAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97234787_97234792delAAAAAA	uc010how.1	+						EPHA6_uc011bgo.1_Intron|EPHA6_uc011bgp.1_Intron|EPHA6_uc003drs.3_Intron|EPHA6_uc003drr.3_Intron|EPHA6_uc003drt.2_Intron|EPHA6_uc010hox.1_Intron	NM_001080448	NP_001073917			EPH receptor A6 isoform a							integral to plasma membrane	ATP binding|ephrin receptor activity			stomach(5)|lung(4)|central_nervous_system(3)|breast(1)|skin(1)|ovary(1)|kidney(1)	16																		---	---	---	---
CRYBG3	131544	broad.mit.edu	37	3	97605313	97605313	+	Intron	DEL	A	-	-	rs9862347	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97605313delA	uc003drx.2	+							NM_153605	NP_705833			beta-gamma crystallin domain containing 3												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	98272351	98272351	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98272351delA								GPR15 (20393 upstream) : CPOX (25941 downstream)																																			---	---	---	---
DCBLD2	131566	broad.mit.edu	37	3	98525429	98525429	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98525429delT	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																		---	---	---	---
COL8A1	1295	broad.mit.edu	37	3	99497461	99497461	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:99497461delA	uc003dtg.1	+						COL8A1_uc003dth.1_Intron|COL8A1_uc003dti.1_Intron	NM_001850	NP_001841			alpha 1 type VIII collagen precursor						angiogenesis|cell adhesion	basement membrane|collagen type VIII					0																		---	---	---	---
COL8A1	1295	broad.mit.edu	37	3	99513026	99513027	+	Intron	DEL	TC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:99513026_99513027delTC	uc003dtg.1	+						COL8A1_uc003dth.1_Intron|COL8A1_uc003dti.1_Intron	NM_001850	NP_001841			alpha 1 type VIII collagen precursor						angiogenesis|cell adhesion	basement membrane|collagen type VIII					0																		---	---	---	---
FILIP1L	11259	broad.mit.edu	37	3	99648358	99648359	+	Intron	DEL	GT	-	-	rs34865104		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:99648358_99648359delGT	uc003dtm.2	-						C3orf26_uc003dtk.1_Intron|C3orf26_uc003dtl.2_Intron|FILIP1L_uc003dto.2_Intron	NM_182909	NP_878913			filamin A interacting protein 1-like isoform 1							cytoplasm|membrane|myosin complex|nucleus				ovary(1)	1																		---	---	---	---
FILIP1L	11259	broad.mit.edu	37	3	99783243	99783244	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:99783243_99783244delTT	uc003dtm.2	-						C3orf26_uc003dtl.2_Intron|FILIP1L_uc003dto.2_Intron	NM_182909	NP_878913			filamin A interacting protein 1-like isoform 1							cytoplasm|membrane|myosin complex|nucleus				ovary(1)	1																		---	---	---	---
LNP1	348801	broad.mit.edu	37	3	100122892	100122892	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100122892delT	uc003dtx.3	+						LNP1_uc003dty.3_Intron|LNP1_uc011bhb.1_Intron|TOMM70A_uc003dtw.2_5'Flank	NM_001085451	NP_001078920			leukemia NUP98 fusion partner 1												0																		---	---	---	---
TMEM45A	55076	broad.mit.edu	37	3	100253972	100253972	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100253972delT	uc003dtz.1	+						TMEM45A_uc003dua.1_Intron	NM_018004	NP_060474			transmembrane protein 45A							integral to membrane				skin(2)|ovary(1)	3																		---	---	---	---
ABI3BP	25890	broad.mit.edu	37	3	100595247	100595247	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100595247delA	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																		---	---	---	---
SENP7	57337	broad.mit.edu	37	3	101161485	101161485	+	Intron	DEL	A	-	-	rs79832386		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:101161485delA	uc003dut.2	-						SENP7_uc003duu.2_Intron|SENP7_uc003duv.2_Intron|SENP7_uc003duw.2_Intron|SENP7_uc003dux.2_Intron	NM_020654	NP_065705			sentrin/SUMO-specific protease 7 isoform 1						proteolysis	nucleus	cysteine-type peptidase activity			ovary(3)|lung(2)	5																		---	---	---	---
SENP7	57337	broad.mit.edu	37	3	101181711	101181711	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:101181711delA	uc003dut.2	-						SENP7_uc003duu.2_Intron|SENP7_uc003duv.2_Intron|SENP7_uc003duw.2_Intron|SENP7_uc003dux.2_Intron	NM_020654	NP_065705			sentrin/SUMO-specific protease 7 isoform 1						proteolysis	nucleus	cysteine-type peptidase activity			ovary(3)|lung(2)	5																		---	---	---	---
PCNP	57092	broad.mit.edu	37	3	101305125	101305125	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:101305125delA	uc003dva.2	+						PCNP_uc003dvb.2_Intron|PCNP_uc003dvc.2_Intron|PCNP_uc003dvd.2_Intron	NM_020357	NP_065090			PEST proteolytic signal containing nuclear						cell cycle|proteasomal ubiquitin-dependent protein catabolic process|protein ubiquitination	nucleus	protein binding				0																		---	---	---	---
ZPLD1	131368	broad.mit.edu	37	3	102008729	102008730	+	Intron	INS	-	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:102008729_102008730insC	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	102480042	102480042	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:102480042delA								ZPLD1 (281357 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	102663749	102663750	+	IGR	DEL	AA	-	-	rs112004228		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:102663749_102663750delAA								ZPLD1 (465064 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	103514987	103514988	+	IGR	DEL	GT	-	-	rs67877767		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:103514987_103514988delGT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	103768182	103768183	+	IGR	DEL	CA	-	-	rs76506407		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:103768182_103768183delCA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	105051727	105051727	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:105051727delA								None (None upstream) : ALCAM (33986 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	106148172	106148172	+	IGR	DEL	T	-	-	rs146766813		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:106148172delT								CBLB (559906 upstream) : LOC100302640 (407488 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	107539165	107539165	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:107539165delA								BBX (9118 upstream) : LOC151658 (21346 downstream)																																			---	---	---	---
MORC1	27136	broad.mit.edu	37	3	108690160	108690160	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108690160delA	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	108952917	108952917	+	IGR	DEL	A	-	-	rs72078298		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108952917delA								C3orf66 (48810 upstream) : DPPA2 (59719 downstream)																																			---	---	---	---
FLJ25363	401082	broad.mit.edu	37	3	109196336	109196336	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:109196336delT	uc003dxr.1	+							NM_001145553	NP_001139025			hypothetical protein LOC401082												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	109753072	109753072	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:109753072delT								FLJ25363 (539058 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	109769842	109769842	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:109769842delT								FLJ25363 (555828 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	110783734	110783734	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:110783734delT								None (None upstream) : PVRL3 (7131 downstream)																																			---	---	---	---
PLCXD2	257068	broad.mit.edu	37	3	111433013	111433013	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111433013delA	uc003dya.2	+						PLCXD2_uc003dyb.2_Intron|PLCXD2_uc003dxz.2_Intron	NM_001134478	NP_001127950			phosphatidylinositol-specific phospholipase C, X						intracellular signal transduction|lipid catabolic process		phospholipase C activity|signal transducer activity			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	112599630	112599632	+	IGR	DEL	GTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112599630_112599632delGTT								CD200R1L (34833 upstream) : CD200R1 (41900 downstream)																																			---	---	---	---
CCDC52	152185	broad.mit.edu	37	3	113167135	113167137	+	Intron	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113167135_113167137delTTT	uc003eag.3	-						CCDC52_uc003eaf.3_Intron	NM_144718	NP_653319			coiled-coil domain containing 52						cell division|mitosis	centriole|spindle	protein binding				0																		---	---	---	---
KIAA2018	205717	broad.mit.edu	37	3	113371901	113371901	+	3'UTR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113371901delA	uc003eam.2	-	7					KIAA2018_uc003eal.2_3'UTR	NM_001009899	NP_001009899			hypothetical protein LOC205717						regulation of transcription, DNA-dependent	membrane|nucleus	calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity			skin(2)|ovary(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	113433901	113433901	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113433901delT								KIAA2018 (18408 upstream) : NAA50 (3940 downstream)																																			---	---	---	---
GRAMD1C	54762	broad.mit.edu	37	3	113610734	113610734	+	Intron	DEL	A	-	-	rs79617145		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113610734delA	uc003eaq.3	+						GRAMD1C_uc011bil.1_Intron|GRAMD1C_uc011bim.1_Intron|GRAMD1C_uc003ear.2_Intron	NM_017577	NP_060047			GRAM domain containing 1C							integral to membrane				ovary(2)|skin(1)	3																		---	---	---	---
GRAMD1C	54762	broad.mit.edu	37	3	113643950	113643950	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113643950delT	uc003eaq.3	+						GRAMD1C_uc011bil.1_Intron|GRAMD1C_uc011bim.1_Intron|GRAMD1C_uc003ear.2_Intron|GRAMD1C_uc003eas.2_Intron|GRAMD1C_uc003eat.2_Intron	NM_017577	NP_060047			GRAM domain containing 1C							integral to membrane				ovary(2)|skin(1)	3																		---	---	---	---
KIAA1407	57577	broad.mit.edu	37	3	113707649	113707649	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113707649delT	uc003eax.2	-						KIAA1407_uc011bin.1_Intron	NM_020817	NP_065868			hypothetical protein LOC57577											ovary(2)	2																		---	---	---	---
ZBTB20	26137	broad.mit.edu	37	3	114066214	114066214	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:114066214delT	uc003ebi.2	-						ZBTB20_uc003ebj.2_Intron|ZBTB20_uc010hqp.2_Intron|ZBTB20_uc003ebk.2_Intron|ZBTB20_uc003ebl.2_Intron|ZBTB20_uc003ebm.2_Intron|ZBTB20_uc003ebn.2_Intron	NM_015642	NP_056457			zinc finger and BTB domain containing 20 isoform						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)|skin(1)	5				LUSC - Lung squamous cell carcinoma(41;0.0581)|Lung(219;0.191)														---	---	---	---
ZBTB20	26137	broad.mit.edu	37	3	114292528	114292528	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:114292528delG	uc003ebj.2	-						ZBTB20_uc010hqp.2_Intron|ZBTB20_uc003ebk.2_Intron|ZBTB20_uc003ebl.2_Intron|ZBTB20_uc003ebm.2_Intron|ZBTB20_uc003ebn.2_Intron	NM_015642	NP_056457			zinc finger and BTB domain containing 20 isoform						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)|skin(1)	5				LUSC - Lung squamous cell carcinoma(41;0.0581)|Lung(219;0.191)														---	---	---	---
ZBTB20	26137	broad.mit.edu	37	3	114684841	114684841	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:114684841delA	uc003ebm.2	-						ZBTB20_uc003ebn.2_Intron|ZBTB20_uc003ebp.2_Intron	NM_015642	NP_056457			zinc finger and BTB domain containing 20 isoform						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)|skin(1)	5				LUSC - Lung squamous cell carcinoma(41;0.0581)|Lung(219;0.191)														---	---	---	---
LSAMP	4045	broad.mit.edu	37	3	115946516	115946517	+	Intron	DEL	TT	-	-	rs11357383		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:115946516_115946517delTT	uc003ebt.2	-						LSAMP_uc011bis.1_Intron	NM_002338	NP_002329			limbic system-associated membrane protein						cell adhesion|nervous system development	anchored to membrane|plasma membrane					0		all_cancers(1;0.00189)|all_epithelial(1;0.0366)|Myeloproliferative disorder(1037;0.17)|all_neural(597;0.208)|Lung NSC(201;0.215)		GBM - Glioblastoma multiforme(114;0.00117)|LUSC - Lung squamous cell carcinoma(41;0.0407)|Lung(219;0.152)														---	---	---	---
LSAMP	4045	broad.mit.edu	37	3	116017276	116017276	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:116017276delA	uc003ebt.2	-						LSAMP_uc011bis.1_Intron	NM_002338	NP_002329			limbic system-associated membrane protein						cell adhesion|nervous system development	anchored to membrane|plasma membrane					0		all_cancers(1;0.00189)|all_epithelial(1;0.0366)|Myeloproliferative disorder(1037;0.17)|all_neural(597;0.208)|Lung NSC(201;0.215)		GBM - Glioblastoma multiforme(114;0.00117)|LUSC - Lung squamous cell carcinoma(41;0.0407)|Lung(219;0.152)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	116581850	116581850	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:116581850delT								LOC285194 (145965 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	117154856	117154856	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:117154856delT								LOC285194 (718971 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	117420395	117420395	+	IGR	DEL	T	-	-	rs11355600		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:117420395delT								LOC285194 (984510 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	117742801	117742804	+	IGR	DEL	GTGT	-	-	rs66600563		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:117742801_117742804delGTGT								None (None upstream) : IGSF11 (876677 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	117941004	117941004	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:117941004delA								None (None upstream) : IGSF11 (678477 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	118358512	118358512	+	Intron	DEL	T	-	-	rs79693717		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:118358512delT	uc011biu.1	-											Homo sapiens clone HA_003061 mRNA sequence.																														---	---	---	---
IGSF11	152404	broad.mit.edu	37	3	118631958	118631958	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:118631958delA	uc003ebw.2	-						IGSF11_uc011biv.1_Intron|IGSF11_uc003ebx.2_Intron|IGSF11_uc003eby.2_Intron|IGSF11_uc003ebz.2_Intron|IGSF11_uc010hqs.2_Intron	NM_001015887	NP_001015887			immunoglobulin superfamily, member 11 isoform b						cell adhesion|regulation of growth	integral to membrane|plasma membrane	receptor activity				0																		---	---	---	---
IGSF11	152404	broad.mit.edu	37	3	118743520	118743520	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:118743520delT	uc003ebw.2	-						IGSF11_uc011biv.1_Intron|IGSF11_uc003ebx.2_Intron|IGSF11_uc003eby.2_Intron|IGSF11_uc003ebz.2_Intron|IGSF11_uc010hqs.2_Intron	NM_001015887	NP_001015887			immunoglobulin superfamily, member 11 isoform b						cell adhesion|regulation of growth	integral to membrane|plasma membrane	receptor activity				0																		---	---	---	---
ARHGAP31	57514	broad.mit.edu	37	3	119012551	119012552	+	5'Flank	DEL	GT	-	-	rs71964788		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119012551_119012552delGT	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																		---	---	---	---
C3orf15	89876	broad.mit.edu	37	3	119480645	119480645	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119480645delA	uc003ede.3	+						C3orf15_uc010hqz.2_Intron|C3orf15_uc011bjd.1_Intron|C3orf15_uc011bje.1_Intron|C3orf15_uc003edg.3_Intron|C3orf15_uc003edh.3_Intron	NM_033364	NP_203528			AAT1-alpha							mitochondrion	protein binding			ovary(2)|pancreas(1)	3				GBM - Glioblastoma multiforme(114;0.186)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	120325507	120325508	+	IGR	INS	-	T	T	rs150361695		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120325507_120325508insT								NDUFB4 (4334 upstream) : HGD (21508 downstream)																																			---	---	---	---
FAM162A	26355	broad.mit.edu	37	3	122117148	122117148	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122117148delA	uc003eez.2	+						FAM162A_uc011bjq.1_Intron	NM_014367	NP_055182			growth and transformation-dependent protein							integral to membrane				ovary(1)	1																		---	---	---	---
PARP9	83666	broad.mit.edu	37	3	122257706	122257706	+	Intron	DEL	T	-	-	rs11366135		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122257706delT	uc010hri.2	-						PARP9_uc003eff.3_Intron|PARP9_uc011bjs.1_Intron|PARP9_uc003efg.2_Intron|PARP9_uc003efi.2_Intron|PARP9_uc003efh.2_Intron|PARP9_uc003efj.2_Intron	NM_001146102	NP_001139574			poly (ADP-ribose) polymerase family, member 9						cell migration	cytosol|nucleus	NAD+ ADP-ribosyltransferase activity|protein binding			ovary(1)|pancreas(1)|prostate(1)|skin(1)	4				GBM - Glioblastoma multiforme(114;0.0519)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	122618612	122618613	+	IGR	INS	-	A	A	rs1821101	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122618612_122618613insA								LOC100129550 (7350 upstream) : SEMA5B (9430 downstream)																																			---	---	---	---
SEC22A	26984	broad.mit.edu	37	3	122924523	122924527	+	Intron	DEL	CAAAA	-	-	rs66811125		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122924523_122924527delCAAAA	uc003ege.2	+						SEC22A_uc003egf.2_5'Flank	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)														---	---	---	---
PTPLB	201562	broad.mit.edu	37	3	123256431	123256432	+	Intron	INS	-	AC	AC	rs3109652		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123256431_123256432insAC	uc003egj.2	-							NM_198402	NP_940684			protein tyrosine phosphatase-like (proline						fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	lyase activity|protein binding			kidney(1)	1				GBM - Glioblastoma multiforme(114;0.1)														---	---	---	---
MYLK	4638	broad.mit.edu	37	3	123601587	123601587	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123601587delC	uc003ego.2	-						MYLK_uc003egp.2_Intron|MYLK_uc003egq.2_Intron|MYLK_uc003egr.2_Intron|MYLK_uc003egs.2_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	124177122	124177123	+	Intron	INS	-	A	A	rs67396845		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124177122_124177123insA	uc003ehg.2	+						KALRN_uc010hrv.1_Intron|KALRN_uc003ehf.1_Intron|KALRN_uc011bjy.1_Intron|KALRN_uc003ehh.1_Intron	NM_001024660	NP_001019831			kalirin, RhoGEF kinase isoform 1						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|vesicle-mediated transport	actin cytoskeleton|cytosol	ATP binding|GTPase activator activity|metal ion binding|protein binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			large_intestine(2)|ovary(2)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
KALRN	8997	broad.mit.edu	37	3	124371433	124371433	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124371433delT	uc003ehg.2	+						KALRN_uc003ehi.2_Intron|KALRN_uc003ehk.2_Intron|KALRN_uc011bjz.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																		---	---	---	---
MUC13	56667	broad.mit.edu	37	3	124655870	124655870	+	5'Flank	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124655870delA	uc003ehq.1	-							NM_033049	NP_149038			mucin 13, epithelial transmembrane							extracellular region|integral to membrane|plasma membrane					0																		---	---	---	---
ZNF148	7707	broad.mit.edu	37	3	124989186	124989187	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124989186_124989187delAA	uc003ehx.3	-						SLC12A8_uc003ehw.3_Intron|ZNF148_uc003ehz.3_Intron|ZNF148_uc010hsa.2_Intron|ZNF148_uc003eia.3_Intron|ZNF148_uc003ehy.2_Intron	NM_021964	NP_068799			zinc finger protein 148						cellular defense response|negative regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	Golgi apparatus|nucleus	protein binding|sequence-specific DNA binding|zinc ion binding			skin(2)|ovary(1)|pancreas(1)	4																		---	---	---	---
ZNF148	7707	broad.mit.edu	37	3	125062847	125062847	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125062847delA	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																		---	---	---	---
ZNF148	7707	broad.mit.edu	37	3	125069172	125069172	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125069172delT	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																		---	---	---	---
ZNF148	7707	broad.mit.edu	37	3	125071020	125071020	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125071020delA	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	125549468	125549468	+	IGR	DEL	A	-	-	rs112764611		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125549468delA								MIR548I1 (40073 upstream) : LOC100125556 (85976 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	125991268	125991269	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125991268_125991269delAA								ALDH1L1 (91783 upstream) : KLF15 (70209 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	126047135	126047136	+	IGR	INS	-	AT	AT			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126047135_126047136insAT								ALDH1L1 (147650 upstream) : KLF15 (14342 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	126858922	126858922	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126858922delG								PLXNA1 (102694 upstream) : TPRA1 (432986 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	127085088	127085088	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127085088delA	uc003ejj.2	-											Homo sapiens, clone IMAGE:4618125, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	127086170	127086170	+	Intron	DEL	A	-	-	rs76979444		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127086170delA	uc003ejj.2	-											Homo sapiens, clone IMAGE:4618125, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	127115605	127115606	+	IGR	INS	-	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127115605_127115606insC								PLXNA1 (359377 upstream) : TPRA1 (176302 downstream)																																			---	---	---	---
EEFSEC	60678	broad.mit.edu	37	3	127916784	127916784	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127916784delA	uc003eki.2	+						EEFSEC_uc003ekj.2_Intron	NM_021937	NP_068756			eukaryotic elongation factor,							cytoplasm|nucleus	GTP binding|GTPase activity|translation elongation factor activity			ovary(1)	1																		---	---	---	---
GATA2	2624	broad.mit.edu	37	3	128212625	128212625	+	5'Flank	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128212625delC	uc003eko.2	-						uc003ekp.2_Intron	NM_032638	NP_116027			GATA binding protein 2 isoform 1						blood coagulation|negative regulation of fat cell differentiation|negative regulation of fat cell proliferation|negative regulation of neural precursor cell proliferation|negative regulation of Notch signaling pathway|phagocytosis|positive regulation of angiogenesis|positive regulation of phagocytosis|positive regulation of transcription from RNA polymerase II promoter	nucleoplasm	C2H2 zinc finger domain binding|chromatin binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|zinc ion binding			haematopoietic_and_lymphoid_tissue(13)|lung(1)|skin(1)	15				GBM - Glioblastoma multiforme(114;0.173)				Mis		AML(CML blast transformation)								---	---	---	---
ACAD9	28976	broad.mit.edu	37	3	128614030	128614030	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128614030delT	uc003ela.3	+						ACAD9_uc010hsw.1_Intron|ACAD9_uc011bks.1_Intron|ACAD9_uc003elb.2_Intron|ACAD9_uc003elc.1_5'Flank	NM_014049	NP_054768			acyl-Coenzyme A dehydrogenase family, member 9							mitochondrion	acyl-CoA dehydrogenase activity|flavin adenine dinucleotide binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
KIAA1257	57501	broad.mit.edu	37	3	128707386	128707387	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128707386_128707387delAA	uc003elj.3	-						KIAA1257_uc003elg.1_Intron|KIAA1257_uc003eli.3_Intron	NM_020741	NP_065792			hypothetical protein LOC57501												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	129350108	129350108	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129350108delA								PLXND1 (24526 upstream) : TMCC1 (16529 downstream)																																			---	---	---	---
TMCC1	23023	broad.mit.edu	37	3	129582728	129582728	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129582728delA	uc003emz.3	-						TMCC1_uc010htg.2_Intron	NM_001017395	NP_001017395			transmembrane and coiled-coil domain family 1							integral to membrane				skin(1)	1																		---	---	---	---
COL6A6	131873	broad.mit.edu	37	3	130381353	130381353	+	Intron	DEL	T	-	-	rs146981165		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130381353delT	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	131160455	131160455	+	IGR	DEL	C	-	-	rs12635604	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:131160455delC								NUDT16 (55526 upstream) : MRPL3 (20591 downstream)																																			---	---	---	---
CPNE4	131034	broad.mit.edu	37	3	131504364	131504364	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:131504364delT	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																		---	---	---	---
TF	7018	broad.mit.edu	37	3	133419816	133419816	+	5'UTR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133419816delT	uc003epu.1	+	2						NM_001063	NP_001054			transferrin precursor						cellular iron ion homeostasis|platelet activation|platelet degranulation|transferrin transport|transmembrane transport	apical plasma membrane|basal plasma membrane|coated pit|early endosome|endocytic vesicle|endosome membrane|extracellular region|late endosome|perinuclear region of cytoplasm|recycling endosome|stored secretory granule	ferric iron binding			ovary(1)|skin(1)	2					Aluminium(DB01370)|Bismuth(DB01402)|Iron Dextran(DB00893)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	133813053	133813053	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133813053delT								SLCO2A1 (64133 upstream) : RYK (62925 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	134137461	134137461	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134137461delA								AMOTL2 (43202 upstream) : ANAPC13 (59086 downstream)																																			---	---	---	---
KY	339855	broad.mit.edu	37	3	134369290	134369290	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134369290delG	uc010hty.2	-						KY_uc011blw.1_Intron|KY_uc011blx.1_Intron|KY_uc003eqs.1_Intron	NM_178554	NP_848649			kyphoscoliosis peptidase							cytoskeleton|Z disc	peptidase activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	134503216	134503216	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134503216delT								KY (132738 upstream) : EPHB1 (11044 downstream)																																			---	---	---	---
EPHB1	2047	broad.mit.edu	37	3	134577220	134577220	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134577220delG	uc003eqt.2	+						EPHB1_uc010htz.1_Intron|EPHB1_uc011bly.1_Intron	NM_004441	NP_004432			ephrin receptor EphB1 precursor							integral to plasma membrane	ATP binding|ephrin receptor activity|protein binding			lung(11)|ovary(6)|stomach(4)|breast(3)|central_nervous_system(2)|skin(2)|large_intestine(1)|pancreas(1)	30																		---	---	---	---
EPHB1	2047	broad.mit.edu	37	3	134725664	134725665	+	Intron	DEL	TT	-	-	rs63729162		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134725664_134725665delTT	uc003eqt.2	+						EPHB1_uc010htz.1_Intron|EPHB1_uc011bly.1_Intron	NM_004441	NP_004432			ephrin receptor EphB1 precursor							integral to plasma membrane	ATP binding|ephrin receptor activity|protein binding			lung(11)|ovary(6)|stomach(4)|breast(3)|central_nervous_system(2)|skin(2)|large_intestine(1)|pancreas(1)	30																		---	---	---	---
EPHB1	2047	broad.mit.edu	37	3	134945680	134945680	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134945680delA	uc003eqt.2	+						EPHB1_uc003equ.2_Intron	NM_004441	NP_004432			ephrin receptor EphB1 precursor							integral to plasma membrane	ATP binding|ephrin receptor activity|protein binding			lung(11)|ovary(6)|stomach(4)|breast(3)|central_nervous_system(2)|skin(2)|large_intestine(1)|pancreas(1)	30																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	135562126	135562127	+	IGR	DEL	AA	-	-	rs140143610	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:135562126_135562127delAA								EPHB1 (582821 upstream) : PPP2R3A (122440 downstream)																																			---	---	---	---
PCCB	5096	broad.mit.edu	37	3	135975659	135975659	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:135975659delG	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	136279788	136279788	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136279788delT	uc003era.1	-						STAG1_uc003erb.1_Intron|STAG1_uc003erc.1_Intron|STAG1_uc010hua.1_Intron|STAG1_uc003erd.2_Intron|STAG1_uc003ere.2_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	137300483	137300484	+	IGR	DEL	TC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137300483_137300484delTC								IL20RB (570563 upstream) : SOX14 (183095 downstream)																																			---	---	---	---
PIK3CB	5291	broad.mit.edu	37	3	138418346	138418346	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138418346delA	uc011bmq.1	-						PIK3CB_uc011bmn.1_Intron|PIK3CB_uc011bmo.1_Intron|PIK3CB_uc011bmp.1_Intron	NM_006219	NP_006210			catalytic phosphatidylinositol 3-kinase beta						activation of MAPK activity|chemotaxis|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell receptor signaling pathway	phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity			breast(2)|ovary(1)|lung(1)|skin(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	138606619	138606620	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138606619_138606620insT								PIK3CB (128434 upstream) : FOXL2 (56447 downstream)																																			---	---	---	---
CLSTN2	64084	broad.mit.edu	37	3	139955698	139955707	+	Intron	DEL	TGTGTGTGTA	-	-	rs60145180	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:139955698_139955707delTGTGTGTGTA	uc003etn.2	+						CLSTN2_uc003etm.2_Intron	NM_022131	NP_071414			calsyntenin 2 precursor						homophilic cell adhesion	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|plasma membrane	calcium ion binding			skin(3)|large_intestine(2)|pancreas(1)|central_nervous_system(1)	7															HNSCC(16;0.037)			---	---	---	---
Unknown	0	broad.mit.edu	37	3	140306518	140306518	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140306518delT								CLSTN2 (19601 upstream) : TRIM42 (90363 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	140477316	140477317	+	IGR	DEL	AG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140477316_140477317delAG								TRIM42 (57325 upstream) : SLC25A36 (183345 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	141388175	141388175	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141388175delA								RASA2 (56978 upstream) : RNF7 (68876 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	141546800	141546801	+	IGR	DEL	GA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141546800_141546801delGA								GRK7 (10910 upstream) : ATP1B3 (48669 downstream)																																			---	---	---	---
GK5	256356	broad.mit.edu	37	3	141876800	141876800	+	3'UTR	DEL	T	-	-	rs67398474		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141876800delT	uc003euq.1	-	16					GK5_uc003eup.1_3'UTR	NM_001039547	NP_001034636			glycerol kinase 5 (putative)						glycerol metabolic process		ATP binding|glycerol kinase activity				0																		---	---	---	---
XRN1	54464	broad.mit.edu	37	3	142108156	142108156	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142108156delT	uc003eus.2	-						XRN1_uc010huu.2_Intron|XRN1_uc003eut.2_Intron|XRN1_uc003euu.2_Intron|XRN1_uc003euv.1_Intron	NM_019001	NP_061874			5'-3' exoribonuclease 1 isoform a						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|histone mRNA catabolic process|nuclear mRNA surveillance|rRNA catabolic process	cytosol|Golgi apparatus|intermediate filament cytoskeleton|plasma membrane	5'-3' exonuclease activity|DNA binding|protein binding|RNA binding			ovary(3)	3																		---	---	---	---
SLC9A9	285195	broad.mit.edu	37	3	143149967	143149967	+	Intron	DEL	A	-	-	rs74655192		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:143149967delA	uc003evn.2	-							NM_173653	NP_775924			solute carrier family 9 (sodium/hydrogen						regulation of pH	integral to membrane|late endosome membrane|recycling endosome	sodium:hydrogen antiporter activity			ovary(2)|skin(1)	3																		---	---	---	---
SLC9A9	285195	broad.mit.edu	37	3	143441856	143441856	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:143441856delT	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																		---	---	---	---
SLC9A9	285195	broad.mit.edu	37	3	143537161	143537161	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:143537161delT	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	144538515	144538516	+	IGR	DEL	TT	-	-	rs111657763		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:144538515_144538516delTT								C3orf58 (827306 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	145166980	145166981	+	IGR	INS	-	GT	GT	rs140449413	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:145166980_145166981insGT								None (None upstream) : PLOD2 (620247 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	145529019	145529019	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:145529019delT								None (None upstream) : PLOD2 (258209 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	146430746	146430746	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:146430746delT								PLSCR5 (106743 upstream) : ZIC4 (673091 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	147303463	147303463	+	IGR	DEL	T	-	-	rs73866450	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:147303463delT								ZIC1 (168959 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	147345056	147345057	+	IGR	INS	-	T	T	rs138832509	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:147345056_147345057insT								ZIC1 (210552 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	148112943	148112943	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148112943delA								ZIC1 (978439 upstream) : AGTR1 (302715 downstream)																																			---	---	---	---
AGTR1	185	broad.mit.edu	37	3	148415382	148415382	+	5'Flank	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148415382delA	uc003ewg.2	+						AGTR1_uc003ewh.2_5'Flank|AGTR1_uc003ewi.2_5'Flank|AGTR1_uc003ewj.2_5'Flank	NM_031850	NP_114038			angiotensin II receptor, type 1						calcium-mediated signaling|cell chemotaxis|elevation of cytosolic calcium ion concentration involved in G-protein signaling coupled to IP3 second messenger|kidney development|low-density lipoprotein particle remodeling|positive regulation of cellular protein metabolic process|positive regulation of cholesterol esterification|positive regulation of inflammatory response|positive regulation of NAD(P)H oxidase activity|positive regulation of phospholipase A2 activity|positive regulation of reactive oxygen species metabolic process|regulation of cell growth|regulation of cell proliferation|regulation of renal sodium excretion|regulation of vasoconstriction|renin-angiotensin regulation of aldosterone production|Rho protein signal transduction		acetyltransferase activator activity|angiotensin type I receptor activity|angiotensin type II receptor activity|bradykinin receptor binding|protein heterodimerization activity				0			LUSC - Lung squamous cell carcinoma(72;0.127)|Lung(72;0.152)		Candesartan(DB00796)|Eprosartan(DB00876)|Forasartan(DB01342)|Irbesartan(DB01029)|Losartan(DB00678)|Olmesartan(DB00275)|Saprisartan(DB01347)|Spironolactone(DB00421)|Tasosartan(DB01349)|Telmisartan(DB00966)|Valsartan(DB00177)													---	---	---	---
CPA3	1359	broad.mit.edu	37	3	148582960	148582960	+	5'Flank	DEL	A	-	-	rs143382113		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148582960delA	uc003ewm.2	+							NM_001870	NP_001861			carboxypeptidase A3 precursor						proteolysis	stored secretory granule|transport vesicle	metallocarboxypeptidase activity|zinc ion binding			breast(1)|skin(1)	2			LUSC - Lung squamous cell carcinoma(72;0.0934)|Lung(72;0.115)															---	---	---	---
GYG1	2992	broad.mit.edu	37	3	148726946	148726951	+	Intron	DEL	AAAAAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148726946_148726951delAAAAAA	uc003ewn.2	+						GYG1_uc011bnp.1_Intron|GYG1_uc003ewo.2_Intron|GYG1_uc003ewp.2_Intron	NM_004130	NP_004121			glycogenin 1						glucose metabolic process|glycogen biosynthetic process|glycogen catabolic process	cytosol	glycogenin glucosyltransferase activity|metal ion binding|protein binding			ovary(1)	1			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)															---	---	---	---
HLTF	6596	broad.mit.edu	37	3	148757291	148757291	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148757291delT	uc003ewq.1	-						HLTF_uc003ewr.1_Intron|HLTF_uc003ews.1_Intron|HLTF_uc010hve.1_Intron	NM_139048	NP_620636			helicase-like transcription factor						chromatin modification|transcription, DNA-dependent	nucleus	ATP binding|DNA binding|helicase activity|ligase activity|zinc ion binding			ovary(1)	1			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	149083231	149083232	+	IGR	DEL	TT	-	-	rs10587180		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149083231_149083232delTT								TM4SF18 (31812 upstream) : TM4SF1 (3573 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	149109996	149109997	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149109996_149109997delTT								TM4SF1 (14428 upstream) : TM4SF4 (82437 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	149174504	149174507	+	IGR	DEL	ACAC	-	-	rs145053251		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149174504_149174507delACAC								TM4SF1 (78936 upstream) : TM4SF4 (17927 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	149223518	149223518	+	IGR	DEL	A	-	-	rs111356096		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149223518delA								TM4SF4 (2450 upstream) : WWTR1 (14515 downstream)																																			---	---	---	---
RNF13	11342	broad.mit.edu	37	3	149672223	149672224	+	Intron	INS	-	AC	AC			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149672223_149672224insAC	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	149945958	149945958	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149945958delT								PFN2 (257217 upstream) : TSC22D2 (180830 downstream)																																	OREG0015875	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
CLRN1OS	116933	broad.mit.edu	37	3	150586272	150586272	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150586272delC	uc011bny.1	+											Homo sapiens usher critical region protein (UCRP) pseudogene mRNA, complete sequence.												0																		---	---	---	---
CLRN1OS	116933	broad.mit.edu	37	3	150778321	150778322	+	Intron	INS	-	TGGGCCC	TGGGCCC	rs145593710	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150778321_150778322insTGGGCCC	uc011bny.1	+						CLRN1OS_uc003eyl.2_Intron					Homo sapiens usher critical region protein (UCRP) pseudogene mRNA, complete sequence.												0																		---	---	---	---
MED12L	116931	broad.mit.edu	37	3	150845342	150845342	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150845342delT	uc003eyp.2	+						MED12L_uc011bnz.1_Intron|MED12L_uc003eym.1_Intron|MED12L_uc003eyn.2_Intron|MED12L_uc003eyo.2_Intron	NM_053002	NP_443728			mediator of RNA polymerase II transcription,						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex				ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1)	7			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)															---	---	---	---
MBNL1	4154	broad.mit.edu	37	3	151987516	151987519	+	Intron	DEL	TTCT	-	-	rs60360711		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151987516_151987519delTTCT	uc003ezh.2	+						MBNL1_uc003ezi.2_Intron|MBNL1_uc003ezj.2_Intron|LOC401093_uc011boe.1_5'Flank|LOC401093_uc011bof.1_5'Flank|MBNL1_uc003ezg.1_Intron	NM_021038	NP_066368			muscleblind-like 1 isoform a						embryonic limb morphogenesis|in utero embryonic development|myoblast differentiation|nervous system development	nucleus|stress granule	double-stranded RNA binding|protein binding|zinc ion binding			ovary(1)	1			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	152233152	152233153	+	IGR	DEL	CG	-	-	rs72291284		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:152233152_152233153delCG								MBNL1 (49584 upstream) : P2RY1 (319583 downstream)																																			---	---	---	---
SGEF	26084	broad.mit.edu	37	3	153852806	153852806	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:153852806delA	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)															---	---	---	---
SGEF	26084	broad.mit.edu	37	3	153887162	153887163	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:153887162_153887163delAA	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	154048453	154048453	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154048453delT								DHX36 (6167 upstream) : GPR149 (7009 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	154253986	154253988	+	IGR	DEL	CTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154253986_154253988delCTT								GPR149 (106482 upstream) : MME (487925 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	154932782	154932783	+	IGR	DEL	AA	-	-	rs145615012		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154932782_154932783delAA								MME (31264 upstream) : PLCH1 (264888 downstream)																																			---	---	---	---
PLCH1	23007	broad.mit.edu	37	3	155384682	155384683	+	Intron	INS	-	GTGT	GTGT	rs138179427	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155384682_155384683insGTGT	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)															---	---	---	---
C3orf33	285315	broad.mit.edu	37	3	155511780	155511781	+	Intron	INS	-	T	T	rs139321214	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155511780_155511781insT	uc003fal.1	-						C3orf33_uc003fam.1_Intron	NM_173657	NP_775928			hypothetical protein LOC285315								hydrolase activity, acting on ester bonds|nucleic acid binding				0			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)															---	---	---	---
GMPS	8833	broad.mit.edu	37	3	155632553	155632554	+	Intron	INS	-	T	T	rs111398667		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155632553_155632554insT	uc003faq.2	+						GMPS_uc011bom.1_Intron	NM_003875	NP_003866			guanine monophosphate synthetase						glutamine metabolic process|purine base biosynthetic process	cytosol	ATP binding|GMP synthase (glutamine-hydrolyzing) activity|GMP synthase activity			ovary(2)|lung(1)	3			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)		L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)			T	MLL	AML								---	---	---	---
Unknown	0	broad.mit.edu	37	3	156302715	156302716	+	IGR	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:156302715_156302716delAC								SSR3 (29780 upstream) : LOC100287227 (88248 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	157438022	157438022	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:157438022delT								C3orf55 (119003 upstream) : SHOX2 (375779 downstream)																																			---	---	---	---
RSRC1	51319	broad.mit.edu	37	3	157957511	157957511	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:157957511delA	uc003fbt.2	+						RSRC1_uc011bou.1_Intron|RSRC1_uc003fbu.1_Intron|RSRC1_uc003fbv.2_Intron	NM_016625	NP_057709			arginine/serine-rich coiled-coil 1						nucleocytoplasmic transport	cytoplasm|nuclear speck	protein binding				0			Lung(72;0.00416)|LUSC - Lung squamous cell carcinoma(72;0.00575)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	158678941	158678941	+	IGR	DEL	T	-	-	rs10717356		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158678941delT								MFSD1 (131437 upstream) : SCHIP1 (108176 downstream)																																			---	---	---	---
SCHIP1	29970	broad.mit.edu	37	3	159544310	159544310	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:159544310delC	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)															---	---	---	---
IFT80	57560	broad.mit.edu	37	3	160102250	160102250	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160102250delA	uc011boy.1	-						IFT80_uc003fda.2_Intron|IFT80_uc003fdb.1_5'UTR|IFT80_uc003fdd.1_5'UTR|IFT80_uc003fde.1_5'UTR	NM_020800	NP_065851			WD repeat domain 56							cilium axoneme|microtubule basal body				ovary(1)	1			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)															---	---	---	---
SMC4	10051	broad.mit.edu	37	3	160141144	160141147	+	Intron	DEL	TTTG	-	-	rs4679884		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160141144_160141147delTTTG	uc003fdh.2	+						IFT80_uc003fda.2_Intron|SMC4_uc010hwc.1_Intron|SMC4_uc003fdi.2_Intron|SMC4_uc003fdj.2_Intron|SMC4_uc010hwd.2_Intron|SMC4_uc003fdl.2_Intron	NM_001002800	NP_001002800			SMC4 structural maintenance of chromosomes						cell division|mitotic chromosome condensation	condensin complex|cytoplasm|nucleus	ATP binding|protein heterodimerization activity			ovary(1)|breast(1)	2			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)															---	---	---	---
NMD3	51068	broad.mit.edu	37	3	160937830	160937830	+	5'Flank	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160937830delC	uc003feb.1	+						NMD3_uc003fec.2_5'Flank|NMD3_uc003fed.1_5'Flank	NM_015938	NP_057022			NMD3 homolog						protein transport	cytoplasm|nucleolus|nucleoplasm				ovary(1)	1			Lung(72;0.00111)|LUSC - Lung squamous cell carcinoma(72;0.00156)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	161502302	161502302	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:161502302delA								OTOL1 (280574 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	161625010	161625010	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:161625010delT								OTOL1 (403282 upstream) : None (None downstream)																																			---	---	---	---
SI	6476	broad.mit.edu	37	3	164755956	164755956	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164755956delT	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	164924102	164924102	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164924102delT								SLITRK3 (9633 upstream) : BCHE (566592 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	165254408	165254408	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:165254408delA								SLITRK3 (339939 upstream) : BCHE (236286 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	165357697	165357697	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:165357697delA								SLITRK3 (443228 upstream) : BCHE (132997 downstream)																																			---	---	---	---
ZBBX	79740	broad.mit.edu	37	3	167020323	167020324	+	Intron	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167020323_167020324delAC	uc003fep.2	-						ZBBX_uc011bpc.1_Intron|ZBBX_uc003feq.2_Intron	NM_024687	NP_078963			zinc finger, B-box domain containing							intracellular	zinc ion binding			ovary(2)	2																		---	---	---	---
WDR49	151790	broad.mit.edu	37	3	167321852	167321852	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167321852delA	uc003fev.1	-						WDR49_uc011bpd.1_Intron|WDR49_uc003few.1_Intron	NM_178824	NP_849146			WD repeat domain 49											large_intestine(1)|ovary(1)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	167691944	167691944	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167691944delT								SERPINI1 (148588 upstream) : GOLIM4 (35710 downstream)																																			---	---	---	---
MECOM	2122	broad.mit.edu	37	3	168926684	168926684	+	Intron	DEL	A	-	-	rs34058483		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:168926684delA	uc011bpj.1	-						MECOM_uc003ffl.2_Intron|MECOM_uc011bpk.1_Intron|MECOM_uc010hwn.2_Intron|MECOM_uc011bpl.1_Intron	NM_004991	NP_004982			MDS1 and EVI1 complex locus isoform c						apoptosis|cell differentiation|hemopoietic stem cell proliferation|negative regulation of JNK cascade|negative regulation of programmed cell death|negative regulation of transcription, DNA-dependent|regulation of cell cycle	nuclear speck	DNA binding|protein binding|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(5)|skin(5)|upper_aerodigestive_tract(1)|central_nervous_system(1)|ovary(1)|pancreas(1)	14																		---	---	---	---
MECOM	2122	broad.mit.edu	37	3	169306644	169306644	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169306644delT	uc011bpj.1	-						MECOM_uc011bpk.1_Intron|MECOM_uc010hwn.2_Intron|MECOM_uc011bpl.1_Intron	NM_004991	NP_004982			MDS1 and EVI1 complex locus isoform c						apoptosis|cell differentiation|hemopoietic stem cell proliferation|negative regulation of JNK cascade|negative regulation of programmed cell death|negative regulation of transcription, DNA-dependent|regulation of cell cycle	nuclear speck	DNA binding|protein binding|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(5)|skin(5)|upper_aerodigestive_tract(1)|central_nervous_system(1)|ovary(1)|pancreas(1)	14																		---	---	---	---
PRKCI	5584	broad.mit.edu	37	3	169953309	169953309	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169953309delT	uc003fgs.2	+							NM_002740	NP_002731			protein kinase C, iota						anti-apoptosis|cellular membrane organization|cellular response to insulin stimulus|establishment or maintenance of epithelial cell apical/basal polarity|intracellular signal transduction|nerve growth factor receptor signaling pathway|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|protein targeting to membrane|secretion|tight junction assembly|vesicle-mediated transport	cytosol|endosome|nucleus|polarisome	ATP binding|phospholipid binding|protein binding|protein kinase C activity|zinc ion binding			lung(2)|ovary(1)|breast(1)|skin(1)	5	all_cancers(22;6.45e-23)|all_epithelial(15;8.52e-28)|all_lung(20;6.31e-17)|Lung NSC(18;2.61e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)															---	---	---	---
TNIK	23043	broad.mit.edu	37	3	170958336	170958338	+	Intron	DEL	CTA	-	-	rs139533372		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170958336_170958338delCTA	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)															---	---	---	---
PLD1	5337	broad.mit.edu	37	3	171416767	171416767	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:171416767delA	uc003fhs.2	-						PLD1_uc003fht.2_Intron	NM_002662	NP_002653			phospholipase D1 isoform a						cell communication|chemotaxis|Ras protein signal transduction	endoplasmic reticulum membrane|Golgi membrane|late endosome membrane|perinuclear region of cytoplasm	NAPE-specific phospholipase D activity|phosphatidylinositol binding|phospholipase D activity			ovary(2)|lung(1)	3	all_cancers(22;4.53e-19)|Ovarian(172;0.00197)|Breast(254;0.186)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)		Choline(DB00122)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	172578537	172578537	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172578537delA								ECT2 (39274 upstream) : SPATA16 (28611 downstream)																																			---	---	---	---
NLGN1	22871	broad.mit.edu	37	3	173694883	173694884	+	Intron	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:173694883_173694884delAC	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	173851635	173851635	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:173851635delA	uc003fio.1	+						NLGN1_uc010hww.1_Intron|NLGN1_uc003fip.1_Intron	NM_014932	NP_055747			neuroligin 1						calcium-dependent cell-cell adhesion|neuron cell-cell adhesion|neuronal signal transduction|positive regulation of dendritic spine development|positive regulation of excitatory postsynaptic membrane potential|positive regulation of intracellular protein kinase cascade|positive regulation of synaptogenesis|protein targeting|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|regulation of N-methyl-D-aspartate selective glutamate receptor activity|synapse assembly|synaptic vesicle targeting	cell junction|cell surface|dendrite|integral to plasma membrane|postsynaptic density|postsynaptic membrane	cell adhesion molecule binding|neurexin binding|receptor activity			lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)|ovary(1)|pancreas(1)	7	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	174544926	174544926	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:174544926delT								NLGN1 (543810 upstream) : NAALADL2 (32185 downstream)																																			---	---	---	---
NAALADL2	254827	broad.mit.edu	37	3	175161643	175161643	+	Intron	DEL	A	-	-	rs68035522		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:175161643delA	uc003fit.2	+						NAALADL2_uc003fiu.1_Intron|NAALADL2_uc010hwy.1_Intron|NAALADL2_uc010hwz.1_Intron	NM_207015	NP_996898			N-acetylated alpha-linked acidic dipeptidase 2						proteolysis	integral to membrane	peptidase activity			pancreas(1)	1	Ovarian(172;0.0102)	all_cancers(1;0.0272)|all_epithelial(1;0.0553)	OV - Ovarian serous cystadenocarcinoma(80;9.26e-28)	Colorectal(1;1.66e-10)|COAD - Colon adenocarcinoma(1;2.1e-07)|STAD - Stomach adenocarcinoma(1;0.00261)|READ - Rectum adenocarcinoma(3;0.0284)														---	---	---	---
NAALADL2	254827	broad.mit.edu	37	3	175392216	175392217	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:175392216_175392217insT	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	176073061	176073064	+	IGR	DEL	AAAC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:176073061_176073064delAAAC								NAALADL2 (549635 upstream) : TBL1XR1 (665479 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	176347634	176347634	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:176347634delA								NAALADL2 (824208 upstream) : TBL1XR1 (390909 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	177592513	177592514	+	Intron	DEL	TT	-	-	rs67420726		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:177592513_177592514delTT	uc003fiz.1	+											Homo sapiens cDNA FLJ31690 fis, clone NT2RI2005621.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	178252909	178252910	+	Intron	DEL	AG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178252909_178252910delAG	uc003fjb.1	-						KCNMB2_uc003fjd.2_5'Flank					Homo sapiens clone N11 NTera2D1 teratocarcinoma mRNA.																														---	---	---	---
KCNMB2	10242	broad.mit.edu	37	3	178559905	178559905	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178559905delT	uc003fjd.2	+						uc003fjb.1_Intron|uc003fjc.1_Intron|KCNMB2_uc003fje.2_Intron|KCNMB2_uc003fjf.2_Intron|KCNMB2_uc011bqa.1_Intron|KCNMB2_uc011bqb.1_Intron	NM_181361	NP_852006			calcium-activated potassium channel beta 2						detection of calcium ion|platelet activation|regulation of action potential in neuron|regulation of vasoconstriction	voltage-gated potassium channel complex	calcium-activated potassium channel activity|ion channel inhibitor activity|potassium channel regulator activity			ovary(1)	1	all_cancers(143;5.38e-18)|Ovarian(172;0.00769)|Breast(254;0.125)		OV - Ovarian serous cystadenocarcinoma(80;1.32e-27)|GBM - Glioblastoma multiforme(14;0.0321)|BRCA - Breast invasive adenocarcinoma(182;0.0841)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	179273025	179273025	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179273025delA								GNB4 (103654 upstream) : ACTL6A (7683 downstream)																																			---	---	---	---
USP13	8975	broad.mit.edu	37	3	179437650	179437652	+	Intron	DEL	AGG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179437650_179437652delAGG	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	180551253	180551253	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180551253delT	uc003fko.2	-											Homo sapiens mRNA; cDNA DKFZp434A128 (from clone DKFZp434A128).																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	181082208	181082209	+	IGR	DEL	GA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181082208_181082209delGA								DNAJC19 (374678 upstream) : SOX2OT (199300 downstream)																																			---	---	---	---
SOX2OT	347689	broad.mit.edu	37	3	181417311	181417312	+	Intron	DEL	CT	-	-	rs62289995		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181417311_181417312delCT	uc003fkv.2	+						SOX2OT_uc003fkw.3_Intron					Homo sapiens cDNA FLJ12764 fis, clone NT2RP2001506.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	181599356	181599356	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181599356delT								SOX2OT (140353 upstream) : ATP11B (911935 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	181689606	181689606	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181689606delT	uc003fky.2	+											Homo sapiens cDNA clone IMAGE:5296886.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	181914589	181914590	+	IGR	DEL	AG	-	-	rs80328934		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181914589_181914590delAG								SOX2OT (455586 upstream) : ATP11B (596701 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	182003287	182003287	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182003287delA								SOX2OT (544284 upstream) : ATP11B (508004 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	182135079	182135079	+	IGR	DEL	T	-	-	rs75327279		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182135079delT								SOX2OT (676076 upstream) : ATP11B (376212 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	182404361	182404361	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182404361delA								SOX2OT (945358 upstream) : ATP11B (106930 downstream)																																			---	---	---	---
MCCC1	56922	broad.mit.edu	37	3	182779041	182779041	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182779041delT	uc003fle.2	-						MCCC1_uc010hxi.2_Intron|MCCC1_uc011bqo.1_Intron|MCCC1_uc003flf.2_Intron|MCCC1_uc003flg.2_Intron|MCCC1_uc011bqp.1_Intron|MCCC1_uc011bqq.1_Intron	NM_020166	NP_064551			methylcrotonoyl-Coenzyme A carboxylase 1 (alpha)						biotin metabolic process|leucine catabolic process	mitochondrial inner membrane|mitochondrial matrix	ATP binding|biotin binding|biotin carboxylase activity|metal ion binding|methylcrotonoyl-CoA carboxylase activity			ovary(1)|central_nervous_system(1)|skin(1)	3	all_cancers(143;1.84e-14)|Ovarian(172;0.0355)		all cancers(12;1.8e-44)|Epithelial(37;3.23e-38)|LUSC - Lung squamous cell carcinoma(7;5.04e-25)|Lung(8;5.03e-23)|OV - Ovarian serous cystadenocarcinoma(80;5.07e-21)		Biotin(DB00121)													---	---	---	---
MCF2L2	23101	broad.mit.edu	37	3	182938888	182938888	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182938888delC	uc003fli.1	-							NM_015078	NP_055893			Rho family guanine-nucleotide exchange factor						regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(2)|large_intestine(2)|breast(1)	5	all_cancers(143;1.26e-12)|Ovarian(172;0.0355)		all cancers(12;3.35e-44)|Epithelial(37;6.48e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21)															---	---	---	---
MCF2L2	23101	broad.mit.edu	37	3	182958838	182958838	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182958838delA	uc003fli.1	-						MCF2L2_uc003flj.1_Intron|MCF2L2_uc011bqr.1_Intron	NM_015078	NP_055893			Rho family guanine-nucleotide exchange factor						regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(2)|large_intestine(2)|breast(1)	5	all_cancers(143;1.26e-12)|Ovarian(172;0.0355)		all cancers(12;3.35e-44)|Epithelial(37;6.48e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21)															---	---	---	---
YEATS2	55689	broad.mit.edu	37	3	183521660	183521660	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183521660delA	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	183615733	183615733	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183615733delT								PARL (13040 upstream) : ABCC5 (21993 downstream)																																			---	---	---	---
ABCC5	10057	broad.mit.edu	37	3	183638030	183638031	+	3'UTR	DEL	GA	-	-	rs111657478		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183638030_183638031delGA	uc003fmg.2	-	30					ABCC5_uc011bqt.1_3'UTR|ABCC5_uc010hxl.2_3'UTR	NM_005688	NP_005679			ATP-binding cassette, sub-family C, member 5							integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of substances|organic anion transmembrane transporter activity			ovary(2)|large_intestine(1)|central_nervous_system(1)	4	all_cancers(143;1.85e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)															---	---	---	---
ABCC5	10057	broad.mit.edu	37	3	183696103	183696103	+	Intron	DEL	T	-	-	rs67116575		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183696103delT	uc003fmg.2	-						ABCC5_uc011bqt.1_Intron|ABCC5_uc010hxl.2_Intron	NM_005688	NP_005679			ATP-binding cassette, sub-family C, member 5							integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of substances|organic anion transmembrane transporter activity			ovary(2)|large_intestine(1)|central_nervous_system(1)	4	all_cancers(143;1.85e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)															---	---	---	---
HTR3C	170572	broad.mit.edu	37	3	183768398	183768399	+	5'Flank	DEL	TC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183768398_183768399delTC	uc003fmk.2	+							NM_130770	NP_570126			5-hydroxytryptamine receptor 3 subunit C							integral to membrane|plasma membrane|postsynaptic membrane	extracellular ligand-gated ion channel activity|receptor activity			large_intestine(1)|ovary(1)|central_nervous_system(1)	3	all_cancers(143;2.33e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;3.11e-22)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	184173952	184173952	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184173952delT								CHRD (66333 upstream) : EPHB3 (105635 downstream)																																			---	---	---	---
VPS8	23355	broad.mit.edu	37	3	184711930	184711930	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184711930delA	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	184770795	184770796	+	IGR	DEL	TT	-	-	rs11359249		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184770795_184770796delTT								VPS8 (393 upstream) : C3orf70 (25044 downstream)																																			---	---	---	---
MAP3K13	9175	broad.mit.edu	37	3	185149742	185149743	+	Intron	DEL	TC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185149742_185149743delTC	uc010hyf.2	+						MAP3K13_uc011brt.1_Intron|MAP3K13_uc003fph.3_Intron|MAP3K13_uc011bru.1_Intron|MAP3K13_uc003fpi.2_Intron|MAP3K13_uc010hyg.2_Intron	NM_004721	NP_004712			mitogen-activated protein kinase kinase kinase						activation of MAPKK activity|JNK cascade|positive regulation of NF-kappaB transcription factor activity|protein autophosphorylation	cytoplasm|membrane|membrane fraction	ATP binding|magnesium ion binding|MAP kinase kinase kinase activity|protein homodimerization activity|protein kinase binding			ovary(2)|skin(1)	3	all_cancers(143;7.21e-11)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)															---	---	---	---
LIPH	200879	broad.mit.edu	37	3	185265614	185265615	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185265614_185265615insA	uc003fpm.2	-						LIPH_uc010hyh.2_Intron	NM_139248	NP_640341			lipase, member H precursor						lipid catabolic process	extracellular space|plasma membrane	heparin binding|phospholipase activity			ovary(1)|pancreas(1)	2	all_cancers(143;8.87e-11)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;1.31e-21)															---	---	---	---
LIPH	200879	broad.mit.edu	37	3	185266202	185266202	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185266202delA	uc003fpm.2	-						LIPH_uc010hyh.2_Intron	NM_139248	NP_640341			lipase, member H precursor						lipid catabolic process	extracellular space|plasma membrane	heparin binding|phospholipase activity			ovary(1)|pancreas(1)	2	all_cancers(143;8.87e-11)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;1.31e-21)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	185560763	185560763	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185560763delT								IGF2BP2 (17936 upstream) : TRA2B (71597 downstream)																																			---	---	---	---
DGKG	1608	broad.mit.edu	37	3	185900491	185900491	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185900491delT	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	186122970	186122971	+	IGR	INS	-	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186122970_186122971insC								DGKG (42947 upstream) : CRYGS (133262 downstream)																																			---	---	---	---
HRG	3273	broad.mit.edu	37	3	186393097	186393098	+	Intron	INS	-	GA	GA	rs59016663		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186393097_186393098insGA	uc003fqq.2	+							NM_000412	NP_000403			histidine-rich glycoprotein precursor						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	186879650	186879650	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186879650delT								RPL39L (22387 upstream) : RTP1 (35624 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	187048266	187048266	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187048266delA								MASP1 (38514 upstream) : RTP4 (37902 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	187432754	187432754	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187432754delA								RTP2 (12409 upstream) : BCL6 (6411 downstream)																																	OREG0015976	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	187691066	187691066	+	Intron	DEL	A	-	-	rs79515682		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187691066delA	uc003frr.1	-											full-length cDNA clone CS0DL012YA13 of B cells (Ramos cell line) Cot 25-normalized of Homo sapiens (human).																														---	---	---	---
LPP	4026	broad.mit.edu	37	3	188096879	188096879	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188096879delT	uc003frs.1	+						LPP_uc011bsg.1_Intron|LPP_uc011bsi.1_Intron|LPP_uc003frt.2_Intron	NM_005578	NP_005569			LIM domain containing preferred translocation						cell adhesion	cytoplasm|focal adhesion|nucleus	protein binding|zinc ion binding		HMGA2/LPP(161)	soft_tissue(134)|bone(27)|lung(2)|ovary(1)|breast(1)	165	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)				T	HMGA2|MLL|C12orf9	lipoma|leukemia								---	---	---	---
LPP	4026	broad.mit.edu	37	3	188295533	188295540	+	Intron	DEL	GTTCCTTC	-	-	rs67188827		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188295533_188295540delGTTCCTTC	uc003frs.1	+						LPP_uc011bsg.1_Intron|LPP_uc011bsi.1_Intron|LPP_uc003frt.2_Intron|LPP_uc011bsj.1_Intron	NM_005578	NP_005569			LIM domain containing preferred translocation						cell adhesion	cytoplasm|focal adhesion|nucleus	protein binding|zinc ion binding		HMGA2/LPP(161)	soft_tissue(134)|bone(27)|lung(2)|ovary(1)|breast(1)	165	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)				T	HMGA2|MLL|C12orf9	lipoma|leukemia								---	---	---	---
LPP	4026	broad.mit.edu	37	3	188539158	188539158	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188539158delT	uc003frs.1	+						LPP_uc011bsg.1_Intron|LPP_uc011bsi.1_Intron|LPP_uc011bsj.1_Intron	NM_005578	NP_005569			LIM domain containing preferred translocation						cell adhesion	cytoplasm|focal adhesion|nucleus	protein binding|zinc ion binding		HMGA2/LPP(161)	soft_tissue(134)|bone(27)|lung(2)|ovary(1)|breast(1)	165	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)				T	HMGA2|MLL|C12orf9	lipoma|leukemia								---	---	---	---
TPRG1	285386	broad.mit.edu	37	3	188697480	188697481	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188697480_188697481insA	uc003frv.1	+							NM_198485	NP_940887			tumor protein p63 regulated 1												0	all_cancers(143;6.12e-12)|all_hematologic(3;0.0359)|Ovarian(172;0.0925)	all_lung(153;8.23e-09)|Lung NSC(153;3.55e-06)|all_neural(597;0.0019)|Myeloproliferative disorder(1037;0.0255)	Lung(62;6.93e-06)	GBM - Glioblastoma multiforme(93;4.77e-14)														---	---	---	---
TPRG1	285386	broad.mit.edu	37	3	188703897	188703897	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188703897delT	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)														---	---	---	---
TP63	8626	broad.mit.edu	37	3	189598274	189598274	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189598274delG	uc003fry.2	+						TP63_uc003frx.2_3'UTR|TP63_uc003frz.2_Intron|TP63_uc010hzc.1_Intron|TP63_uc003fsb.2_3'UTR|TP63_uc003fsc.2_Intron|TP63_uc003fsd.2_Intron|TP63_uc010hzd.1_Intron	NM_003722	NP_003713			tumor protein p63 isoform 1						anti-apoptosis|cellular response to UV|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|mitotic cell cycle G1/S transition DNA damage checkpoint|negative regulation of transcription from RNA polymerase II promoter|Notch signaling pathway|positive regulation of Notch signaling pathway|protein homotetramerization|regulation of neuron apoptosis|response to gamma radiation|response to X-ray	chromatin|cytosol|dendrite|Golgi apparatus|transcription factor complex	chromatin binding|damaged DNA binding|double-stranded DNA binding|identical protein binding|metal ion binding|p53 binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			skin(5)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	12	all_cancers(143;3.35e-10)|Ovarian(172;0.0925)		Lung(62;3.33e-05)	GBM - Glioblastoma multiforme(93;0.0227)										Hay-Wells_syndrome	HNSCC(45;0.13)			---	---	---	---
Unknown	0	broad.mit.edu	37	3	190774487	190774487	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:190774487delT								SNAR-I (178648 upstream) : OSTN (155835 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	190828375	190828375	+	IGR	DEL	A	-	-	rs146484826		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:190828375delA								SNAR-I (232536 upstream) : OSTN (101947 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	191173358	191173358	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:191173358delT								CCDC50 (56900 upstream) : PYDC2 (5594 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	191772395	191772395	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:191772395delA								PYDC2 (593152 upstream) : FGF12 (87289 downstream)																																			---	---	---	---
FGF12	2257	broad.mit.edu	37	3	192111657	192111657	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:192111657delA	uc003fsx.2	-						FGF12_uc003fsy.2_Intron	NM_021032	NP_066360			fibroblast growth factor 12 isoform 1						cell-cell signaling|heart development|JNK cascade|nervous system development|signal transduction	extracellular space|nucleus	growth factor activity|heparin binding			ovary(1)|skin(1)|lung(1)|pancreas(1)	4	all_cancers(143;1.72e-08)|Ovarian(172;0.0634)|Breast(254;0.247)	Lung NSC(153;0.21)	LUSC - Lung squamous cell carcinoma(58;5.45e-06)|Lung(62;6.17e-06)	GBM - Glioblastoma multiforme(46;0.00032)														---	---	---	---
FGF12	2257	broad.mit.edu	37	3	192288019	192288019	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:192288019delG	uc003fsy.2	-							NM_004113	NP_004104			fibroblast growth factor 12 isoform 2						cell-cell signaling|heart development|JNK cascade|nervous system development|signal transduction	extracellular space|nucleus	growth factor activity|heparin binding			ovary(1)|skin(1)|lung(1)|pancreas(1)	4	all_cancers(143;1.72e-08)|Ovarian(172;0.0634)|Breast(254;0.247)	Lung NSC(153;0.21)	LUSC - Lung squamous cell carcinoma(58;5.45e-06)|Lung(62;6.17e-06)	GBM - Glioblastoma multiforme(46;0.00032)														---	---	---	---
FGF12	2257	broad.mit.edu	37	3	192293444	192293445	+	Intron	DEL	TT	-	-	rs66592379		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:192293444_192293445delTT	uc003fsy.2	-							NM_004113	NP_004104			fibroblast growth factor 12 isoform 2						cell-cell signaling|heart development|JNK cascade|nervous system development|signal transduction	extracellular space|nucleus	growth factor activity|heparin binding			ovary(1)|skin(1)|lung(1)|pancreas(1)	4	all_cancers(143;1.72e-08)|Ovarian(172;0.0634)|Breast(254;0.247)	Lung NSC(153;0.21)	LUSC - Lung squamous cell carcinoma(58;5.45e-06)|Lung(62;6.17e-06)	GBM - Glioblastoma multiforme(46;0.00032)														---	---	---	---
FGF12	2257	broad.mit.edu	37	3	192350675	192350675	+	Intron	DEL	G	-	-	rs73056205	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:192350675delG	uc003fsy.2	-							NM_004113	NP_004104			fibroblast growth factor 12 isoform 2						cell-cell signaling|heart development|JNK cascade|nervous system development|signal transduction	extracellular space|nucleus	growth factor activity|heparin binding			ovary(1)|skin(1)|lung(1)|pancreas(1)	4	all_cancers(143;1.72e-08)|Ovarian(172;0.0634)|Breast(254;0.247)	Lung NSC(153;0.21)	LUSC - Lung squamous cell carcinoma(58;5.45e-06)|Lung(62;6.17e-06)	GBM - Glioblastoma multiforme(46;0.00032)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	192690591	192690591	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:192690591delC								C3orf59 (54641 upstream) : HRASLS (268327 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	192855753	192855754	+	IGR	INS	-	CT	CT	rs151327730	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:192855753_192855754insCT								C3orf59 (219803 upstream) : HRASLS (103164 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	193108200	193108200	+	IGR	DEL	A	-	-	rs66799303		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193108200delA								ATP13A5 (11686 upstream) : ATP13A4 (11667 downstream)																																			---	---	---	---
ATP13A4	84239	broad.mit.edu	37	3	193216130	193216130	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193216130delA	uc003ftd.2	-						ATP13A4_uc003fte.1_Intron|ATP13A4_uc011bsr.1_Intron	NM_032279	NP_115655			ATPase type 13A4						ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			ovary(2)	2	all_cancers(143;1.76e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;2.72e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000109)														---	---	---	---
ATP13A4	84239	broad.mit.edu	37	3	193269209	193269210	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193269209_193269210delAA	uc003ftd.2	-						ATP13A4_uc003fte.1_Intron|ATP13A4_uc011bsr.1_Intron	NM_032279	NP_115655			ATPase type 13A4						ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			ovary(2)	2	all_cancers(143;1.76e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;2.72e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000109)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	193573695	193573695	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193573695delT								OPA1 (158096 upstream) : LOC100128023 (137189 downstream)																																			---	---	---	---
ATP13A3	79572	broad.mit.edu	37	3	194138715	194138718	+	Intron	DEL	AGGG	-	-	rs57628585	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194138715_194138718delAGGG	uc003fty.3	-						ATP13A3_uc003ftx.3_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	194299483	194299483	+	IGR	DEL	T	-	-	rs71984339		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194299483delT								ATP13A3 (110515 upstream) : TMEM44 (8920 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	194472957	194472957	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194472957delT								FAM43A (63193 upstream) : C3orf21 (316058 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	194486561	194486561	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194486561delT								FAM43A (76797 upstream) : C3orf21 (302454 downstream)																																			---	---	---	---
ACAP2	23527	broad.mit.edu	37	3	195103609	195103612	+	Intron	DEL	AAAA	-	-	rs112190227		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195103609_195103612delAAAA	uc003fun.3	-						ACAP2_uc003fuo.2_Intron	NM_012287	NP_036419			centaurin, beta 2						regulation of ARF GTPase activity		ARF GTPase activator activity|zinc ion binding			large_intestine(1)|ovary(1)	2																		---	---	---	---
ACAP2	23527	broad.mit.edu	37	3	195138670	195138671	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195138670_195138671delAA	uc003fun.3	-						ACAP2_uc003fuo.2_Intron	NM_012287	NP_036419			centaurin, beta 2						regulation of ARF GTPase activity		ARF GTPase activator activity|zinc ion binding			large_intestine(1)|ovary(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	195418092	195418092	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195418092delG								SDHAP2 (2359 upstream) : MIR570 (8180 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	195427758	195427758	+	RNA	DEL	T	-	-	rs111735076		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195427758delT	uc011btd.1	+	1		c.937delT			uc003fux.1_RNA					Homo sapiens cDNA FLJ46488 fis, clone THYMU3026869.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	195440599	195440599	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195440599delT								MIR570 (14231 upstream) : MUC20 (7154 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	195443773	195443781	+	IGR	DEL	GAGAGATCC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195443773_195443781delGAGAGATCC								MIR570 (17405 upstream) : MUC20 (3972 downstream)																																			---	---	---	---
MUC20	200958	broad.mit.edu	37	3	195446286	195446287	+	5'Flank	DEL	TT	-	-	rs112041723		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195446286_195446287delTT	uc010hzo.2	+							NM_152673	NP_689886			mucin 20 isoform L						protein homooligomerization	apical plasma membrane|basal plasma membrane|extracellular region|microvillus membrane					0	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)														---	---	---	---
TFRC	7037	broad.mit.edu	37	3	195798775	195798775	+	Intron	DEL	A	-	-	rs80325185		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195798775delA	uc003fvz.3	-						TFRC_uc003fwa.3_Intron|TFRC_uc010hzy.2_Intron|TFRC_uc011btr.1_Intron	NM_003234	NP_003225			transferrin receptor						cellular iron ion homeostasis|endocytosis|interspecies interaction between organisms|proteolysis|transferrin transport|transmembrane transport	coated pit|endosome|integral to plasma membrane|melanosome	peptidase activity|transferrin receptor activity			ovary(3)	3	all_cancers(143;1.94e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.36e-24)|all cancers(36;3.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.17e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00233)				T	BCL6	NHL								---	---	---	---
Unknown	0	broad.mit.edu	37	3	196270622	196270623	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196270622_196270623delTT								C3orf43 (28385 upstream) : WDR53 (10438 downstream)																																			---	---	---	---
FBXO45	200933	broad.mit.edu	37	3	196299801	196299801	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196299801delT	uc010iai.2	+							NM_001105573	NP_001099043			F-box protein 45						nervous system development|proteasomal ubiquitin-dependent protein catabolic process|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to DNA damage stimulus	cell junction|postsynaptic membrane|presynaptic membrane	protein binding			skin(1)	1	all_cancers(143;8.88e-09)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;2.75e-23)|all cancers(36;2.47e-21)|OV - Ovarian serous cystadenocarcinoma(49;2.32e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00314)														---	---	---	---
PIGX	54965	broad.mit.edu	37	3	196458053	196458055	+	Intron	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196458053_196458055delTTT	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)														---	---	---	---
DLG1	1739	broad.mit.edu	37	3	196876426	196876426	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196876426delA	uc003fxo.3	-						DLG1_uc011bub.1_Intron|DLG1_uc011buc.1_Intron|DLG1_uc011bud.1_Intron|DLG1_uc003fxn.3_Intron|DLG1_uc011bue.1_Intron|DLG1_uc010ial.2_Intron|DLG1_uc011buf.1_Intron|DLG1_uc003fxp.2_Intron|DLG1_uc010iam.1_Intron|DLG1_uc010ian.2_Intron	NM_001098424	NP_001091894			discs, large homolog 1 isoform 1						actin filament organization|axon guidance|cell-cell adhesion|cortical actin cytoskeleton organization|endothelial cell proliferation|establishment or maintenance of cell polarity|interspecies interaction between organisms|mitotic cell cycle G1/S transition checkpoint|negative regulation of mitotic cell cycle|protein localization in plasma membrane|synaptic transmission|tight junction assembly	basolateral plasma membrane|cytosol|endoplasmic reticulum membrane|immunological synapse|MPP7-DLG1-LIN7 complex|nucleus|postsynaptic density|postsynaptic membrane|sarcolemma|tight junction	cytoskeletal protein binding|guanylate kinase activity|L27 domain binding|phosphatase binding|phosphoprotein phosphatase activity|potassium channel regulator activity|protein binding|protein C-terminus binding|protein kinase binding			ovary(3)	3	all_cancers(143;6.22e-10)|Ovarian(172;0.0418)|Breast(254;0.0589)	Lung NSC(153;0.133)	Epithelial(36;3.23e-24)|all cancers(36;2.15e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.0148)														---	---	---	---
LRCH3	84859	broad.mit.edu	37	3	197600896	197600903	+	Intron	DEL	AAAAAAAA	-	-	rs66968502		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197600896_197600903delAAAAAAAA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	197844376	197844376	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197844376delC								LOC348840 (36834 upstream) : FAM157A (34861 downstream)																																			---	---	---	---
ZNF732	654254	broad.mit.edu	37	4	260415	260417	+	Intron	DEL	TTT	-	-	rs74271677		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:260415_260417delTTT	uc010ibb.1	-											Homo sapiens chromosome 4 isolate HA_003619 mRNA sequence.						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
GAK	2580	broad.mit.edu	37	4	883234	883234	+	Intron	DEL	A	-	-	rs33930949		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:883234delA	uc003gbm.3	-						GAK_uc003gbn.3_Intron|GAK_uc010ibk.1_Intron|GAK_uc003gbl.3_Intron	NM_005255	NP_005246			cyclin G associated kinase						cell cycle	focal adhesion|Golgi apparatus|perinuclear region of cytoplasm	ATP binding|heat shock protein binding|protein serine/threonine kinase activity			lung(2)|central_nervous_system(1)|skin(1)	4				Colorectal(103;0.219)														---	---	---	---
MAEA	10296	broad.mit.edu	37	4	1298916	1298916	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1298916delT	uc003gda.2	+						MAEA_uc010ibs.1_Intron|MAEA_uc003gdb.2_Intron|MAEA_uc011bvb.1_Intron|MAEA_uc003gdc.2_Intron|MAEA_uc003gdd.2_Intron	NM_001017405	NP_001017405			macrophage erythroblast attacher isoform 1						cell adhesion|cell cycle|cell division|erythrocyte maturation|negative regulation of myeloid cell apoptosis|regulation of mitotic cell cycle	actomyosin contractile ring|integral to plasma membrane|membrane fraction|nuclear matrix|spindle	actin binding			ovary(1)|central_nervous_system(1)	2			OV - Ovarian serous cystadenocarcinoma(23;0.0201)															---	---	---	---
Unknown	0	broad.mit.edu	37	4	1635576	1635576	+	IGR	DEL	A	-	-	rs144556169	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1635576delA								CRIPAK (245794 upstream) : FAM53A (6033 downstream)																																			---	---	---	---
LETM1	3954	broad.mit.edu	37	4	1834030	1834030	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1834030delA	uc003gdv.2	-							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)															---	---	---	---
WHSC1	7468	broad.mit.edu	37	4	1911366	1911367	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1911366_1911367delTT	uc003gdz.3	+						WHSC1_uc003geb.3_Intron|WHSC1_uc003gec.3_Intron|WHSC1_uc003ged.3_Intron|WHSC1_uc003gee.3_Intron|WHSC1_uc003gef.3_Intron|WHSC1_uc003gdx.2_Intron|WHSC1_uc003gdy.1_Intron|WHSC1_uc010icd.1_Intron|WHSC1_uc003gea.1_Intron|WHSC1_uc010ice.1_Intron|WHSC1_uc003geg.1_Intron|WHSC1_uc003geh.1_Intron	NM_001042424	NP_001035889			Wolf-Hirschhorn syndrome candidate 1 protein						anatomical structure morphogenesis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|cytoplasm|nuclear membrane|nucleolus	DNA binding|histone-lysine N-methyltransferase activity|zinc ion binding			ovary(3)|lung(3)|skin(2)|pancreas(1)	9		all_epithelial(65;1.34e-05)	OV - Ovarian serous cystadenocarcinoma(23;0.00606)	STAD - Stomach adenocarcinoma(129;0.232)				T	IGH@	MM								---	---	---	---
POLN	353497	broad.mit.edu	37	4	2167511	2167511	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2167511delT	uc003ger.2	-						POLN_uc010ich.1_Intron|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					---	---	---	---
POLN	353497	broad.mit.edu	37	4	2223882	2223882	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2223882delT	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					---	---	---	---
POLN	353497	broad.mit.edu	37	4	2240173	2240173	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2240173delA	uc011bvi.1	-						HAUS3_uc011bvj.1_Intron|HAUS3_uc003ges.1_Intron|HAUS3_uc003get.1_Intron	NM_181808	NP_861524			DNA-directed DNA polymerase nu						DNA repair|DNA replication	nucleus	DNA binding|DNA-directed DNA polymerase activity			kidney(2)|ovary(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(23;0.0955)										DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					---	---	---	---
NOP14	8602	broad.mit.edu	37	4	2958002	2958002	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2958002delG	uc003ggj.1	-						C4orf10_uc003ggi.1_Intron|NOP14_uc010icp.2_5'Flank|NOP14_uc003ggk.3_Intron|NOP14_uc003ggl.2_Intron|NOP14_uc010icq.1_Intron	NM_003703	NP_003694			probable nucleolar complex protein 14						endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	mitochondrion|Noc4p-Nop14p complex|small-subunit processome	snoRNA binding			pancreas(1)	1																		---	---	---	---
GRK4	2868	broad.mit.edu	37	4	2977961	2977962	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2977961_2977962delTT	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)														---	---	---	---
GRK4	2868	broad.mit.edu	37	4	2978895	2978895	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2978895delT	uc003ggn.1	+						GRK4_uc003ggo.1_Intron|GRK4_uc003ggp.1_Intron|GRK4_uc003ggq.1_Intron	NM_182982	NP_892027			G protein-coupled receptor kinase 4 isoform							cell cortex	ATP binding|G-protein coupled receptor kinase activity|signal transducer activity			lung(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)														---	---	---	---
HTT	3064	broad.mit.edu	37	4	3111611	3111611	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3111611delG	uc011bvq.1	+							NM_002111	NP_002102			huntingtin						establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule	autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex	beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding			skin(2)|ovary(1)|lung(1)	4		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	3619807	3619808	+	IGR	INS	-	A	A	rs150577781	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3619807_3619808insA								LRPAP1 (85583 upstream) : ADRA2C (148267 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	4727322	4727323	+	IGR	DEL	GT	-	-	rs36110957		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:4727322_4727323delGT								STX18 (183547 upstream) : MSX1 (134069 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	4887176	4887177	+	IGR	INS	-	A	A	rs112456511		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:4887176_4887177insA								MSX1 (21518 upstream) : CYTL1 (129139 downstream)																																			---	---	---	---
STK32B	55351	broad.mit.edu	37	4	5068908	5068908	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5068908delT	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																		---	---	---	---
STK32B	55351	broad.mit.edu	37	4	5192984	5192985	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5192984_5192985delTT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	6630613	6630614	+	IGR	INS	-	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6630613_6630614insG								MAN2B2 (6425 upstream) : MRFAP1 (11204 downstream)																																			---	---	---	---
TBC1D14	57533	broad.mit.edu	37	4	6998263	6998265	+	Intron	DEL	AAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6998263_6998265delAAA	uc011bwg.1	+						TBC1D14_uc003gjs.3_Intron|TBC1D14_uc010idh.2_Intron|TBC1D14_uc011bwh.1_5'Flank	NM_001113361	NP_001106832			TBC1 domain family, member 14 isoform a							intracellular	Rab GTPase activator activity			ovary(1)|pancreas(1)	2																		---	---	---	---
SORCS2	57537	broad.mit.edu	37	4	7220151	7220151	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7220151delT	uc003gkb.3	+							NM_020777	NP_065828			VPS10 domain receptor protein SORCS 2 precursor							integral to membrane	neuropeptide receptor activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
SORCS2	57537	broad.mit.edu	37	4	7357771	7357771	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7357771delC	uc003gkb.3	+							NM_020777	NP_065828			VPS10 domain receptor protein SORCS 2 precursor							integral to membrane	neuropeptide receptor activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
AFAP1	60312	broad.mit.edu	37	4	7811544	7811544	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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																		---	---	---	---
AFAP1	60312	broad.mit.edu	37	4	7942336	7942337	+	5'Flank	DEL	AA	-	-	rs34073371		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7942336_7942337delAA	uc003gkg.1	-						AFAP1_uc011bwk.1_5'Flank	NM_198595	NP_940997			actin filament associated protein 1							actin cytoskeleton|cytoplasm|focal adhesion	actin binding				0																		---	---	---	---
ABLIM2	84448	broad.mit.edu	37	4	8106996	8106997	+	Intron	INS	-	C	C	rs139971889	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:8106996_8106997insC	uc003gko.2	-						ABLIM2_uc003gkj.3_Intron|ABLIM2_uc003gkm.3_Intron|ABLIM2_uc003gkp.2_Intron|ABLIM2_uc003gkq.2_Intron|ABLIM2_uc003gkr.2_Intron|ABLIM2_uc003gks.3_Intron|ABLIM2_uc011bwl.1_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																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	8751482	8751482	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:8751482delG								CPZ (129996 upstream) : HMX1 (117291 downstream)																																			---	---	---	---
SLC2A9	56606	broad.mit.edu	37	4	9981309	9981309	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:9981309delC	uc003gmc.2	-						SLC2A9_uc003gmd.2_Intron	NM_020041	NP_064425			solute carrier family 2, member 9 protein						glucose transport|urate metabolic process	integral to membrane|plasma membrane	sugar:hydrogen symporter activity			ovary(3)	3																		---	---	---	---
WDR1	9948	broad.mit.edu	37	4	10111722	10111722	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:10111722delG	uc003gmf.2	-						WDR1_uc003gmg.2_Intron	NM_017491	NP_059830			WD repeat-containing protein 1 isoform 1						platelet activation|platelet degranulation|sensory perception of sound	cytoskeleton|cytosol|extracellular region	actin binding			ovary(2)|pancreas(1)	3				STAD - Stomach adenocarcinoma(129;0.000703)|Colorectal(103;0.0057)|LUSC - Lung squamous cell carcinoma(721;0.0232)														---	---	---	---
CLNK	116449	broad.mit.edu	37	4	10543504	10543504	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:10543504delT	uc003gmo.3	-						CLNK_uc003gmp.2_Intron	NM_052964	NP_443196			mast cell immunoreceptor signal transducer						immune response|intracellular signal transduction	intracellular	SH3/SH2 adaptor activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	11316851	11316851	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:11316851delA								CLNK (630465 upstream) : MIR572 (53600 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	11672942	11672942	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:11672942delA								HS3ST1 (242405 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	12380004	12380004	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:12380004delC								HS3ST1 (949467 upstream) : HSP90AB2P (955033 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	12517309	12517310	+	IGR	DEL	TC	-	-	rs35419622		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:12517309_12517310delTC								None (None upstream) : HSP90AB2P (817727 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	12577583	12577583	+	IGR	DEL	T	-	-	rs1156833	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:12577583delT								None (None upstream) : HSP90AB2P (757454 downstream)																																			---	---	---	---
BOD1L	259282	broad.mit.edu	37	4	13582681	13582682	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13582681_13582682delAA	uc003gmz.1	-							NM_148894	NP_683692			biorientation of chromosomes in cell division								DNA binding			ovary(5)|breast(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	13754928	13754928	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13754928delG	uc003gna.1	+											Homo sapiens cDNA FLJ34570 fis, clone KIDNE2008072.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	13803320	13803320	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13803320delA	uc003gna.1	+											Homo sapiens cDNA FLJ34570 fis, clone KIDNE2008072.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	14104300	14104300	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:14104300delT								BOD1L (474972 upstream) : CPEB2 (901222 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	14320577	14320578	+	IGR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:14320577_14320578insA								BOD1L (691249 upstream) : CPEB2 (684944 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	14728662	14728663	+	Intron	INS	-	T	T	rs139441591		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:14728662_14728663insT	uc003gne.2	-						uc003gnf.2_Intron					Homo sapiens cDNA clone IMAGE:3604199, **** WARNING: chimeric clone ****.																														---	---	---	---
CPEB2	132864	broad.mit.edu	37	4	15047853	15047853	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15047853delT	uc003gni.1	+						CPEB2_uc003gnj.1_Intron|CPEB2_uc003gnk.1_Intron|CPEB2_uc003gnl.1_Intron|CPEB2_uc003gnm.1_Intron|CPEB2_uc003gnn.1_Intron	NM_182485	NP_872291			cytoplasmic polyadenylation element binding						regulation of translation	cytoplasm	nucleotide binding|RNA binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	15195873	15195874	+	IGR	DEL	AA	-	-	rs80100505		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15195873_15195874delAA								CPEB2 (124099 upstream) : C1QTNF7 (145686 downstream)																																			---	---	---	---
C1QTNF7	114905	broad.mit.edu	37	4	15357213	15357213	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15357213delA	uc003gno.2	+							NM_001135170	NP_001128642			C1q and tumor necrosis factor related protein 7							collagen					0																		---	---	---	---
C1QTNF7	114905	broad.mit.edu	37	4	15412982	15412982	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15412982delA	uc011bxb.1	+						C1QTNF7_uc003gno.2_Intron	NM_001135171	NP_001128643			C1q and tumor necrosis factor related protein 7							collagen					0																		---	---	---	---
CC2D2A	57545	broad.mit.edu	37	4	15483568	15483568	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15483568delC	uc010idv.2	+						CC2D2A_uc003gnx.2_Intron|CC2D2A_uc003gns.3_3'UTR|CC2D2A_uc003gnt.3_3'UTR|CC2D2A_uc003gnq.3_3'UTR|CC2D2A_uc003gnr.3_3'UTR|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																		---	---	---	---
BST1	683	broad.mit.edu	37	4	15712420	15712420	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15712420delT	uc003goh.3	+							NM_004334	NP_004325			bone marrow stromal cell antigen 1 precursor						humoral immune response|multicellular organismal development	anchored to membrane|extrinsic to membrane|plasma membrane	binding|NAD+ nucleosidase activity			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	15945419	15945419	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15945419delT								FGFBP1 (5448 upstream) : FGFBP2 (16445 downstream)																																			---	---	---	---
LDB2	9079	broad.mit.edu	37	4	16636911	16636911	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:16636911delA	uc003goz.2	-						LDB2_uc003gpa.2_Intron|LDB2_uc003gpb.2_Intron|LDB2_uc011bxh.1_Intron|LDB2_uc010iee.2_Intron|LDB2_uc011bxi.1_Intron	NM_001290	NP_001281			LIM domain binding 2 isoform a								LIM domain binding|transcription cofactor activity				0																		---	---	---	---
LDB2	9079	broad.mit.edu	37	4	16884053	16884053	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:16884053delA	uc003goz.2	-						LDB2_uc003gpa.2_Intron|LDB2_uc003gpb.2_Intron|LDB2_uc011bxh.1_Intron|LDB2_uc010iee.2_Intron	NM_001290	NP_001281			LIM domain binding 2 isoform a								LIM domain binding|transcription cofactor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	18364758	18364758	+	IGR	DEL	T	-	-	rs78586009		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:18364758delT								LCORL (341373 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	18367805	18367805	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:18367805delT								LCORL (344420 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	20009493	20009493	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:20009493delA								None (None upstream) : SLIT2 (245742 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	20213402	20213403	+	IGR	DEL	TC	-	-	rs72194342		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:20213402_20213403delTC								None (None upstream) : SLIT2 (41832 downstream)																																			---	---	---	---
SLIT2	9353	broad.mit.edu	37	4	20295552	20295552	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:20295552delT	uc003gpr.1	+						SLIT2_uc003gps.1_Intron	NM_004787	NP_004778			slit homolog 2 precursor						apoptosis involved in luteolysis|axon extension involved in axon guidance|branching morphogenesis of a tube|cell migration involved in sprouting angiogenesis|cellular response to heparin|cellular response to hormone stimulus|chemorepulsion involved in postnatal olfactory bulb interneuron migration|corticospinal neuron axon guidance through spinal cord|induction of negative chemotaxis|motor axon guidance|negative regulation of actin filament polymerization|negative regulation of cell growth|negative regulation of cellular response to growth factor stimulus|negative regulation of chemokine-mediated signaling pathway|negative regulation of endothelial cell migration|negative regulation of lamellipodium assembly|negative regulation of mononuclear cell migration|negative regulation of neutrophil chemotaxis|negative regulation of protein phosphorylation|negative regulation of retinal ganglion cell axon guidance|negative regulation of small GTPase mediated signal transduction|negative regulation of smooth muscle cell chemotaxis|negative regulation of vascular permeability|positive regulation of apoptosis|positive regulation of axonogenesis|response to cortisol stimulus|retinal ganglion cell axon guidance|Roundabout signaling pathway|ureteric bud development	cell surface|cytoplasm|extracellular space|plasma membrane	calcium ion binding|GTPase inhibitor activity|heparin binding|laminin-1 binding|protein homodimerization activity|proteoglycan binding|Roundabout binding			central_nervous_system(4)|skin(4)|ovary(3)	11																		---	---	---	---
SLIT2	9353	broad.mit.edu	37	4	20428395	20428395	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:20428395delA	uc003gpr.1	+						SLIT2_uc003gps.1_Intron	NM_004787	NP_004778			slit homolog 2 precursor						apoptosis involved in luteolysis|axon extension involved in axon guidance|branching morphogenesis of a tube|cell migration involved in sprouting angiogenesis|cellular response to heparin|cellular response to hormone stimulus|chemorepulsion involved in postnatal olfactory bulb interneuron migration|corticospinal neuron axon guidance through spinal cord|induction of negative chemotaxis|motor axon guidance|negative regulation of actin filament polymerization|negative regulation of cell growth|negative regulation of cellular response to growth factor stimulus|negative regulation of chemokine-mediated signaling pathway|negative regulation of endothelial cell migration|negative regulation of lamellipodium assembly|negative regulation of mononuclear cell migration|negative regulation of neutrophil chemotaxis|negative regulation of protein phosphorylation|negative regulation of retinal ganglion cell axon guidance|negative regulation of small GTPase mediated signal transduction|negative regulation of smooth muscle cell chemotaxis|negative regulation of vascular permeability|positive regulation of apoptosis|positive regulation of axonogenesis|response to cortisol stimulus|retinal ganglion cell axon guidance|Roundabout signaling pathway|ureteric bud development	cell surface|cytoplasm|extracellular space|plasma membrane	calcium ion binding|GTPase inhibitor activity|heparin binding|laminin-1 binding|protein homodimerization activity|proteoglycan binding|Roundabout binding			central_nervous_system(4)|skin(4)|ovary(3)	11																		---	---	---	---
PACRGL	133015	broad.mit.edu	37	4	20712785	20712786	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:20712785_20712786delTT	uc010iek.2	+						PACRGL_uc003gpu.2_Intron|PACRGL_uc010iei.1_Intron|PACRGL_uc003gpz.2_Intron|PACRGL_uc011bxm.1_Intron|PACRGL_uc003gqa.2_Intron|PACRGL_uc003gpx.3_Intron|PACRGL_uc003gpv.2_Intron|PACRGL_uc003gpw.2_Intron|PACRGL_uc010iej.1_Intron|PACRGL_uc011bxn.1_Intron|PACRGL_uc003gpy.2_Intron	NM_145048	NP_659485			PARK2 co-regulated-like isoform 1								binding				0																		---	---	---	---
KCNIP4	80333	broad.mit.edu	37	4	20805392	20805395	+	Intron	DEL	GGAC	-	-	rs34063674		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:20805392_20805395delGGAC	uc003gqe.2	-						KCNIP4_uc003gqf.1_Intron|KCNIP4_uc003gqg.1_Intron|KCNIP4_uc003gqh.1_Intron|KCNIP4_uc003gqi.1_Intron|KCNIP4_uc010iel.2_Intron|KCNIP4_uc003gqd.3_Intron	NM_147182	NP_671711			Kv channel interacting protein 4 isoform 3							plasma membrane	calcium ion binding|potassium channel activity|protein binding|voltage-gated ion channel activity				0		Breast(46;0.134)																---	---	---	---
KCNIP4	80333	broad.mit.edu	37	4	21039428	21039428	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:21039428delT	uc003gqf.1	-						KCNIP4_uc003gqg.1_Intron|KCNIP4_uc003gqh.1_Intron|KCNIP4_uc003gqi.1_Intron	NM_147183	NP_671712			Kv channel interacting protein 4 isoform 4							plasma membrane	calcium ion binding|potassium channel activity|protein binding|voltage-gated ion channel activity				0		Breast(46;0.134)																---	---	---	---
KCNIP4	80333	broad.mit.edu	37	4	21513788	21513811	+	Intron	DEL	GGAGGGAGGAAGGAAGGAACGAAC	-	-	rs68124536		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:21513788_21513811delGGAGGGAGGAAGGAAGGAACGAAC	uc003gqh.1	-						KCNIP4_uc003gqg.1_Intron|KCNIP4_uc003gqi.1_Intron	NM_001035003	NP_001030175			Kv channel interacting protein 4 isoform 5							plasma membrane	calcium ion binding|potassium channel activity|protein binding|voltage-gated ion channel activity				0		Breast(46;0.134)																---	---	---	---
KCNIP4	80333	broad.mit.edu	37	4	21852622	21852622	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:21852622delA	uc003gqi.1	-						NCRNA00099_uc003gqj.1_RNA	NM_147182	NP_671711			Kv channel interacting protein 4 isoform 3							plasma membrane	calcium ion binding|potassium channel activity|protein binding|voltage-gated ion channel activity				0		Breast(46;0.134)																---	---	---	---
Unknown	0	broad.mit.edu	37	4	23158576	23158576	+	IGR	DEL	T	-	-	rs67602447		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:23158576delT								GBA3 (337385 upstream) : PPARGC1A (635069 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	23925101	23925101	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:23925101delA								PPARGC1A (33401 upstream) : MIR573 (596714 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	23994291	23994292	+	IGR	INS	-	TAAAAGAC	TAAAAGAC	rs146197002	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:23994291_23994292insTAAAAGAC								PPARGC1A (102591 upstream) : MIR573 (527523 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	24458236	24458236	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:24458236delG								PPARGC1A (566536 upstream) : MIR573 (63579 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	24483298	24483298	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:24483298delA								PPARGC1A (591598 upstream) : MIR573 (38517 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	24665328	24665329	+	IGR	DEL	TG	-	-	rs34382541		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:24665328_24665329delTG								DHX15 (79144 upstream) : SOD3 (131756 downstream)																																			---	---	---	---
SEPSECS	51091	broad.mit.edu	37	4	25161430	25161430	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25161430delA	uc003grg.2	-						uc003grj.2_5'Flank|PI4K2B_uc011bxs.1_5'Flank|SEPSECS_uc003gri.2_Intron|SEPSECS_uc003grh.2_Intron	NM_153825	NP_722547			Sep (O-phosphoserine) tRNA:Sec (selenocysteine)						selenocysteine incorporation	cytoplasm|nucleus	pyridoxal phosphate binding|transferase activity, transferring selenium-containing groups|tRNA binding				0		Breast(46;0.173)			Pyridoxal Phosphate(DB00114)													---	---	---	---
Unknown	0	broad.mit.edu	37	4	25497611	25497612	+	IGR	INS	-	CTTT	CTTT	rs144415784	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25497611_25497612insCTTT								ANAPC4 (77492 upstream) : SLC34A2 (159823 downstream)																																			---	---	---	---
RBPJ	3516	broad.mit.edu	37	4	26433200	26433201	+	3'UTR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:26433200_26433201delTT	uc003grx.1	+	12					RBPJ_uc003gry.1_3'UTR|RBPJ_uc003grz.1_3'UTR|RBPJ_uc003gsa.1_3'UTR|RBPJ_uc003gsb.1_3'UTR|RBPJ_uc003gsc.1_3'UTR|uc003gsd.2_5'Flank	NM_005349	NP_005340			recombining binding protein suppressor of						DNA recombination|negative regulation of transcription, DNA-dependent|positive regulation of transcription of Notch receptor target	cytoplasm|nucleolus|nucleoplasm	DNA binding|protein binding|recombinase activity|sequence-specific DNA binding transcription factor activity			ovary(1)|lung(1)|central_nervous_system(1)	3		Breast(46;0.0503)																---	---	---	---
Unknown	0	broad.mit.edu	37	4	27949791	27949791	+	IGR	DEL	T	-	-	rs66952851		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:27949791delT								STIM2 (923983 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	29751861	29751861	+	IGR	DEL	A	-	-	rs113375137		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:29751861delA								None (None upstream) : PCDH7 (970176 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	29988068	29988068	+	IGR	DEL	A	-	-	rs112225030		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:29988068delA								None (None upstream) : PCDH7 (733969 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	30270391	30270395	+	IGR	DEL	TAGAA	-	-	rs36221656		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:30270391_30270395delTAGAA								None (None upstream) : PCDH7 (451642 downstream)																																			---	---	---	---
PCDH7	5099	broad.mit.edu	37	4	31122011	31122011	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:31122011delT	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	31510447	31510447	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:31510447delT								PCDH7 (362026 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	32385449	32385449	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:32385449delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	32487900	32487900	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:32487900delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	32554671	32554672	+	IGR	DEL	TT	-	-	rs34294785		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:32554671_32554672delTT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	32580548	32580548	+	IGR	DEL	A	-	-	rs34320369		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:32580548delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	33717748	33717749	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:33717748_33717749insT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	35356948	35356949	+	IGR	INS	-	AAT	AAT	rs142793524	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:35356948_35356949insAAT								None (None upstream) : ARAP2 (592895 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	35500876	35500876	+	IGR	DEL	C	-	-	rs71655269		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:35500876delC								None (None upstream) : ARAP2 (448968 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	36466644	36466644	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:36466644delT								MIR1255B-1 (38594 upstream) : KIAA1239 (780046 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	37077750	37077750	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:37077750delA								MIR1255B-1 (649700 upstream) : KIAA1239 (168940 downstream)																																			---	---	---	---
RELL1	768211	broad.mit.edu	37	4	37648669	37648669	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:37648669delT	uc003gsz.2	-						RELL1_uc010ifc.2_Intron	NM_001085399	NP_001078868			receptor expressed in lymphoid tissues like 1							cytoplasm|integral to membrane|microtubule cytoskeleton|plasma membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	37751961	37751964	+	IGR	DEL	ACAT	-	-	rs35022540		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:37751961_37751964delACAT								RELL1 (63962 upstream) : PGM2 (76318 downstream)																																			---	---	---	---
FAM114A1	92689	broad.mit.edu	37	4	38928079	38928084	+	Intron	DEL	TTTTTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38928079_38928084delTTTTTT	uc003gtn.2	+						FAM114A1_uc011byh.1_Intron	NM_138389	NP_612398			hypothetical protein LOC92689							cytoplasm				ovary(1)	1																		---	---	---	---
RPL9	6133	broad.mit.edu	37	4	39455984	39455984	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39455984delG	uc003gub.2	-						RPL9_uc003guc.2_Intron|RPL9_uc011byk.1_Intron	NM_001024921	NP_001020092			ribosomal protein L9						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosol|nucleolus|ribosome	rRNA binding|structural constituent of ribosome			skin(1)	1																		---	---	---	---
UGDH	7358	broad.mit.edu	37	4	39506147	39506148	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39506147_39506148insA	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)													---	---	---	---
UBE2K	3093	broad.mit.edu	37	4	39742891	39742891	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39742891delA	uc003guu.3	+						UBE2K_uc003gus.3_Intron|UBE2K_uc003gut.3_Intron|UBE2K_uc010ifn.2_Intron|UBE2K_uc011byq.1_Intron|UBE2K_uc003guq.3_Intron	NM_005339	NP_005330			ubiquitin-conjugating enzyme E2K isoform 1						protein K48-linked ubiquitination|ubiquitin-dependent protein catabolic process	cytoplasm	ATP binding|ubiquitin protein ligase binding|ubiquitin-ubiquitin ligase activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	40296173	40296184	+	IGR	DEL	TCTCCACCTCAG	-	-	rs147396408		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40296173_40296184delTCTCCACCTCAG								RHOH (49892 upstream) : CHRNA9 (41285 downstream)																																			---	---	---	---
SLC30A9	10463	broad.mit.edu	37	4	42077874	42077874	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42077874delT	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	43052524	43052525	+	IGR	INS	-	AG	AG	rs1436466	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:43052524_43052525insAG								GRXCR1 (19851 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	43838980	43838980	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:43838980delA								GRXCR1 (806307 upstream) : KCTD8 (336942 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	44075628	44075628	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:44075628delT								None (None upstream) : KCTD8 (100294 downstream)																																			---	---	---	---
KCTD8	386617	broad.mit.edu	37	4	44321479	44321480	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:44321479_44321480delAA	uc003gwu.2	-							NM_198353	NP_938167			potassium channel tetramerisation domain							cell junction|postsynaptic membrane|presynaptic membrane|voltage-gated potassium channel complex	voltage-gated potassium channel activity			central_nervous_system(2)|ovary(1)	3															HNSCC(17;0.042)			---	---	---	---
Unknown	0	broad.mit.edu	37	4	45233988	45233988	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:45233988delT								GNPDA2 (505376 upstream) : GABRG1 (803801 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	46184843	46184843	+	IGR	DEL	A	-	-	rs113323674		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:46184843delA								GABRG1 (58761 upstream) : GABRA2 (66738 downstream)																																			---	---	---	---
COX7B2	170712	broad.mit.edu	37	4	46842946	46842946	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:46842946delA	uc003gxf.2	-						COX7B2_uc010ige.2_Intron	NM_130902	NP_570972			cytochrome c oxidase subunit VIIb2 precursor							integral to membrane|mitochondrial respiratory chain	cytochrome-c oxidase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	48928904	48928904	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48928904delT								OCIAD2 (20089 upstream) : CWH43 (59361 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	49095672	49095672	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49095672delG								CWH43 (31579 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	49107047	49107061	+	IGR	DEL	ATTCCATTCCATTCA	-	-	rs56261870		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49107047_49107061delATTCCATTCCATTCA								CWH43 (42954 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	49200238	49200239	+	IGR	DEL	TC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49200238_49200239delTC								CWH43 (136145 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	49651741	49651745	+	IGR	DEL	AATTT	-	-	rs111675613		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49651741_49651745delAATTT								CWH43 (587648 upstream) : None (None downstream)																																			---	---	---	---
DCUN1D4	23142	broad.mit.edu	37	4	52731147	52731147	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:52731147delT	uc003gze.2	+						DCUN1D4_uc003gzf.2_Intron|DCUN1D4_uc011bzn.1_Intron|DCUN1D4_uc003gzg.2_Intron|DCUN1D4_uc003gzh.2_Intron|DCUN1D4_uc011bzo.1_Intron	NM_001040402	NP_001035492			DCN1, defective in cullin neddylation 1, domain											ovary(2)	2			GBM - Glioblastoma multiforme(4;1.93e-11)|LUSC - Lung squamous cell carcinoma(32;0.00654)															---	---	---	---
SGCB	6443	broad.mit.edu	37	4	52891527	52891528	+	Intron	DEL	CA	-	-	rs146084109		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:52891527_52891528delCA	uc003gzj.2	-						SGCB_uc011bzp.1_Intron	NM_000232	NP_000223			sarcoglycan, beta						cytoskeleton organization|muscle organ development	cytoplasm|cytoskeleton|integral to plasma membrane|sarcoglycan complex|sarcolemma					0			GBM - Glioblastoma multiforme(4;7.63e-12)|LUSC - Lung squamous cell carcinoma(32;0.00204)															---	---	---	---
USP46	64854	broad.mit.edu	37	4	53496461	53496461	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:53496461delT	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	4	53623449	53623449	+	IGR	DEL	G	-	-	rs9999908	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:53623449delG								KIAA0114 (43144 upstream) : RASL11B (105046 downstream)																																			---	---	---	---
RASL11B	65997	broad.mit.edu	37	4	53729814	53729814	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:53729814delA	uc003gzt.2	+							NM_023940	NP_076429			RAS-like family 11 member B						small GTPase mediated signal transduction	membrane	GTP binding|GTPase activity			central_nervous_system(1)	1			LUSC - Lung squamous cell carcinoma(32;0.0302)															---	---	---	---
PDGFRA	5156	broad.mit.edu	37	4	55087242	55087242	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55087242delA	uc003haa.2	+							NM_006206	NP_006197			platelet-derived growth factor receptor alpha						cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye	cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity			soft_tissue(572)|small_intestine(40)|stomach(16)|lung(16)|central_nervous_system(13)|haematopoietic_and_lymphoid_tissue(7)|skin(3)|ovary(3)|gastrointestinal_tract_(site_indeterminate)(1)|autonomic_ganglia(1)|prostate(1)|bone(1)	674	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Sunitinib(DB01268)			Mis|O|T	FIP1L1	GIST|idiopathic hypereosinophilic syndrome				Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Intestinal_Neurofibromatosis	TSP Lung(21;0.16)			---	---	---	---
Unknown	0	broad.mit.edu	37	4	55314018	55314019	+	IGR	DEL	AA	-	-	rs10553731		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55314018_55314019delAA								PDGFRA (149607 upstream) : KIT (210076 downstream)																																			---	---	---	---
TMEM165	55858	broad.mit.edu	37	4	56277767	56277767	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:56277767delT	uc003hax.2	+						TMEM165_uc011bzy.1_Intron	NM_018475	NP_060945			transmembrane protein 165							integral to membrane					0	Lung NSC(11;0.00545)|Glioma(25;0.08)|all_neural(26;0.101)|all_epithelial(27;0.135)		LUSC - Lung squamous cell carcinoma(4;1.62e-07)|Lung(4;1.34e-06)|Epithelial(7;0.0103)															---	---	---	---
CLOCK	9575	broad.mit.edu	37	4	56367648	56367648	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:56367648delA	uc003haz.1	-						CLOCK_uc003hba.1_Intron	NM_004898	NP_004889			clock						circadian rhythm|photoperiodism|positive regulation of transcription from RNA polymerase II promoter	cytoplasm|transcription factor complex	DNA binding|histone acetyltransferase activity|sequence-specific DNA binding transcription factor activity|signal transducer activity			central_nervous_system(2)|ovary(1)	3	Lung NSC(11;0.00335)|Glioma(25;0.08)|all_epithelial(27;0.0992)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(4;1.62e-07)|Lung(4;1.34e-06)|Epithelial(7;0.0107)															---	---	---	---
SRP72	6731	broad.mit.edu	37	4	57366537	57366537	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57366537delA	uc003hbv.2	+						SRP72_uc010ihe.2_Intron|SRP72_uc003hbx.2_5'Flank	NM_006947	NP_008878			signal recognition particle 72kDa						response to drug|SRP-dependent cotranslational protein targeting to membrane	cytosol|nucleolus|plasma membrane|signal recognition particle, endoplasmic reticulum targeting	7S RNA binding|signal recognition particle binding			ovary(1)	1	Glioma(25;0.08)|all_neural(26;0.101)																	---	---	---	---
Unknown	0	broad.mit.edu	37	4	57743815	57743815	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57743815delT								SPINK2 (55922 upstream) : REST (30227 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	58724819	58724820	+	IGR	INS	-	TA	TA	rs144416775	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:58724819_58724820insTA								IGFBP7 (748280 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	59449610	59449610	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:59449610delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	59960445	59960445	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:59960445delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	60257511	60257512	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:60257511_60257512insT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	60284038	60284039	+	IGR	INS	-	GT	GT	rs143676347	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:60284038_60284039insGT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	63756544	63756544	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:63756544delA								LPHN3 (818377 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	64010865	64010865	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:64010865delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	64014350	64014351	+	IGR	DEL	TT	-	-	rs71666950		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:64014350_64014351delTT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	64187699	64187699	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:64187699delA								None (None upstream) : TECRL (956486 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	65962425	65962425	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:65962425delA								TECRL (687247 upstream) : EPHA5 (222857 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	66787807	66787807	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:66787807delA								EPHA5 (252154 upstream) : MIR1269 (354735 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	66901124	66901124	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:66901124delT								EPHA5 (365471 upstream) : MIR1269 (241418 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	66943655	66943656	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:66943655_66943656delAA								EPHA5 (408002 upstream) : MIR1269 (198886 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	67157895	67157896	+	IGR	INS	-	A	A	rs143065856	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:67157895_67157896insA								MIR1269 (15249 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	67761339	67761339	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:67761339delT								MIR1269 (618693 upstream) : CENPC1 (576650 downstream)																																			---	---	---	---
CENPC1	1060	broad.mit.edu	37	4	68389371	68389372	+	Intron	INS	-	AC	AC	rs149688825	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68389371_68389372insAC	uc003hdd.1	-						CENPC1_uc010ihj.1_Intron|CENPC1_uc010ihk.1_Intron|CENPC1_uc010ihm.1_Intron	NM_001812	NP_001803			centromere protein C 1						mitotic prometaphase	condensed chromosome kinetochore|condensed nuclear chromosome, centromeric region|cytosol	DNA binding			urinary_tract(1)|lung(1)	2																		---	---	---	---
LOC550112	550112	broad.mit.edu	37	4	68621945	68621954	+	Intron	DEL	TTCCTTCCCT	-	-	rs62303137		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68621945_68621954delTTCCTTCCCT	uc003hdl.3	+						GNRHR_uc003hdm.2_5'Flank|GNRHR_uc003hdn.2_5'Flank					Homo sapiens chromosome 4 cDNA.												0																		---	---	---	---
YTHDC1	91746	broad.mit.edu	37	4	69212173	69212173	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69212173delC	uc003hdx.2	-						YTHDC1_uc003hdy.2_Intron	NM_001031732	NP_001026902			splicing factor YT521-B isoform 1											upper_aerodigestive_tract(1)|ovary(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	69861248	69861248	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69861248delT								UGT2A3 (43739 upstream) : UGT2B7 (100945 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	70040965	70040965	+	IGR	DEL	T	-	-	rs61414063		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70040965delT								UGT2B7 (62261 upstream) : UGT2B11 (25088 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	70452170	70452171	+	IGR	INS	-	A	A	rs141773813	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70452170_70452171insA								UGT2B4 (60438 upstream) : UGT2A1 (1965 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	70784579	70784583	+	IGR	DEL	TTTTT	-	-	rs33971462		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70784579_70784583delTTTTT								SULT1E1 (58709 upstream) : CSN1S1 (12216 downstream)																																			---	---	---	---
PROL1	58503	broad.mit.edu	37	4	71270139	71270140	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71270139_71270140insA	uc003hfi.2	+							NM_021225	NP_067048			proline rich, lacrimal 1						regulation of sensory perception of pain	extracellular region	endopeptidase inhibitor activity			large_intestine(1)	1		all_hematologic(202;0.196)																---	---	---	---
Unknown	0	broad.mit.edu	37	4	71376056	71376056	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71376056delA								MUC7 (27343 upstream) : AMTN (8242 downstream)																																			---	---	---	---
RUFY3	22902	broad.mit.edu	37	4	71665743	71665744	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71665743_71665744insA	uc003hfr.2	+						RUFY3_uc011cay.1_Intron	NM_001037442	NP_001032519			RUN and FYVE domain containing 3 isoform 1						negative regulation of axonogenesis	filopodium|growth cone					0		all_hematologic(202;0.248)	Lung(101;0.235)															---	---	---	---
MOBKL1A	92597	broad.mit.edu	37	4	71837726	71837726	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71837726delT	uc003hfw.2	+						MOBKL1A_uc003hfv.1_Intron|MOBKL1A_uc011cba.1_Intron	NM_173468	NP_775739			MOB1, Mps One Binder kinase activator-like 1A						hippo signaling cascade|protein autophosphorylation	cytoplasm|nucleus	kinase activator activity|kinase binding|metal ion binding				0		all_hematologic(202;0.21)	Lung(101;0.235)															---	---	---	---
Unknown	0	broad.mit.edu	37	4	71934284	71934284	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71934284delT								DCK (37657 upstream) : SLC4A4 (118719 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	71939460	71939460	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71939460delA								DCK (42833 upstream) : SLC4A4 (113543 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	71994651	71994652	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71994651_71994652insT								DCK (98024 upstream) : SLC4A4 (58351 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	72037977	72037979	+	IGR	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:72037977_72037979delTTT								DCK (141350 upstream) : SLC4A4 (15024 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	72460725	72460726	+	IGR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:72460725_72460726insA								SLC4A4 (22922 upstream) : GC (146687 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	72547009	72547009	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:72547009delA								SLC4A4 (109206 upstream) : GC (60404 downstream)																																			---	---	---	---
ANKRD17	26057	broad.mit.edu	37	4	73981830	73981830	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:73981830delA	uc003hgp.2	-						ANKRD17_uc003hgo.2_Intron|ANKRD17_uc003hgq.2_Intron|ANKRD17_uc003hgr.2_Intron|ANKRD17_uc011cbd.1_Intron	NM_032217	NP_115593			ankyrin repeat domain protein 17 isoform a						interspecies interaction between organisms	cytoplasm|nucleus	RNA binding			ovary(5)|skin(3)|upper_aerodigestive_tract(1)|lung(1)	10	Breast(15;0.000295)		Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)															---	---	---	---
ANKRD17	26057	broad.mit.edu	37	4	74103027	74103027	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:74103027delT	uc003hgp.2	-						ANKRD17_uc003hgq.2_Intron|ANKRD17_uc003hgr.2_Intron	NM_032217	NP_115593			ankyrin repeat domain protein 17 isoform a						interspecies interaction between organisms	cytoplasm|nucleus	RNA binding			ovary(5)|skin(3)|upper_aerodigestive_tract(1)|lung(1)	10	Breast(15;0.000295)		Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)															---	---	---	---
Unknown	0	broad.mit.edu	37	4	76010090	76010091	+	IGR	INS	-	GAAG	GAAG	rs34335133		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76010090_76010091insGAAG								PARM1 (34767 upstream) : RCHY1 (394264 downstream)																																			---	---	---	---
CDKL2	8999	broad.mit.edu	37	4	76530988	76530989	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76530988_76530989insA	uc003hiq.2	-						CDKL2_uc011cbp.1_Intron|CDKL2_uc010iix.1_Intron	NM_003948	NP_003939			cyclin-dependent kinase-like 2						sex differentiation|signal transduction	cytoplasm|nucleus	ATP binding|cyclin-dependent protein kinase activity			ovary(2)|stomach(2)|breast(2)|skin(1)	7			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)															---	---	---	---
Unknown	0	broad.mit.edu	37	4	76828568	76828570	+	IGR	DEL	AAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76828568_76828570delAAA								PPEF2 (4887 upstream) : NAAA (3239 downstream)																																			---	---	---	---
CXCL9	4283	broad.mit.edu	37	4	76926198	76926198	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76926198delT	uc003hjh.1	-							NM_002416	NP_002407			small inducible cytokine B9 precursor						cell-cell signaling|cellular defense response|chemotaxis|G-protein coupled receptor protein signaling pathway|immune response|inflammatory response	extracellular space	chemokine activity			ovary(1)	1			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)															---	---	---	---
SHROOM3	57619	broad.mit.edu	37	4	77380160	77380160	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77380160delG	uc011cbx.1	+							NM_020859	NP_065910			shroom family member 3 protein						apical protein localization|cell morphogenesis|cellular pigment accumulation|pattern specification process|regulation of cell shape	adherens junction|apical junction complex|apical plasma membrane|cytoplasm|microtubule	actin binding			skin(2)|ovary(1)	3			Lung(101;0.0903)															---	---	---	---
CCNI	10983	broad.mit.edu	37	4	77985383	77985383	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77985383delA	uc003hkm.2	-						CCNI_uc011ccb.1_Intron	NM_006835	NP_006826			cyclin I						spermatogenesis					ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	78372137	78372142	+	IGR	DEL	CCTCTT	-	-	rs36228645		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:78372137_78372142delCCTCTT								CCNG2 (280927 upstream) : CXCL13 (60765 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	78622091	78622091	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:78622091delT								CXCL13 (89105 upstream) : CNOT6L (12451 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	78941599	78941599	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:78941599delA								MRPL1 (67655 upstream) : FRAS1 (37125 downstream)																																			---	---	---	---
FRAS1	80144	broad.mit.edu	37	4	79309794	79309797	+	Intron	DEL	TTTT	-	-	rs5859620		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79309794_79309797delTTTT	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	79357844	79357844	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79357844delA	uc003hlb.2	+						FRAS1_uc003hkw.2_Intron|FRAS1_uc010ijj.1_Intron	NM_025074	NP_079350			Fraser syndrome 1						cell communication	integral to membrane|plasma membrane	metal ion binding			large_intestine(5)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	79577674	79577675	+	Intron	DEL	AA	-	-	rs79511247		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79577674_79577675delAA	uc003hlf.2	+						uc003hlg.2_Intron|uc003hlh.2_Intron|uc003hli.2_Intron					Homo sapiens cDNA FLJ32651 fis, clone SYNOV2001581.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	80104810	80104810	+	Intron	DEL	T	-	-	rs35395296		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:80104810delT	uc003hlr.1	+											Homo sapiens full length insert cDNA clone YY75G10.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	81019887	81019888	+	IGR	INS	-	GGAA	GGAA	rs143935207	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:81019887_81019888insGGAA								ANTXR2 (25410 upstream) : PRDM8 (85551 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	81179764	81179765	+	IGR	DEL	TT	-	-	rs72234450		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:81179764_81179765delTT								PRDM8 (54284 upstream) : FGF5 (7977 downstream)																																			---	---	---	---
C4orf22	255119	broad.mit.edu	37	4	81651433	81651434	+	Intron	DEL	TA	-	-	rs57000466		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:81651433_81651434delTA	uc003hmf.2	+						C4orf22_uc010ijp.2_Intron	NM_152770	NP_689983			hypothetical protein LOC255119											skin(2)	2																		---	---	---	---
C4orf22	255119	broad.mit.edu	37	4	81681030	81681030	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:81681030delT	uc003hmf.2	+						C4orf22_uc010ijp.2_Intron	NM_152770	NP_689983			hypothetical protein LOC255119											skin(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	83323764	83323764	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83323764delT								HNRNPD (28615 upstream) : HNRPDL (20585 downstream)																																			---	---	---	---
SEC31A	22872	broad.mit.edu	37	4	83786509	83786510	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83786509_83786510insA	uc003hnf.2	-						SEC31A_uc003hne.2_Intron|SEC31A_uc011ccl.1_Intron|SEC31A_uc003hnl.2_Intron|SEC31A_uc003hng.2_Intron|SEC31A_uc003hnh.2_Intron|SEC31A_uc003hni.2_Intron|SEC31A_uc003hnj.2_Intron|SEC31A_uc011ccm.1_Intron|SEC31A_uc011ccn.1_Intron|SEC31A_uc003hnk.2_Intron|SEC31A_uc003hnm.2_Intron|SEC31A_uc003hnn.1_Intron|SEC31A_uc003hno.2_Intron	NM_001077207	NP_001070675			SEC31 homolog A isoform 1						COPII vesicle coating|post-translational protein modification|protein N-linked glycosylation via asparagine|protein transport|response to calcium ion	COPII vesicle coat|cytosol|endoplasmic reticulum membrane|perinuclear region of cytoplasm	calcium-dependent protein binding		SEC31A/JAK2(4)|SEC31A/ALK(3)	haematopoietic_and_lymphoid_tissue(4)|soft_tissue(3)|breast(1)	8		Hepatocellular(203;0.114)																---	---	---	---
COPS4	51138	broad.mit.edu	37	4	83989279	83989279	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83989279delT	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	84041553	84041553	+	IGR	DEL	T	-	-	rs112666677		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84041553delT								PLAC8 (5642 upstream) : COQ2 (141136 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	84078902	84078902	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84078902delT								PLAC8 (42991 upstream) : COQ2 (103787 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	84094863	84094863	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84094863delT								PLAC8 (58952 upstream) : COQ2 (87826 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	85372600	85372601	+	IGR	DEL	TC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85372600_85372601delTC								AGPAT9 (845575 upstream) : NKX6-1 (41835 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	86308401	86308402	+	IGR	INS	-	AC	AC	rs146652881	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:86308401_86308402insAC								C4orf12 (380233 upstream) : ARHGAP24 (87882 downstream)																																			---	---	---	---
MAPK10	5602	broad.mit.edu	37	4	87488377	87488378	+	Intron	DEL	TT	-	-	rs139082508		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87488377_87488378delTT	uc010ikh.1	-											Synthetic construct DNA, clone: pF1KB9001, Homo sapiens MAPK10 gene for mitogen-activated protein kinase 10, without stop codon, in Flexi system.						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	87635587	87635587	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87635587delT	uc003hpz.2	+						PTPN13_uc003hpy.2_Intron|PTPN13_uc003hqa.2_Intron|PTPN13_uc003hqb.2_Intron	NM_080683	NP_542414			protein tyrosine phosphatase, non-receptor type							cytoplasm|cytoskeleton|plasma membrane	protein binding|protein binding|protein tyrosine phosphatase activity			ovary(4)|breast(1)|kidney(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	88551381	88551381	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88551381delA								DSPP (13358 upstream) : DMP1 (20073 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	88653140	88653141	+	IGR	INS	-	A	A	rs34713097		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88653140_88653141insA								DMP1 (67630 upstream) : IBSP (67561 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	89246657	89246658	+	Intron	INS	-	CC	CC	rs143217735	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89246657_89246658insCC	uc003hro.2	+											Homo sapiens, clone IMAGE:5199401, mRNA.																														---	---	---	---
HERC6	55008	broad.mit.edu	37	4	89358213	89358213	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89358213delT	uc011cdi.1	+						HERC6_uc011cdj.1_Intron|HERC6_uc011cdk.1_Intron|HERC6_uc011cdl.1_Intron	NM_017912	NP_060382			hect domain and RLD 6 isoform 1						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytosol	ubiquitin-protein ligase activity			lung(3)|ovary(1)|kidney(1)	5		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000222)														---	---	---	---
HERC5	51191	broad.mit.edu	37	4	89380299	89380300	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89380299_89380300insA	uc003hrt.2	+							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	89407537	89407537	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89407537delA	uc003hrt.2	+						HERC5_uc011cdm.1_Intron	NM_016323	NP_057407			hect domain and RLD 5						innate immune response|ISG15-protein conjugation|negative regulation of type I interferon production|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of cyclin-dependent protein kinase activity|regulation of defense response to virus|response to virus	cytosol|perinuclear region of cytoplasm	ISG15 ligase activity|protein binding|ubiquitin-protein ligase activity			ovary(4)|lung(3)|skin(2)	9		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000209)														---	---	---	---
HERC3	8916	broad.mit.edu	37	4	89532496	89532496	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89532496delG	uc003hrw.1	+						HERC3_uc003hrv.2_Intron|HERC3_uc011cdn.1_Intron	NM_014606	NP_055421			hect domain and RLD 3						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasmic membrane-bounded vesicle	ubiquitin-protein ligase activity			lung(2)|prostate(1)|skin(1)	4				OV - Ovarian serous cystadenocarcinoma(123;0.000319)														---	---	---	---
HERC3	8916	broad.mit.edu	37	4	89627723	89627724	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89627723_89627724delTT	uc003hrw.1	+						HERC3_uc011cdn.1_Intron|HERC3_uc011cdo.1_Intron	NM_014606	NP_055421			hect domain and RLD 3						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasmic membrane-bounded vesicle	ubiquitin-protein ligase activity			lung(2)|prostate(1)|skin(1)	4				OV - Ovarian serous cystadenocarcinoma(123;0.000319)												OREG0016265	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	4	90259809	90259809	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:90259809delT								GPRIN3 (30648 upstream) : SNCA (385442 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	90360128	90360131	+	IGR	DEL	TGTG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:90360128_90360131delTGTG								GPRIN3 (130967 upstream) : SNCA (285120 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	90433852	90433854	+	IGR	DEL	AAG	-	-	rs10608411		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:90433852_90433854delAAG								GPRIN3 (204691 upstream) : SNCA (211397 downstream)																																			---	---	---	---
SNCA	6622	broad.mit.edu	37	4	90650173	90650173	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:90650173delT	uc003hsq.2	-						SNCA_uc010ikt.2_Intron|SNCA_uc003hso.2_Intron|SNCA_uc003hsp.2_Intron|SNCA_uc003hsr.2_Intron|uc011cdr.1_5'Flank	NM_001146054	NP_001139526			alpha-synuclein isoform NACP140						activation of caspase activity|anti-apoptosis|negative regulation of dopamine uptake|negative regulation of exocytosis|negative regulation of histone acetylation|negative regulation of microtubule polymerization|negative regulation of monooxygenase activity|negative regulation of norepinephrine uptake|negative regulation of platelet-derived growth factor receptor signaling pathway|negative regulation of serotonin uptake|negative regulation of thrombin receptor signaling pathway|negative regulation of transporter activity|positive regulation of endocytosis|positive regulation of inositol phosphate biosynthetic process|positive regulation of peptidyl-serine phosphorylation|positive regulation of protein serine/threonine kinase activity|positive regulation of receptor recycling|positive regulation of release of sequestered calcium ion into cytosol|receptor internalization|regulation of phospholipase activity|response to interferon-gamma|response to interleukin-1|response to iron(II) ion|response to lipopolysaccharide|response to magnesium ion|synaptic vesicle endocytosis	actin cytoskeleton|axon|cell cortex|cell junction|cytosol|fibril|growth cone|nucleus|synapse	alpha-tubulin binding|calcium ion binding|caspase inhibitor activity|dynein binding|ferrous iron binding|histone binding|Hsp70 protein binding|kinesin binding|magnesium ion binding|phosphoprotein binding|tau protein binding|zinc ion binding				0		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;7.42e-05)	Melatonin(DB01065)													---	---	---	---
FAM190A	401145	broad.mit.edu	37	4	91534339	91534339	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:91534339delA	uc003hsv.3	+						FAM190A_uc010ikv.2_Intron|FAM190A_uc003hsw.2_Intron	NM_001145065	NP_001138537			KIAA1680 protein isoform 1											large_intestine(1)|ovary(1)	2																		---	---	---	---
FAM190A	401145	broad.mit.edu	37	4	91642360	91642361	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:91642360_91642361delTT	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	91820044	91820045	+	Intron	DEL	TG	-	-	rs139768445	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:91820044_91820045delTG	uc003hsv.3	+						FAM190A_uc010ikv.2_Intron|FAM190A_uc003hsx.2_Intron	NM_001145065	NP_001138537			KIAA1680 protein isoform 1											large_intestine(1)|ovary(1)	2																		---	---	---	---
GRID2	2895	broad.mit.edu	37	4	94328860	94328861	+	Intron	INS	-	TCC	TCC	rs148280882	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:94328860_94328861insTCC	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	94978790	94978791	+	IGR	DEL	TC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:94978790_94978791delTC								ATOH1 (227648 upstream) : SMARCAD1 (149968 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	95344194	95344194	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:95344194delA								HPGDS (80167 upstream) : PDLIM5 (28844 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	95625493	95625493	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:95625493delA								PDLIM5 (36117 upstream) : BMPR1B (53635 downstream)																																			---	---	---	---
UNC5C	8633	broad.mit.edu	37	4	96349226	96349227	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:96349226_96349227insT	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	97658431	97658431	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:97658431delA								PDHA2 (895807 upstream) : C4orf37 (821603 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	97693521	97693526	+	IGR	DEL	ACACAA	-	-	rs57830434		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:97693521_97693526delACACAA								PDHA2 (930897 upstream) : C4orf37 (786508 downstream)																																			---	---	---	---
C4orf37	285555	broad.mit.edu	37	4	98495593	98495594	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:98495593_98495594delAA	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	99138009	99138011	+	IGR	DEL	AAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99138009_99138011delAAA								C4orf37 (73618 upstream) : RAP1GDS1 (44516 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	99138914	99138914	+	IGR	DEL	A	-	-	rs75321732		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99138914delA								C4orf37 (74523 upstream) : RAP1GDS1 (43613 downstream)																																			---	---	---	---
TSPAN5	10098	broad.mit.edu	37	4	99408302	99408303	+	Intron	INS	-	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99408302_99408303insG	uc003hub.2	-						TSPAN5_uc011cdz.1_Intron	NM_005723	NP_005714			transmembrane 4 superfamily member 9							integral to membrane					0				OV - Ovarian serous cystadenocarcinoma(123;1.89e-07)														---	---	---	---
TSPAN5	10098	broad.mit.edu	37	4	99541324	99541325	+	Intron	INS	-	CTT	CTT	rs143269781	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99541324_99541325insCTT	uc003hub.2	-						TSPAN5_uc011cdz.1_Intron	NM_005723	NP_005714			transmembrane 4 superfamily member 9							integral to membrane					0				OV - Ovarian serous cystadenocarcinoma(123;1.89e-07)														---	---	---	---
EIF4E	1977	broad.mit.edu	37	4	99823226	99823228	+	Intron	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99823226_99823228delTTT	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	101020209	101020210	+	IGR	DEL	GA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:101020209_101020210delGA								LOC256880 (146589 upstream) : DDIT4L (86819 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	101177053	101177053	+	IGR	DEL	T	-	-	rs35310712		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:101177053delT								DDIT4L (65440 upstream) : EMCN (139447 downstream)																																			---	---	---	---
NHEDC1	150159	broad.mit.edu	37	4	103919762	103919764	+	Intron	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103919762_103919764delTTT	uc003hww.2	-						NHEDC1_uc003hwu.2_Intron|NHEDC1_uc010ilm.2_Intron|NHEDC1_uc003hwv.2_Intron|NHEDC1_uc011cev.1_Intron	NM_139173	NP_631912			Na+/H+ exchanger domain containing 1 isoform 1							integral to membrane	solute:hydrogen antiporter activity			ovary(1)|skin(1)	2		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;1.5e-08)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	104171159	104171160	+	IGR	INS	-	T	T	rs138333011	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:104171159_104171160insT								CENPE (51593 upstream) : TACR3 (339465 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	107695838	107695839	+	IGR	INS	-	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:107695838_107695839insC								AIMP1 (425459 upstream) : DKK2 (147121 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	108513838	108513838	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:108513838delA								DKK2 (308992 upstream) : PAPSS1 (20985 downstream)																																			---	---	---	---
SGMS2	166929	broad.mit.edu	37	4	108809480	108809480	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:108809480delA	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	4	109114862	109114862	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109114862delA								LEF1 (25284 upstream) : LOC285456 (344484 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	109122991	109122991	+	IGR	DEL	A	-	-	rs140925192		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109122991delA								LEF1 (33413 upstream) : LOC285456 (336355 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	109138768	109138769	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109138768_109138769delTT								LEF1 (49190 upstream) : LOC285456 (320577 downstream)																																			---	---	---	---
COL25A1	84570	broad.mit.edu	37	4	109878296	109878296	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109878296delC	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	110137485	110137485	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110137485delG	uc003hze.1	-						COL25A1_uc003hzg.2_Intron|COL25A1_uc003hzh.1_Intron	NM_198721	NP_942014			collagen, type XXV, alpha 1 isoform 1							collagen|extracellular space	beta-amyloid binding|heparin binding			ovary(2)	2		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000173)														---	---	---	---
SEC24B	10427	broad.mit.edu	37	4	110438461	110438461	+	Intron	DEL	T	-	-	rs34345091		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110438461delT	uc003hzk.2	+						SEC24B_uc003hzl.2_Intron|SEC24B_uc011cfp.1_Intron|SEC24B_uc011cfq.1_Intron|SEC24B_uc011cfr.1_Intron	NM_006323	NP_006314			SEC24 (S. cerevisiae) homolog B isoform a						COPII vesicle coating|intracellular protein transport|post-translational protein modification|protein N-linked glycosylation via asparagine	COPII vesicle coat|cytosol|endoplasmic reticulum membrane|Golgi membrane|perinuclear region of cytoplasm	protein binding|transporter activity|zinc ion binding			ovary(2)|large_intestine(1)	3		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;3.03e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	111291048	111291048	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:111291048delT								ELOVL6 (171228 upstream) : ENPEP (106181 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	111323431	111323447	+	IGR	DEL	TTCCTTCCTTCCTCCCT	-	-	rs6817024		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:111323431_111323447delTTCCTTCCTTCCTCCCT								ELOVL6 (203611 upstream) : ENPEP (73782 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	111497917	111497918	+	IGR	INS	-	T	T	rs112981457		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:111497917_111497918insT								ENPEP (13426 upstream) : PITX2 (40664 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	111530364	111530364	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:111530364delG								ENPEP (45873 upstream) : PITX2 (8218 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	111959205	111959205	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:111959205delA								MIR297 (177402 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	111993000	111993000	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:111993000delT								MIR297 (211197 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	112098504	112098507	+	IGR	DEL	AAAA	-	-	rs113275239		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:112098504_112098507delAAAA								MIR297 (316701 upstream) : C4orf32 (968046 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	112754633	112754633	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:112754633delA								MIR297 (972830 upstream) : C4orf32 (311920 downstream)																																			---	---	---	---
ANK2	287	broad.mit.edu	37	4	114062134	114062135	+	Intron	DEL	AA	-	-	rs112473521		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:114062134_114062135delAA	uc003ibe.3	+						ANK2_uc003ibd.3_Intron|ANK2_uc003ibf.3_Intron|ANK2_uc003ibc.2_Intron|ANK2_uc011cgb.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)														---	---	---	---
ANK2	287	broad.mit.edu	37	4	114209316	114209317	+	Intron	DEL	CT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:114209316_114209317delCT	uc003ibe.3	+						ANK2_uc003ibd.3_Intron|ANK2_uc003ibf.3_Intron|ANK2_uc003ibc.2_Intron|ANK2_uc011cgb.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)														---	---	---	---
ANK2	287	broad.mit.edu	37	4	114231581	114231582	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:114231581_114231582delTT	uc003ibe.3	+						ANK2_uc003ibd.3_Intron|ANK2_uc003ibf.3_Intron|ANK2_uc011cgc.1_Intron|ANK2_uc003ibc.2_Intron|ANK2_uc011cgb.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)														---	---	---	---
ANK2	287	broad.mit.edu	37	4	114234449	114234449	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:114234449delT	uc003ibe.3	+						ANK2_uc003ibd.3_Intron|ANK2_uc003ibf.3_Intron|ANK2_uc011cgc.1_Intron|ANK2_uc003ibc.2_Intron|ANK2_uc011cgb.1_Intron	NM_001148	NP_001139			ankyrin 2 isoform 1						axon guidance|signal transduction	apical plasma membrane|basolateral plasma membrane|cytoskeleton|cytosol|sarcomere	protein binding|protein binding			central_nervous_system(7)|ovary(3)|large_intestine(2)|breast(1)|skin(1)	14		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)														---	---	---	---
CAMK2D	817	broad.mit.edu	37	4	114585961	114585962	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:114585961_114585962insT	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	115267947	115267948	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:115267947_115267948delTT								ARSJ (367069 upstream) : UGT8 (251663 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	115316939	115316939	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:115316939delA								ARSJ (416061 upstream) : UGT8 (202672 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	115381816	115381816	+	IGR	DEL	T	-	-	rs112310606		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:115381816delT								ARSJ (480938 upstream) : UGT8 (137795 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	115743029	115743029	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:115743029delT								UGT8 (144827 upstream) : NDST4 (5902 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	116220607	116220607	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:116220607delT								NDST4 (185575 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	116775969	116775969	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:116775969delA								NDST4 (740937 upstream) : MIR1973 (444912 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	117358519	117358519	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:117358519delC								MIR1973 (137595 upstream) : TRAM1L1 (646197 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	117839641	117839641	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:117839641delT								MIR1973 (618717 upstream) : TRAM1L1 (165075 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	117867767	117867768	+	IGR	INS	-	TA	TA			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:117867767_117867768insTA								MIR1973 (646843 upstream) : TRAM1L1 (136948 downstream)																																			---	---	---	---
PRSS12	8492	broad.mit.edu	37	4	119239769	119239770	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119239769_119239770delTT	uc003ica.1	-							NM_003619	NP_003610			neurotrypsin precursor							membrane	scavenger receptor activity			skin(1)	1																		---	---	---	---
MYOZ2	51778	broad.mit.edu	37	4	120104578	120104578	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:120104578delA	uc003icp.3	+							NM_016599	NP_057683			myozenin 2								protein phosphatase 2B binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	120405398	120405398	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:120405398delT								FABP2 (162082 upstream) : PDE5A (10154 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	120691443	120691443	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:120691443delA								PDE5A (141462 upstream) : MAD2L1 (289136 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	121204381	121204381	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:121204381delT								MAD2L1 (216368 upstream) : PRDM5 (411549 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	121288936	121288937	+	IGR	INS	-	GAA	GAA	rs146373610	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:121288936_121288937insGAA								MAD2L1 (300923 upstream) : PRDM5 (326993 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	121402804	121402804	+	IGR	DEL	A	-	-	rs141324282		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:121402804delA								MAD2L1 (414791 upstream) : PRDM5 (213126 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	121542921	121542921	+	IGR	DEL	A	-	-	rs75303261		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:121542921delA								MAD2L1 (554908 upstream) : PRDM5 (73009 downstream)																																			---	---	---	---
PRDM5	11107	broad.mit.edu	37	4	121639460	121639461	+	Intron	DEL	CA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:121639460_121639461delCA	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																		---	---	---	---
PRDM5	11107	broad.mit.edu	37	4	121768477	121768478	+	Intron	DEL	TC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:121768477_121768478delTC	uc003idn.2	-						PRDM5_uc003ido.2_Intron|PRDM5_uc010ine.2_Intron|PRDM5_uc010inf.2_Intron|PRDM5_uc003idp.1_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																		---	---	---	---
TNIP3	79931	broad.mit.edu	37	4	122071541	122071541	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:122071541delT	uc010ing.2	-						TNIP3_uc010inh.2_Intron|TNIP3_uc011cgj.1_Intron	NM_024873	NP_079149			TNFAIP3 interacting protein 3											ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	122579113	122579113	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:122579113delA								QRFPR (276932 upstream) : ANXA5 (10040 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	122692306	122692306	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:122692306delT								LOC100192379 (4344 upstream) : EXOSC9 (30166 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	122898151	122898151	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:122898151delT								TRPC3 (25242 upstream) : KIAA1109 (193607 downstream)																																			---	---	---	---
KIAA1109	84162	broad.mit.edu	37	4	123090635	123090635	+	5'Flank	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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	123227333	123227333	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123227333delA	uc003ieh.2	+						KIAA1109_uc003iel.1_Intron	NM_015312	NP_056127			fragile site-associated protein						regulation of cell growth|regulation of epithelial cell differentiation	integral to membrane|nucleus				ovary(8)|skin(2)|pancreas(1)|central_nervous_system(1)	12																		---	---	---	---
KIAA1109	84162	broad.mit.edu	37	4	123252061	123252061	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123252061delT	uc003ieh.2	+						KIAA1109_uc003iem.2_Intron	NM_015312	NP_056127			fragile site-associated protein						regulation of cell growth|regulation of epithelial cell differentiation	integral to membrane|nucleus				ovary(8)|skin(2)|pancreas(1)|central_nervous_system(1)	12																		---	---	---	---
ADAD1	132612	broad.mit.edu	37	4	123301135	123301135	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123301135delG	uc003ieo.2	+						ADAD1_uc003iep.2_Intron|ADAD1_uc003ieq.2_Intron	NM_139243	NP_640336			adenosine deaminase domain containing 1						multicellular organismal development|RNA processing	nucleus	adenosine deaminase activity|double-stranded RNA binding				0																		---	---	---	---
SPATA5	166378	broad.mit.edu	37	4	123914317	123914317	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123914317delT	uc003iez.3	+						SPATA5_uc003iey.2_Intron	NM_145207	NP_660208			spermatogenesis associated 5						cell differentiation|multicellular organismal development|spermatogenesis	mitochondrion	ATP binding|nucleoside-triphosphatase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	124393891	124393892	+	IGR	INS	-	TTG	TTG	rs148506842	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:124393891_124393892insTTG								SPRY1 (68984 upstream) : LOC285419 (177530 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	125435129	125435129	+	Intron	DEL	A	-	-	rs5861666		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:125435129delA	uc003ife.1	-											Homo sapiens cDNA FLJ32893 fis, clone TESTI2004993.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	126101851	126101852	+	IGR	INS	-	AAAA	AAAA	rs7662216		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:126101851_126101852insAAAA								ANKRD50 (467964 upstream) : FAT4 (135715 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	126948841	126948842	+	IGR	DEL	AA	-	-	rs76260504		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:126948841_126948842delAA								MIR2054 (520379 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	128162631	128162635	+	IGR	DEL	AAATT	-	-	rs75262099		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:128162631_128162635delAAATT								None (None upstream) : INTU (391485 downstream)																																			---	---	---	---
HSPA4L	22824	broad.mit.edu	37	4	128716189	128716189	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:128716189delT	uc003ifm.2	+						HSPA4L_uc010iny.1_Intron|HSPA4L_uc011cgr.1_Intron	NM_014278	NP_055093			heat shock 70kDa protein 4-like						protein folding|response to unfolded protein	cytoplasm|nucleus	ATP binding|protein binding			ovary(2)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
SCLT1	132320	broad.mit.edu	37	4	129996214	129996214	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:129996214delA	uc003igp.2	-						SCLT1_uc003igq.2_Intron|SCLT1_uc010iob.1_Intron|SCLT1_uc003igr.2_Intron|SCLT1_uc003igs.2_Intron|SCLT1_uc003igt.3_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	130034754	130034754	+	IGR	DEL	T	-	-	rs11335742		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:130034754delT								C4orf33 (912 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	130154135	130154135	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:130154135delA								C4orf33 (120293 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	131355191	131355193	+	IGR	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:131355191_131355193delTTT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	133545740	133545741	+	IGR	INS	-	CTCCTT	CTCCTT	rs143517636	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:133545740_133545741insCTCCTT								None (None upstream) : PCDH10 (524729 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	134060513	134060513	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:134060513delT	uc003igy.2	-											Homo sapiens cDNA clone IMAGE:4818734.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	134493151	134493152	+	IGR	INS	-	AT	AT	rs146796471	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:134493151_134493152insAT								PCDH10 (380420 upstream) : PABPC4L (624339 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	134694320	134694320	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:134694320delA								PCDH10 (581589 upstream) : PABPC4L (423171 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	134819193	134819194	+	IGR	DEL	GT	-	-	rs12503334	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:134819193_134819194delGT								PCDH10 (706462 upstream) : PABPC4L (298297 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	134997171	134997172	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:134997171_134997172delAA								PCDH10 (884440 upstream) : PABPC4L (120319 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	135394064	135394064	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:135394064delA								PABPC4L (271161 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	135826923	135826923	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:135826923delT								PABPC4L (704020 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	136138779	136138779	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:136138779delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	137091399	137091401	+	IGR	DEL	AAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:137091399_137091401delAAA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	138284178	138284178	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:138284178delT								None (None upstream) : PCDH18 (155898 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	138821648	138821648	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:138821648delT								PCDH18 (368000 upstream) : SLC7A11 (263600 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	139557256	139557256	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:139557256delT								SLC7A11 (393753 upstream) : CCRN4L (379687 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	139621075	139621075	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:139621075delA								SLC7A11 (457572 upstream) : CCRN4L (315868 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	140340171	140340172	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:140340171_140340172delTT								NAA15 (28236 upstream) : RAB33B (34789 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	140426748	140426749	+	IGR	DEL	AA	-	-	rs57572140		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:140426748_140426749delAA								RAB33B (29685 upstream) : SETD7 (444 downstream)																																			---	---	---	---
SETD7	80854	broad.mit.edu	37	4	140470929	140470929	+	Intron	DEL	A	-	-	rs35804679		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:140470929delA	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)																	---	---	---	---
MAML3	55534	broad.mit.edu	37	4	141040782	141040783	+	Intron	DEL	TT	-	-	rs58340523		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:141040782_141040783delTT	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)																	---	---	---	---
TBC1D9	23158	broad.mit.edu	37	4	141648961	141648961	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:141648961delA	uc010ioj.2	-							NM_015130	NP_055945			TBC1 domain family, member 9 (with GRAM domain)							intracellular	calcium ion binding|Rab GTPase activator activity			ovary(1)	1	all_hematologic(180;0.162)	Medulloblastoma(177;0.00498)																---	---	---	---
Unknown	0	broad.mit.edu	37	4	142063497	142063499	+	IGR	DEL	CTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:142063497_142063499delCTT								RNF150 (8881 upstream) : ZNF330 (78550 downstream)																																			---	---	---	---
INPP4B	8821	broad.mit.edu	37	4	143087848	143087848	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:143087848delA	uc003iix.3	-						INPP4B_uc003iiw.3_Intron|INPP4B_uc011chm.1_Intron|INPP4B_uc011chn.1_Intron|INPP4B_uc011cho.1_Intron|INPP4B_uc011chp.1_Intron	NM_003866	NP_003857			inositol polyphosphate-4-phosphatase, type II,						signal transduction		phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity			ovary(1)|lung(1)	2	all_hematologic(180;0.158)																	---	---	---	---
INPP4B	8821	broad.mit.edu	37	4	143327824	143327824	+	Intron	DEL	T	-	-	rs67834807		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:143327824delT	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)																	---	---	---	---
INPP4B	8821	broad.mit.edu	37	4	143565352	143565353	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:143565352_143565353insA	uc003iix.3	-						INPP4B_uc003iiw.3_Intron	NM_003866	NP_003857			inositol polyphosphate-4-phosphatase, type II,						signal transduction		phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity			ovary(1)|lung(1)	2	all_hematologic(180;0.158)																	---	---	---	---
GAB1	2549	broad.mit.edu	37	4	144381841	144381841	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:144381841delA	uc003ije.2	+						GAB1_uc003ijd.2_Intron|GAB1_uc011chq.1_Intron	NM_002039	NP_002030			GRB2-associated binding protein 1 isoform b						cell proliferation|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway	cytosol	SH3/SH2 adaptor activity			breast(2)|lung(1)|skin(1)	4	all_hematologic(180;0.158)																	---	---	---	---
Unknown	0	broad.mit.edu	37	4	144498147	144498148	+	IGR	DEL	TA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:144498147_144498148delTA								LOC441046 (8834 upstream) : GYPE (293872 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	144687239	144687240	+	IGR	INS	-	T	T	rs146010732	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:144687239_144687240insT								LOC441046 (197926 upstream) : GYPE (104780 downstream)																																			---	---	---	---
GYPA	2993	broad.mit.edu	37	4	144921229	144921230	+	Intron	INS	-	C	C	rs34487421		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:144921229_144921230insC	uc003ijn.2	-						GYPB_uc011chs.1_Intron|GYPB_uc011cht.1_Intron|GYPB_uc011chu.1_Intron|GYPB_uc010ioo.1_Intron|GYPB_uc010iop.2_Intron|GYPB_uc011chv.1_Intron|GYPB_uc011chw.1_Intron|GYPB_uc011chx.1_Intron|GYPB_uc003ijm.1_Intron|GYPB_uc011chy.1_Intron|GYPB_uc011chz.1_Intron					SubName: Full=Glycophorin MiX; Flags: Fragment;						interspecies interaction between organisms	membrane fraction	receptor activity			central_nervous_system(2)	2	all_hematologic(180;0.15)																	---	---	---	---
Unknown	0	broad.mit.edu	37	4	145455216	145455216	+	IGR	DEL	A	-	-	rs71590460		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:145455216delA								GYPA (393312 upstream) : HHIP (111957 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	145556461	145556465	+	IGR	DEL	AAAAA	-	-	rs76663205	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:145556461_145556465delAAAAA								GYPA (494557 upstream) : HHIP (10708 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	145754839	145754839	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:145754839delA								HHIP (94958 upstream) : ANAPC10 (161475 downstream)																																			---	---	---	---
ANAPC10	10393	broad.mit.edu	37	4	145966767	145966767	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:145966767delT	uc003iju.3	-						ANAPC10_uc003ijv.3_Intron|ANAPC10_uc003ijw.3_Intron	NM_014885	NP_055700			anaphase promoting complex subunit 10						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|G2/M transition of mitotic cell cycle|mitotic anaphase|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|cytosol|nucleoplasm	ubiquitin-protein ligase activity				0	all_hematologic(180;0.151)																	---	---	---	---
ANAPC10	10393	broad.mit.edu	37	4	145972386	145972389	+	Intron	DEL	AGAG	-	-	rs57384763		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:145972386_145972389delAGAG	uc003iju.3	-						ANAPC10_uc003ijv.3_Intron|ANAPC10_uc003ijw.3_Intron	NM_014885	NP_055700			anaphase promoting complex subunit 10						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|G2/M transition of mitotic cell cycle|mitotic anaphase|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|cytosol|nucleoplasm	ubiquitin-protein ligase activity				0	all_hematologic(180;0.151)																	---	---	---	---
ANAPC10	10393	broad.mit.edu	37	4	145993172	145993172	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:145993172delA	uc003iju.3	-						ANAPC10_uc003ijv.3_Intron|ANAPC10_uc003ijw.3_Intron	NM_014885	NP_055700			anaphase promoting complex subunit 10						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|G2/M transition of mitotic cell cycle|mitotic anaphase|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|cytosol|nucleoplasm	ubiquitin-protein ligase activity				0	all_hematologic(180;0.151)																	---	---	---	---
Unknown	0	broad.mit.edu	37	4	146377226	146377227	+	IGR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146377226_146377227insA								OTUD4 (276394 upstream) : SMAD1 (25724 downstream)																																			---	---	---	---
SMAD1	4086	broad.mit.edu	37	4	146401459	146401459	+	5'Flank	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146401459delT	uc003ikc.2	+						SMAD1_uc003ikd.2_5'Flank|SMAD1_uc010iov.2_5'Flank	NM_005900	NP_005891			Sma- and Mad-related protein 1						BMP signaling pathway|embryonic pattern specification|primary miRNA processing|SMAD protein complex assembly|transforming growth factor beta receptor signaling pathway	cytosol|integral to membrane|nuclear inner membrane	co-SMAD binding|I-SMAD binding|identical protein binding|protein kinase binding|sequence-specific DNA binding transcription factor activity|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity			ovary(1)	1	all_hematologic(180;0.151)																	---	---	---	---
SMAD1	4086	broad.mit.edu	37	4	146442479	146442479	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146442479delT	uc003ikc.2	+						SMAD1_uc003ikd.2_Intron|SMAD1_uc010iov.2_Intron|SMAD1_uc011cic.1_Intron	NM_005900	NP_005891			Sma- and Mad-related protein 1						BMP signaling pathway|embryonic pattern specification|primary miRNA processing|SMAD protein complex assembly|transforming growth factor beta receptor signaling pathway	cytosol|integral to membrane|nuclear inner membrane	co-SMAD binding|I-SMAD binding|identical protein binding|protein kinase binding|sequence-specific DNA binding transcription factor activity|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity			ovary(1)	1	all_hematologic(180;0.151)																	---	---	---	---
Unknown	0	broad.mit.edu	37	4	147958230	147958230	+	IGR	DEL	A	-	-	rs145207887		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:147958230delA								TTC29 (91196 upstream) : MIR548G (307551 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	148073537	148073537	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:148073537delA								TTC29 (206503 upstream) : MIR548G (192244 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	148518780	148518780	+	IGR	DEL	A	-	-	rs11301239		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:148518780delA								EDNRA (52674 upstream) : TMEM184C (19759 downstream)																																			---	---	---	---
ARHGAP10	79658	broad.mit.edu	37	4	148830794	148830794	+	Intron	DEL	T	-	-	rs77063685		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:148830794delT	uc003ilf.2	+						ARHGAP10_uc003ilg.2_Intron	NM_024605	NP_078881			Rho GTPase activating protein 10						apoptosis|filopodium assembly|regulation of apoptosis|small GTPase mediated signal transduction	cytosol|perinuclear region of cytoplasm|plasma membrane	cytoskeletal adaptor activity|SH3 domain binding			skin(2)|pancreas(1)|lung(1)	4	all_hematologic(180;0.151)	Renal(17;0.0166)		GBM - Glioblastoma multiforme(119;0.0423)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	150968073	150968074	+	IGR	DEL	TC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:150968073_150968074delTC								None (None upstream) : DCLK2 (32006 downstream)																																			---	---	---	---
LRBA	987	broad.mit.edu	37	4	151833280	151833280	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151833280delA	uc010ipj.2	-						LRBA_uc003ilu.3_Intron|LRBA_uc010ipk.1_Intron	NM_006726	NP_006717			LPS-responsive vesicle trafficking, beach and							endoplasmic reticulum|Golgi apparatus|integral to membrane|lysosome|plasma membrane	protein binding			ovary(3)|breast(3)|skin(1)	7	all_hematologic(180;0.151)																	---	---	---	---
Unknown	0	broad.mit.edu	37	4	151989453	151989453	+	IGR	DEL	T	-	-	rs150391514	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151989453delT								LRBA (52574 upstream) : RPS3A (31301 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	152026204	152026205	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152026204_152026205delTT								RPS3A (402 upstream) : SH3D19 (15228 downstream)																																			---	---	---	---
SH3D19	152503	broad.mit.edu	37	4	152048929	152048930	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152048929_152048930insT	uc010ipl.1	-						SH3D19_uc003imb.2_Intron|SH3D19_uc003imc.2_Intron|SH3D19_uc003ime.2_Intron|SH3D19_uc010ipm.2_Intron	NM_001009555	NP_001009555			SH3 domain containing 19 isoform a						cellular membrane organization|positive regulation of membrane protein ectodomain proteolysis|post-Golgi vesicle-mediated transport	cytosol|Golgi apparatus|nucleus|plasma membrane	proline-rich region binding			ovary(1)|skin(1)	2	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.138)																---	---	---	---
SH3D19	152503	broad.mit.edu	37	4	152061073	152061073	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152061073delT	uc010ipl.1	-						SH3D19_uc003imb.2_Intron|SH3D19_uc003imc.2_Intron|SH3D19_uc003ime.2_Intron|SH3D19_uc010ipm.2_Intron	NM_001009555	NP_001009555			SH3 domain containing 19 isoform a						cellular membrane organization|positive regulation of membrane protein ectodomain proteolysis|post-Golgi vesicle-mediated transport	cytosol|Golgi apparatus|nucleus|plasma membrane	proline-rich region binding			ovary(1)|skin(1)	2	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.138)																---	---	---	---
FAM160A1	729830	broad.mit.edu	37	4	152498455	152498456	+	Intron	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152498455_152498456delAC	uc003imj.2	+							NM_001109977	NP_001103447			hypothetical protein LOC729830												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	152838637	152838637	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152838637delT								PET112L (156491 upstream) : FBXW7 (403774 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	152925389	152925389	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152925389delA								PET112L (243243 upstream) : FBXW7 (317022 downstream)																																			---	---	---	---
TMEM154	201799	broad.mit.edu	37	4	153549745	153549745	+	Intron	DEL	C	-	-	rs72117571		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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)																---	---	---	---
TRIM2	23321	broad.mit.edu	37	4	154171261	154171262	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154171261_154171262delTT	uc003ing.2	+						TRIM2_uc003inh.2_Intron	NM_001130067	NP_001123539			tripartite motif-containing 2 isoform 2							cytoplasm	zinc ion binding			central_nervous_system(1)	1	all_hematologic(180;0.093)	Medulloblastoma(177;0.00225)		GBM - Glioblastoma multiforme(119;0.0102)|LUSC - Lung squamous cell carcinoma(193;0.0703)														---	---	---	---
TRIM2	23321	broad.mit.edu	37	4	154221412	154221412	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154221412delT	uc003ing.2	+						TRIM2_uc003inh.2_Intron	NM_001130067	NP_001123539			tripartite motif-containing 2 isoform 2							cytoplasm	zinc ion binding			central_nervous_system(1)	1	all_hematologic(180;0.093)	Medulloblastoma(177;0.00225)		GBM - Glioblastoma multiforme(119;0.0102)|LUSC - Lung squamous cell carcinoma(193;0.0703)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	154573648	154573648	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154573648delC								KIAA0922 (15788 upstream) : TLR2 (31793 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	154748395	154748396	+	IGR	INS	-	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154748395_154748396insG								SFRP2 (38167 upstream) : DCHS2 (407131 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	155588402	155588402	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155588402delA	uc003iol.2	+											Homo sapiens cDNA FLJ31672 fis, clone NT2RI2005048.																														---	---	---	---
MAP9	79884	broad.mit.edu	37	4	156291801	156291801	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:156291801delT	uc003ios.2	-						MAP9_uc011cin.1_Intron|MAP9_uc010iqa.1_Intron|MAP9_uc003iot.1_Intron|MAP9_uc010iqb.1_Intron	NM_001039580	NP_001034669			aster-associated protein						cell division|mitosis	cytoplasm|microtubule|spindle				ovary(1)|central_nervous_system(1)	2	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.143)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	156798423	156798423	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:156798423delA								ACCN5 (10998 upstream) : TDO2 (26424 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	157246854	157246856	+	IGR	DEL	AAA	-	-	rs113182336		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:157246854_157246856delAAA								CTSO (371806 upstream) : PDGFC (435908 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	157305066	157305066	+	IGR	DEL	T	-	-	rs76814838		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:157305066delT								CTSO (430018 upstream) : PDGFC (377698 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	158926848	158926849	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:158926848_158926849insT								LOC340017 (429553 upstream) : FAM198B (118884 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	159213283	159213283	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159213283delA								TMEM144 (36845 upstream) : RXFP1 (229764 downstream)																																			---	---	---	---
RAPGEF2	9693	broad.mit.edu	37	4	160220028	160220028	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:160220028delC	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	160306337	160306341	+	IGR	DEL	AAACA	-	-	rs67303926		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:160306337_160306341delAAACA								RAPGEF2 (25038 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	160380508	160380509	+	IGR	INS	-	T	T	rs140715307	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:160380508_160380509insT								RAPGEF2 (99209 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	160457019	160457019	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:160457019delT								RAPGEF2 (175720 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	161533479	161533479	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:161533479delA								None (None upstream) : FSTL5 (771572 downstream)																																			---	---	---	---
MARCH1	55016	broad.mit.edu	37	4	165230116	165230118	+	Intron	DEL	AAA	-	-	rs146523850		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:165230116_165230118delAAA	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)																---	---	---	---
TMEM192	201931	broad.mit.edu	37	4	166011534	166011535	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166011534_166011535delAA	uc003iqz.3	-							NM_001100389	NP_001093859			transmembrane protein 192							Golgi apparatus|integral to membrane|late endosome|lysosomal membrane|nucleus				skin(1)	1	all_hematologic(180;0.221)	Prostate(90;0.0959)|Melanoma(52;0.18)		GBM - Glioblastoma multiforme(119;0.0926)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	166514893	166514893	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166514893delA								CPE (95412 upstream) : TLL1 (279517 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	168618771	168618771	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:168618771delA								SPOCK3 (463030 upstream) : ANXA10 (394936 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	168772847	168772847	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:168772847delT								SPOCK3 (617106 upstream) : ANXA10 (240860 downstream)																																			---	---	---	---
PALLD	23022	broad.mit.edu	37	4	169453045	169453045	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169453045delT	uc011cjx.1	+						PALLD_uc003iru.2_Intron	NM_016081	NP_057165			palladin isoform 2						cytoskeleton organization	actin filament|focal adhesion|lamellipodium|nucleus|ruffle|sarcomere	actin binding|muscle alpha-actinin binding			ovary(1)	1		Prostate(90;0.00996)|Renal(120;0.0203)|Melanoma(52;0.144)		GBM - Glioblastoma multiforme(119;0.204)										Pancreatic_Cancer_Familial_Clustering_of				---	---	---	---
PALLD	23022	broad.mit.edu	37	4	169537274	169537275	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169537274_169537275insA	uc011cjx.1	+						PALLD_uc003iru.2_Intron	NM_016081	NP_057165			palladin isoform 2						cytoskeleton organization	actin filament|focal adhesion|lamellipodium|nucleus|ruffle|sarcomere	actin binding|muscle alpha-actinin binding			ovary(1)	1		Prostate(90;0.00996)|Renal(120;0.0203)|Melanoma(52;0.144)		GBM - Glioblastoma multiforme(119;0.204)										Pancreatic_Cancer_Familial_Clustering_of				---	---	---	---
PALLD	23022	broad.mit.edu	37	4	169828992	169828993	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169828992_169828993delAA	uc011cjx.1	+						CBR4_uc011cjy.1_Intron|PALLD_uc003iru.2_Intron|PALLD_uc003irv.2_Intron|PALLD_uc003irw.2_Intron|PALLD_uc003irx.2_Intron	NM_016081	NP_057165			palladin isoform 2						cytoskeleton organization	actin filament|focal adhesion|lamellipodium|nucleus|ruffle|sarcomere	actin binding|muscle alpha-actinin binding			ovary(1)	1		Prostate(90;0.00996)|Renal(120;0.0203)|Melanoma(52;0.144)		GBM - Glioblastoma multiforme(119;0.204)										Pancreatic_Cancer_Familial_Clustering_of				---	---	---	---
SH3RF1	57630	broad.mit.edu	37	4	170088479	170088479	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170088479delA	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	170366852	170366853	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170366852_170366853insA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	170820422	170820422	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170820422delA								C4orf27 (141329 upstream) : MFAP3L (87328 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	171869710	171869710	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:171869710delC								AADAT (858338 upstream) : GALNTL6 (864865 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	172648845	172648845	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:172648845delA								None (None upstream) : GALNTL6 (85730 downstream)																																			---	---	---	---
GALNTL6	442117	broad.mit.edu	37	4	173658459	173658459	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:173658459delT	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																		---	---	---	---
GALNT7	51809	broad.mit.edu	37	4	174099203	174099204	+	Intron	INS	-	GTGCGCGC	GTGCGCGC	rs71937077		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:174099203_174099204insGTGCGCGC	uc003isz.3	+							NM_017423	NP_059119			polypeptide N-acetylgalactosaminyltransferase 7						protein O-linked glycosylation	Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			central_nervous_system(1)	1		Prostate(90;0.0132)|Renal(120;0.0183)|Melanoma(52;0.0749)|all_hematologic(60;0.107)|all_neural(102;0.122)		all cancers(43;1.87e-18)|Epithelial(43;3.44e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-09)|STAD - Stomach adenocarcinoma(60;0.0019)|GBM - Glioblastoma multiforme(59;0.0119)|LUSC - Lung squamous cell carcinoma(193;0.0199)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	174308456	174308456	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:174308456delT								SAP30 (9774 upstream) : SCRG1 (844 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	174409979	174409980	+	IGR	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:174409979_174409980delTG								SCRG1 (82451 upstream) : HAND2 (37672 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	176214948	176214948	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:176214948delT								ADAM29 (315618 upstream) : GPM6A (339141 downstream)																																			---	---	---	---
WDR17	116966	broad.mit.edu	37	4	177046768	177046769	+	Intron	DEL	AT	-	-	rs142222789		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:177046768_177046769delAT	uc003iuj.2	+						WDR17_uc003iuk.2_Intron|WDR17_uc003ium.3_Intron|WDR17_uc003iul.1_Intron	NM_170710	NP_733828			WD repeat domain 17 isoform 1											ovary(2)|skin(2)|pancreas(1)|central_nervous_system(1)	6		Breast(14;0.00015)|Melanoma(52;0.00886)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;2.21e-20)|Epithelial(43;9.71e-18)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-09)|GBM - Glioblastoma multiforme(59;0.000295)|STAD - Stomach adenocarcinoma(60;0.000703)|LUSC - Lung squamous cell carcinoma(193;0.0232)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	177398834	177398837	+	IGR	DEL	CACA	-	-	rs150182104		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:177398834_177398837delCACA								SPCS3 (145440 upstream) : VEGFC (205854 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	177860499	177860499	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:177860499delA								VEGFC (146604 upstream) : NEIL3 (370492 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	178414490	178414504	+	Intron	DEL	GCTACAATGACAATG	-	-	rs142039120		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:178414490_178414504delGCTACAATGACAATG	uc003iux.1	+											Homo sapiens cDNA FLJ37626 fis, clone BRCOC2014748.																														---	---	---	---
LOC285501	285501	broad.mit.edu	37	4	178853493	178853493	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:178853493delT	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	179354005	179354005	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:179354005delA								LOC285501 (442102 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	179590093	179590094	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:179590093_179590094delAA								LOC285501 (678190 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	180250591	180250593	+	IGR	DEL	AAG	-	-	rs72535443		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:180250591_180250593delAAG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	181005057	181005058	+	IGR	INS	-	C	C	rs145249223	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:181005057_181005058insC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	181134791	181134791	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:181134791delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	181156439	181156440	+	IGR	INS	-	GT	GT	rs141666729	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:181156439_181156440insGT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	181419211	181419211	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:181419211delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	181464154	181464155	+	IGR	INS	-	T	T	rs145745612	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:181464154_181464155insT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	181536316	181536318	+	IGR	DEL	AAC	-	-	rs10563774		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:181536316_181536318delAAC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	182498947	182498947	+	IGR	DEL	T	-	-	rs33944520		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:182498947delT								None (None upstream) : MGC45800 (561212 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	182652391	182652391	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:182652391delT								None (None upstream) : MGC45800 (407768 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	182707851	182707856	+	IGR	DEL	TTTTTT	-	-	rs146629166		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:182707851_182707856delTTTTTT								None (None upstream) : MGC45800 (352303 downstream)																																			---	---	---	---
ODZ3	55714	broad.mit.edu	37	4	183064234	183064234	+	5'Flank	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183064234delT	uc010irv.1	+						MGC45800_uc003ivc.2_RNA					Homo sapiens ODZ3 (ODZ3) mRNA, partial cds.						signal transduction	integral to membrane					0		all_lung(41;2.69e-14)|Lung NSC(41;1.92e-11)|Melanoma(52;1.74e-05)|Colorectal(36;0.0062)|Breast(14;0.00748)|all_hematologic(60;0.0162)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_neural(102;0.155)|Medulloblastoma(177;0.184)		all cancers(43;1.42e-24)|Epithelial(43;6.86e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.16e-11)|Colorectal(24;9.75e-06)|STAD - Stomach adenocarcinoma(60;2.96e-05)|COAD - Colon adenocarcinoma(29;0.00103)|GBM - Glioblastoma multiforme(59;0.00462)|LUSC - Lung squamous cell carcinoma(40;0.0391)|READ - Rectum adenocarcinoma(43;0.0487)														---	---	---	---
ODZ3	55714	broad.mit.edu	37	4	183231825	183231826	+	Intron	DEL	TT	-	-	rs150719795		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183231825_183231826delTT	uc010irv.1	+											Homo sapiens ODZ3 (ODZ3) mRNA, partial cds.						signal transduction	integral to membrane					0		all_lung(41;2.69e-14)|Lung NSC(41;1.92e-11)|Melanoma(52;1.74e-05)|Colorectal(36;0.0062)|Breast(14;0.00748)|all_hematologic(60;0.0162)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_neural(102;0.155)|Medulloblastoma(177;0.184)		all cancers(43;1.42e-24)|Epithelial(43;6.86e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.16e-11)|Colorectal(24;9.75e-06)|STAD - Stomach adenocarcinoma(60;2.96e-05)|COAD - Colon adenocarcinoma(29;0.00103)|GBM - Glioblastoma multiforme(59;0.00462)|LUSC - Lung squamous cell carcinoma(40;0.0391)|READ - Rectum adenocarcinoma(43;0.0487)														---	---	---	---
ODZ3	55714	broad.mit.edu	37	4	183676994	183676995	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183676994_183676995insA	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	184329208	184329213	+	IGR	DEL	TTTTCT	-	-	rs112534299		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184329208_184329213delTTTTCT								WWC2 (87281 upstream) : CDKN2AIP (36576 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	184445213	184445213	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184445213delT								ING2 (12964 upstream) : RWDD4A (115576 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	184490755	184490755	+	IGR	DEL	T	-	-	rs11409582		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184490755delT								ING2 (58506 upstream) : RWDD4A (70034 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	184516052	184516053	+	IGR	DEL	AA	-	-	rs113331571		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184516052_184516053delAA								ING2 (83803 upstream) : RWDD4A (44736 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	184538420	184538427	+	IGR	DEL	CTTCTTCT	-	-	rs143064778	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184538420_184538427delCTTCTTCT								ING2 (106171 upstream) : RWDD4A (22362 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	184789589	184789589	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184789589delA								C4orf41 (154845 upstream) : STOX2 (36920 downstream)																																			---	---	---	---
SORBS2	8470	broad.mit.edu	37	4	186591379	186591379	+	Intron	DEL	A	-	-	rs77054159		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186591379delA	uc003iyl.2	-						SORBS2_uc003iyh.2_Intron|SORBS2_uc011ckw.1_Intron|SORBS2_uc003iyi.2_Intron|SORBS2_uc011ckx.1_Intron|SORBS2_uc003iyk.2_Intron|SORBS2_uc003iym.2_Intron|SORBS2_uc003iyn.1_Intron|SORBS2_uc011cky.1_Intron|SORBS2_uc003iyp.2_Intron|SORBS2_uc003iyd.2_Intron|SORBS2_uc003iye.2_Intron|SORBS2_uc003iya.2_Intron|SORBS2_uc003iyb.2_Intron|SORBS2_uc003iyc.2_Intron|SORBS2_uc003iyg.2_Intron|SORBS2_uc003iyf.2_Intron	NM_021069	NP_066547			sorbin and SH3 domain containing 2 isoform 2							actin cytoskeleton|nucleus|perinuclear region of cytoplasm|Z disc	cytoskeletal adaptor activity|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(1)	1		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205)														---	---	---	---
SORBS2	8470	broad.mit.edu	37	4	186640003	186640003	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186640003delA	uc003iyl.2	-						SORBS2_uc003iyh.2_Intron|SORBS2_uc011ckw.1_Intron|SORBS2_uc003iyi.2_Intron|SORBS2_uc011ckx.1_Intron|SORBS2_uc003iyk.2_Intron|SORBS2_uc003iym.2_Intron|SORBS2_uc003iyn.1_Intron|SORBS2_uc011cky.1_Intron|SORBS2_uc003iyp.2_Intron	NM_021069	NP_066547			sorbin and SH3 domain containing 2 isoform 2							actin cytoskeleton|nucleus|perinuclear region of cytoplasm|Z disc	cytoskeletal adaptor activity|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(1)	1		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205)														---	---	---	---
SORBS2	8470	broad.mit.edu	37	4	186752922	186752922	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186752922delC	uc003iyl.2	-						SORBS2_uc003iym.2_Intron|SORBS2_uc011cky.1_Intron	NM_021069	NP_066547			sorbin and SH3 domain containing 2 isoform 2							actin cytoskeleton|nucleus|perinuclear region of cytoplasm|Z disc	cytoskeletal adaptor activity|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(1)	1		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205)														---	---	---	---
SORBS2	8470	broad.mit.edu	37	4	186783290	186783291	+	Intron	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186783290_186783291delTG	uc003iyl.2	-						SORBS2_uc003iym.2_Intron|SORBS2_uc011cky.1_Intron	NM_021069	NP_066547			sorbin and SH3 domain containing 2 isoform 2							actin cytoskeleton|nucleus|perinuclear region of cytoplasm|Z disc	cytoskeletal adaptor activity|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(1)	1		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205)														---	---	---	---
FAT1	2195	broad.mit.edu	37	4	187641536	187641537	+	Intron	INS	-	A	A	rs139374778	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187641536_187641537insA	uc003izf.2	-						FAT1_uc010iso.1_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)			---	---	---	---
Unknown	0	broad.mit.edu	37	4	187992506	187992507	+	IGR	INS	-	TTCTTTCC	TTCTTTCC	rs150979756	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187992506_187992507insTTCTTTCC								FAT1 (344656 upstream) : ZFP42 (924418 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	188382299	188382300	+	IGR	DEL	GG	-	-	rs72093167		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:188382299_188382300delGG								FAT1 (734449 upstream) : ZFP42 (534625 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	188602166	188602167	+	IGR	INS	-	T	T	rs138720554	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:188602166_188602167insT								FAT1 (954316 upstream) : ZFP42 (314758 downstream)																																			---	---	---	---
ZFP42	132625	broad.mit.edu	37	4	188915137	188915137	+	5'Flank	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:188915137delA	uc003izg.1	+						ZFP42_uc003izh.1_5'Flank|ZFP42_uc003izi.1_5'Flank	NM_174900	NP_777560			zinc finger protein 42						female gonad development|male gonad development|meiosis	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|skin(1)	2		all_cancers(14;6.2e-52)|all_epithelial(14;7.36e-37)|all_lung(41;2.29e-15)|Lung NSC(41;6.7e-15)|Breast(6;1.53e-05)|Melanoma(20;3.01e-05)|Hepatocellular(41;0.00335)|all_hematologic(60;0.014)|Renal(120;0.0183)|Prostate(90;0.0421)|Colorectal(36;0.227)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-11)|BRCA - Breast invasive adenocarcinoma(30;4.21e-06)|GBM - Glioblastoma multiforme(59;8.93e-05)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.157)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	189215487	189215488	+	IGR	DEL	TT	-	-	rs35598610		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:189215487_189215488delTT								TRIML1 (146838 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	189238117	189238118	+	IGR	INS	-	CA	CA	rs62351257		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:189238117_189238118insCA								TRIML1 (169468 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	189421344	189421345	+	Intron	DEL	CA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:189421344_189421345delCA	uc003izp.1	+											Homo sapiens cDNA FLJ38649 fis, clone HHDPC2007302.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	189445117	189445117	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:189445117delA	uc003izp.1	+											Homo sapiens cDNA FLJ38649 fis, clone HHDPC2007302.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	189789343	189789343	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:189789343delG								TRIML1 (720694 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	190364898	190364898	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190364898delA								None (None upstream) : FRG1 (497076 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	190555264	190555291	+	IGR	DEL	CCTCCAGATTTAGGAGATGTCAAGGGAG	-	-	rs28647764	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190555264_190555291delCCTCCAGATTTAGGAGATGTCAAGGGAG								None (None upstream) : FRG1 (306683 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	190621246	190621247	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190621246_190621247insT								None (None upstream) : FRG1 (240727 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	190631428	190631428	+	IGR	DEL	G	-	-	rs5011623		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190631428delG								None (None upstream) : FRG1 (230546 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	190676953	190676954	+	IGR	INS	-	GTAGTGG	GTAGTGG	rs67595208		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190676953_190676954insGTAGTGG								None (None upstream) : FRG1 (185020 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	190827126	190827127	+	Intron	DEL	TA	-	-	rs148029614		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190827126_190827127delTA	uc003izq.2	-											Homo sapiens cDNA clone IMAGE:30384438.																														---	---	---	---
PLEKHG4B	153478	broad.mit.edu	37	5	173747	173748	+	Intron	INS	-	CAC	CAC	rs142627113	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173747_173748insCAC	uc003jak.2	+							NM_052909	NP_443141			pleckstrin homology domain containing, family G						regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			skin(2)	2			all cancers(22;0.0253)|Lung(60;0.113)	Kidney(1;0.119)														---	---	---	---
CEP72	55722	broad.mit.edu	37	5	649980	649981	+	Intron	INS	-	TG	TG	rs142053577		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:649980_649981insTG	uc003jbf.2	+							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)															---	---	---	---
NKD2	85409	broad.mit.edu	37	5	1026147	1026148	+	Intron	INS	-	A	A	rs66703602		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1026147_1026148insA	uc003jbt.1	+						NKD2_uc010itf.1_Intron	NM_033120	NP_149111			naked cuticle homolog 2						exocytosis|Wnt receptor signaling pathway	cytoplasmic membrane-bounded vesicle|plasma membrane	calcium ion binding|ubiquitin protein ligase binding				0	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09)		Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165)															---	---	---	---
SLC12A7	10723	broad.mit.edu	37	5	1081113	1081133	+	Intron	DEL	AGAGAGAGAGACAGACAGACA	-	-	rs70957325		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1081113_1081133delAGAGAGAGAGACAGACAGACA	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)													---	---	---	---
LOC728613	728613	broad.mit.edu	37	5	1603957	1603957	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1603957delT	uc003jcq.3	-						LOC728613_uc003jcp.3_Intron|LOC728613_uc003jcr.2_Intron|LOC728613_uc003jcs.2_Intron|LOC728613_uc010ith.1_Intron	NR_003713				Homo sapiens cDNA, FLJ97024.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	1936480	1936481	+	IGR	INS	-	T	T	rs138822797	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1936480_1936481insT								IRX4 (53600 upstream) : IRX2 (809800 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	3367454	3367457	+	IGR	DEL	AGTG	-	-	rs139447339		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3367454_3367457delAGTG								C5orf38 (611942 upstream) : IRX1 (228711 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	3382116	3382117	+	IGR	INS	-	AA	AA	rs111683412		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3382116_3382117insAA								C5orf38 (626604 upstream) : IRX1 (214051 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	3408999	3408999	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3408999delT								C5orf38 (653487 upstream) : IRX1 (187169 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	3488515	3488515	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3488515delA	uc003jdd.2	-											Homo sapiens cDNA clone IMAGE:4823480.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	3701104	3701106	+	IGR	DEL	TTC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3701104_3701106delTTC								IRX1 (99588 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	3716725	3716725	+	IGR	DEL	A	-	-	rs72287296		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3716725delA								IRX1 (115209 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	4623055	4623056	+	IGR	DEL	TT	-	-	rs72081762		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:4623055_4623056delTT								None (None upstream) : LOC340094 (411416 downstream)																																			---	---	---	---
LOC340094	340094	broad.mit.edu	37	5	5039016	5039016	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5039016delT	uc003jdg.2	+						LOC340094_uc003jdh.2_Intron	NR_026994				Homo sapiens hypothetical protein LOC340094, mRNA (cDNA clone IMAGE:5295461).												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	5836875	5836876	+	IGR	DEL	CC	-	-	rs58040354		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5836875_5836876delCC								KIAA0947 (346538 upstream) : FLJ33360 (473678 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	5988660	5988661	+	IGR	INS	-	AC	AC	rs148590057	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5988660_5988661insAC								KIAA0947 (498323 upstream) : FLJ33360 (321893 downstream)																																			---	---	---	---
FLJ33360	401172	broad.mit.edu	37	5	6322316	6322332	+	Intron	DEL	TGGGAACAGTCTCACAA	-	-	rs73736828	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6322316_6322332delTGGGAACAGTCTCACAA	uc003jdn.1	-							NM_001001702	NP_001001702			SubName: Full=FLJ33360 protein; SubName: Full=cDNA FLJ33360 fis, clone BRACE2005253;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	6699846	6699846	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6699846delG								SRD5A1 (30173 upstream) : PAPD7 (14872 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	7207149	7207157	+	IGR	DEL	TCCCTTCCT	-	-	rs111399864	byFrequency;by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7207149_7207157delTCCCTTCCT								PAPD7 (449988 upstream) : ADCY2 (189186 downstream)																																			---	---	---	---
ADCY2	108	broad.mit.edu	37	5	7434363	7434363	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7434363delA	uc003jdz.1	+							NM_020546	NP_065433			adenylate cyclase 2						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	cytoplasm|dendrite|integral to membrane|plasma membrane	ATP binding|metal ion binding			ovary(5)|pancreas(1)|skin(1)	7																		---	---	---	---
C5orf49	134121	broad.mit.edu	37	5	7840705	7840705	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7840705delG	uc003jea.3	-							NM_001089584	NP_001083053			hypothetical protein LOC134121												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	8497065	8497068	+	IGR	DEL	ACAG	-	-	rs57016068		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:8497065_8497068delACAG								MTRR (595832 upstream) : SEMA5A (538070 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	8541452	8541452	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:8541452delT								MTRR (640219 upstream) : SEMA5A (493686 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	8692255	8692256	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:8692255_8692256insT								MTRR (791022 upstream) : SEMA5A (342882 downstream)																																			---	---	---	---
SEMA5A	9037	broad.mit.edu	37	5	9291717	9291718	+	Intron	INS	-	AG	AG	rs142508804	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9291717_9291718insAG	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	9449697	9449698	+	Intron	DEL	AA	-	-	rs80078361		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9449697_9449698delAA	uc003jek.2	-							NM_003966	NP_003957			semaphorin 5A precursor						cell adhesion|cell-cell signaling	integral to membrane|plasma membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
LOC285692	285692	broad.mit.edu	37	5	9730923	9730923	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9730923delC	uc003jen.2	-							NR_027112				Homo sapiens clone TEE10 Cri-du-chat region mRNA.												0																		---	---	---	---
LOC285692	285692	broad.mit.edu	37	5	9825937	9825937	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9825937delT	uc003jen.2	-							NR_027112				Homo sapiens clone TEE10 Cri-du-chat region mRNA.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	10129801	10129801	+	IGR	DEL	A	-	-	rs79470926		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10129801delA								LOC285692 (225865 upstream) : FAM173B (96637 downstream)																																			---	---	---	---
MARCH6	10299	broad.mit.edu	37	5	10397692	10397693	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10397692_10397693delTT	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	10495521	10495523	+	IGR	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10495521_10495523delTTT								ROPN1L (30384 upstream) : DAP (183820 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	10523141	10523142	+	IGR	DEL	TG	-	-	rs10535296		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10523141_10523142delTG								ROPN1L (58004 upstream) : DAP (156201 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	10551719	10551719	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10551719delA								ROPN1L (86582 upstream) : DAP (127624 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	10962798	10962799	+	IGR	INS	-	AG	AG	rs144196101	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10962798_10962799insAG								DAP (201411 upstream) : CTNND2 (9153 downstream)																																			---	---	---	---
CTNND2	1501	broad.mit.edu	37	5	11259456	11259456	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:11259456delA	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	11312222	11312223	+	Intron	DEL	CA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:11312222_11312223delCA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	12333842	12333842	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:12333842delT								CTNND2 (429732 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	12489191	12489191	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:12489191delA								CTNND2 (585081 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	13385596	13385596	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13385596delA								None (None upstream) : DNAH5 (304841 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	14067494	14067496	+	IGR	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14067494_14067496delTTT								DNAH5 (122905 upstream) : TRIO (76333 downstream)																																			---	---	---	---
TRIO	7204	broad.mit.edu	37	5	14247172	14247172	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14247172delC	uc003jff.2	+						TRIO_uc003jfg.2_Intron|TRIO_uc011cna.1_Intron	NM_007118	NP_009049			triple functional domain (PTPRF interacting)						apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway	cytosol	ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|kidney(1)	18	Lung NSC(4;0.000742)																	---	---	---	---
TRIO	7204	broad.mit.edu	37	5	14265193	14265195	+	Intron	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14265193_14265195delTTT	uc003jff.2	+						TRIO_uc003jfg.2_Intron|TRIO_uc011cna.1_Intron	NM_007118	NP_009049			triple functional domain (PTPRF interacting)						apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway	cytosol	ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|kidney(1)	18	Lung NSC(4;0.000742)																	---	---	---	---
TRIO	7204	broad.mit.edu	37	5	14308893	14308894	+	Intron	INS	-	CCAACCAC	CCAACCAC	rs149330023	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14308893_14308894insCCAACCAC	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	14374173	14374173	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14374173delT	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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	5	15128349	15128349	+	IGR	DEL	T	-	-	rs71603770		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:15128349delT								ANKH (256462 upstream) : FBXL7 (371956 downstream)																																			---	---	---	---
FBXL7	23194	broad.mit.edu	37	5	15578425	15578425	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:15578425delG	uc003jfn.1	+							NM_012304	NP_036436			F-box and leucine-rich repeat protein 7						ubiquitin-dependent protein catabolic process	ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity			ovary(2)|lung(1)	3																		---	---	---	---
FBXL7	23194	broad.mit.edu	37	5	15774684	15774684	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:15774684delG	uc003jfn.1	+							NM_012304	NP_036436			F-box and leucine-rich repeat protein 7						ubiquitin-dependent protein catabolic process	ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity			ovary(2)|lung(1)	3																		---	---	---	---
FBXL7	23194	broad.mit.edu	37	5	15832599	15832599	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:15832599delA	uc003jfn.1	+							NM_012304	NP_036436			F-box and leucine-rich repeat protein 7						ubiquitin-dependent protein catabolic process	ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity			ovary(2)|lung(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	17332404	17332404	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17332404delA								BASP1 (55469 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	18056603	18056604	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:18056603_18056604delAA								BASP1 (779668 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	18161441	18161441	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:18161441delT								BASP1 (884506 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	18279706	18279706	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:18279706delT								None (None upstream) : None (None downstream)																																			---	---	---	---
CDH18	1016	broad.mit.edu	37	5	19518667	19518668	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19518667_19518668insA	uc003jgc.2	-						CDH18_uc003jgd.2_Intron|CDH18_uc011cnm.1_Intron	NM_004934	NP_004925			cadherin 18, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|large_intestine(1)|skin(1)	7	Lung NSC(1;0.00734)|all_lung(1;0.0197)																	---	---	---	---
CDH18	1016	broad.mit.edu	37	5	19709445	19709446	+	Intron	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19709445_19709446delTG	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	20973076	20973076	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:20973076delC								CDH18 (984769 upstream) : GUSBP1 (368866 downstream)																																			---	---	---	---
GUSBP1	728411	broad.mit.edu	37	5	21529100	21529104	+	Intron	DEL	CTCTT	-	-	rs66638629		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21529100_21529104delCTCTT	uc011cnn.1	+						GUSBP1_uc003jgh.3_Intron					Homo sapiens cDNA FLJ38337 fis, clone FCBBF3026692, moderately similar to Homo sapiens WD repeat domain 70 (WDR70), mRNA.												0																		---	---	---	---
GUSBP1	728411	broad.mit.edu	37	5	21557452	21557453	+	Intron	INS	-	TATATCTG	TATATCTG	rs112882822		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21557452_21557453insTATATCTG	uc003jgh.3	+							NR_027026				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	21564316	21564317	+	Intron	DEL	TC	-	-	rs150916520		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21564316_21564317delTC	uc003jgh.3	+							NR_027026				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	21579382	21579382	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21579382delC	uc003jgh.3	+							NR_027026				Homo sapiens cDNA FLJ38337 fis, clone FCBBF3026692, moderately similar to Homo sapiens WD repeat domain 70 (WDR70), mRNA.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	21651103	21651106	+	Intron	DEL	CTTC	-	-	rs72068262		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21651103_21651106delCTTC	uc003jgj.2	+											Homo sapiens, clone IMAGE:5171606, mRNA.																														---	---	---	---
CDH12	1010	broad.mit.edu	37	5	22077157	22077162	+	Intron	DEL	GTGTGT	-	-	rs35598688		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:22077157_22077162delGTGTGT	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	22202275	22202278	+	Intron	DEL	CCTC	-	-	rs72243697		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:22202275_22202278delCCTC	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	22622438	22622438	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:22622438delT	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	23026450	23026451	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:23026450_23026451insT								CDH12 (172719 upstream) : PRDM9 (481273 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	25159222	25159222	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:25159222delT								CDH10 (514311 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	26737008	26737008	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:26737008delA								None (None upstream) : CDH9 (143701 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	27625549	27625549	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:27625549delT								CDH9 (586860 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	27799060	27799067	+	IGR	DEL	AGCAAGAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:27799060_27799067delAGCAAGAA								CDH9 (760371 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	28579633	28579634	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:28579633_28579634delAA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	28705267	28705267	+	IGR	DEL	T	-	-	rs74583572	byFrequency;by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:28705267delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	29431910	29431910	+	IGR	DEL	A	-	-	rs34147754		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:29431910delA								None (None upstream) : None (None downstream)																																			---	---	---	---
RNASEN	29102	broad.mit.edu	37	5	31405766	31405766	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31405766delA	uc003jhg.2	-						RNASEN_uc003jhh.2_Intron	NM_013235	NP_037367			ribonuclease III, nuclear isoform 1						gene silencing by RNA|ribosome biogenesis|RNA processing	nucleolus|nucleoplasm	double-stranded RNA binding|metal ion binding|protein binding|ribonuclease III activity				0																		---	---	---	---
MTMR12	54545	broad.mit.edu	37	5	32233574	32233579	+	Intron	DEL	ACACAA	-	-	rs35760638		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32233574_32233579delACACAA	uc003jhq.2	-						MTMR12_uc010iuk.2_Intron|MTMR12_uc010iul.2_Intron	NM_001040446	NP_001035536			myotubularin related protein 12							cytoplasm	phosphatase activity			ovary(1)	1																		---	---	---	---
MTMR12	54545	broad.mit.edu	37	5	32308714	32308715	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32308714_32308715insT	uc003jhq.2	-						MTMR12_uc010iuk.2_Intron|MTMR12_uc010iul.2_Intron	NM_001040446	NP_001035536			myotubularin related protein 12							cytoplasm	phosphatase activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	32888053	32888053	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32888053delT								C5orf23 (96234 upstream) : TARS (552749 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	34236496	34236496	+	IGR	DEL	A	-	-	rs144323307		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34236496delA								C1QTNF3 (193179 upstream) : RAI14 (419937 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	34423404	34423404	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34423404delA								C1QTNF3 (380087 upstream) : RAI14 (233029 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	34602243	34602244	+	IGR	DEL	AA	-	-	rs10717898		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34602243_34602244delAA								C1QTNF3 (558926 upstream) : RAI14 (54189 downstream)																																			---	---	---	---
AGXT2	64902	broad.mit.edu	37	5	35046348	35046348	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35046348delG	uc003jjf.2	-						AGXT2_uc011com.1_Intron|AGXT2_uc011con.1_Intron	NM_031900	NP_114106			alanine-glyoxylate aminotransferase 2 precursor						glyoxylate metabolic process|pyrimidine base metabolic process|pyrimidine nucleoside catabolic process	mitochondrial matrix	(R)-3-amino-2-methylpropionate-pyruvate transaminase activity|alanine-glyoxylate transaminase activity|pyridoxal phosphate binding			ovary(3)|skin(1)	4	all_lung(31;4.52e-05)		COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)	GBM - Glioblastoma multiforme(108;0.181)	Glycine(DB00145)|L-Alanine(DB00160)|Pyridoxal Phosphate(DB00114)|Pyruvic acid(DB00119)													---	---	---	---
SPEF2	79925	broad.mit.edu	37	5	35693180	35693180	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35693180delG	uc003jjo.2	+						SPEF2_uc003jjq.3_Intron|SPEF2_uc003jjp.1_Intron	NM_024867	NP_079143			KPL2 protein isoform 1						nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		ATP binding|nucleobase, nucleoside, nucleotide kinase activity|protein dimerization activity			skin(2)|ovary(1)|central_nervous_system(1)	4	all_lung(31;7.56e-05)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)															---	---	---	---
SPEF2	79925	broad.mit.edu	37	5	35728052	35728052	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35728052delT	uc003jjo.2	+						SPEF2_uc003jjp.1_Intron	NM_024867	NP_079143			KPL2 protein isoform 1						nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		ATP binding|nucleobase, nucleoside, nucleotide kinase activity|protein dimerization activity			skin(2)|ovary(1)|central_nervous_system(1)	4	all_lung(31;7.56e-05)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)															---	---	---	---
SPEF2	79925	broad.mit.edu	37	5	35802177	35802178	+	Intron	DEL	AG	-	-	rs3061407		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35802177_35802178delAG	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	35816262	35816262	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35816262delT								SPEF2 (1550 upstream) : IL7R (40729 downstream)																																			---	---	---	---
IL7R	3575	broad.mit.edu	37	5	35860320	35860320	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35860320delT	uc003jjs.2	+						IL7R_uc011coo.1_Intron|IL7R_uc011cop.1_Intron	NM_002185	NP_002176			interleukin 7 receptor precursor						immune response|regulation of DNA recombination	extracellular region|integral to membrane	antigen binding|interleukin-7 receptor activity			ovary(3)|breast(1)|skin(1)	5	all_lung(31;0.00015)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.187)|Colorectal(62;0.202)															---	---	---	---
SKP2	6502	broad.mit.edu	37	5	36183774	36183774	+	Intron	DEL	T	-	-	rs141292010		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36183774delT	uc003jkd.2	+							NM_032637	NP_116026			S-phase kinase-associated protein 2 isoform 2						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell proliferation|G1/S transition of mitotic cell cycle|S phase of mitotic cell cycle	nucleoplasm|SCF ubiquitin ligase complex	protein binding			central_nervous_system(2)|ovary(1)|breast(1)	4	all_lung(31;5.63e-05)		Epithelial(62;0.0396)|Lung(74;0.111)|all cancers(62;0.115)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	36488676	36488677	+	IGR	INS	-	CTTT	CTTT	rs13177218	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36488676_36488677insCTTT								RANBP3L (186665 upstream) : SLC1A3 (117780 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	36601895	36601895	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36601895delT								RANBP3L (299884 upstream) : SLC1A3 (4562 downstream)																																			---	---	---	---
NUP155	9631	broad.mit.edu	37	5	37360587	37360587	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37360587delA	uc003jku.1	-						NUP155_uc003jkt.1_Intron|NUP155_uc010iuz.1_Intron	NM_153485	NP_705618			nucleoporin 155kDa isoform 1						carbohydrate metabolic process|glucose transport|mRNA transport|nucleocytoplasmic transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear membrane|nuclear pore	protein binding|structural constituent of nuclear pore|transporter activity			ovary(1)	1	all_lung(31;0.000137)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)															---	---	---	---
EGFLAM	133584	broad.mit.edu	37	5	38399029	38399029	+	Intron	DEL	G	-	-	rs113642316		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38399029delG	uc003jlc.1	+						EGFLAM_uc003jlb.1_Intron	NM_152403	NP_689616			EGF-like, fibronectin type III and laminin G							cell junction|proteinaceous extracellular matrix|synapse				pancreas(3)|skin(3)|ovary(1)	7	all_lung(31;0.000385)																	---	---	---	---
LIFR	3977	broad.mit.edu	37	5	38583777	38583777	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38583777delA	uc003jli.2	-						uc003jlj.2_Intron	NM_002310	NP_002301			leukemia inhibitory factor receptor precursor						positive regulation of cell proliferation	extracellular region|integral to plasma membrane	ciliary neurotrophic factor receptor binding|growth factor binding|leukemia inhibitory factor receptor activity			ovary(3)|large_intestine(1)	4	all_lung(31;0.00021)							T	PLAG1	salivary adenoma								---	---	---	---
Unknown	0	broad.mit.edu	37	5	39275847	39275847	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:39275847delT								FYB (5088 upstream) : C9 (8532 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	39868375	39868375	+	IGR	DEL	G	-	-	rs34204144		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:39868375delG								DAB2 (443040 upstream) : PTGER4 (811657 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	40862712	40862714	+	IGR	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40862712_40862714delTTT								CARD6 (7258 upstream) : C7 (46885 downstream)																																			---	---	---	---
PLCXD3	345557	broad.mit.edu	37	5	41471852	41471853	+	Intron	INS	-	A	A	rs150329176	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41471852_41471853insA	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	41507233	41507234	+	Intron	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41507233_41507234delAC	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																		---	---	---	---
GHR	2690	broad.mit.edu	37	5	42561836	42561836	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:42561836delT	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	5	43051783	43051783	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43051783delA								LOC153684 (6413 upstream) : ZNF131 (69202 downstream)																																			---	---	---	---
FGF10	2255	broad.mit.edu	37	5	44332085	44332085	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:44332085delA	uc003jog.1	-							NM_004465	NP_004456			fibroblast growth factor 10 precursor						actin cytoskeleton reorganization|activation of MAPK activity|bud outgrowth involved in lung branching|ERK1 and ERK2 cascade|fibroblast growth factor receptor signaling pathway involved in mammary gland specification|insulin receptor signaling pathway|lacrimal gland development|lung saccule development|mesonephros development|negative regulation of cell cycle arrest|positive regulation of ATPase activity|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of DNA repair|positive regulation of DNA replication|positive regulation of epithelial cell migration|positive regulation of epithelial cell proliferation involved in wound healing|positive regulation of ERK1 and ERK2 cascade|positive regulation of hair follicle cell proliferation|positive regulation of keratinocyte migration|positive regulation of keratinocyte proliferation|positive regulation of lymphocyte proliferation|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of Ras protein signal transduction|positive regulation of transcription, DNA-dependent|positive regulation of urothelial cell proliferation|protein localization at cell surface|radial glial cell differentiation|regulation of saliva secretion|response to protein stimulus|secretion by lung epithelial cell involved in lung growth|tear secretion|thymus development|urothelial cell proliferation	cell surface|extracellular space|nucleus|plasma membrane	chemoattractant activity|growth factor activity|heparin binding|type 2 fibroblast growth factor receptor binding			lung(3)	3	Lung NSC(6;1.12e-06)																	---	---	---	---
Unknown	0	broad.mit.edu	37	5	45124533	45124534	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:45124533_45124534delTT								MRPS30 (308919 upstream) : HCN1 (134819 downstream)																																			---	---	---	---
HCN1	348980	broad.mit.edu	37	5	45263045	45263045	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:45263045delT	uc003jok.2	-							NM_021072	NP_066550			hyperpolarization activated cyclic							integral to membrane	cAMP binding|sodium channel activity|voltage-gated potassium channel activity			ovary(1)	1																		---	---	---	---
PARP8	79668	broad.mit.edu	37	5	49983689	49983689	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:49983689delG	uc003jon.3	+						PARP8_uc011cpz.1_Intron|PARP8_uc003joo.2_Intron|PARP8_uc003jop.2_Intron	NM_024615	NP_078891			poly (ADP-ribose) polymerase family, member 8							intracellular	NAD+ ADP-ribosyltransferase activity			lung(3)|large_intestine(1)|ovary(1)	5		Lung NSC(810;0.0305)|Breast(144;0.222)																---	---	---	---
Unknown	0	broad.mit.edu	37	5	50440691	50440691	+	IGR	DEL	C	-	-	rs34180958		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:50440691delC								PARP8 (302522 upstream) : ISL1 (238267 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	50994602	50994603	+	IGR	INS	-	T	T	rs143188979	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:50994602_50994603insT								ISL1 (304045 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	51199400	51199400	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:51199400delA								ISL1 (508843 upstream) : ITGA1 (884374 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	51431265	51431265	+	IGR	DEL	A	-	-	rs11345650		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:51431265delA								ISL1 (740708 upstream) : ITGA1 (652509 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	51506798	51506798	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:51506798delT								ISL1 (816241 upstream) : ITGA1 (576976 downstream)																																			---	---	---	---
ITGA2	3673	broad.mit.edu	37	5	52303544	52303544	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:52303544delA	uc003joy.2	+						ITGA2_uc011cqa.1_Intron|ITGA2_uc011cqb.1_Intron|ITGA2_uc011cqc.1_Intron|ITGA2_uc011cqd.1_Intron|ITGA2_uc011cqe.1_Intron	NM_002203	NP_002194			integrin alpha 2 precursor						axon guidance|blood coagulation|cell-matrix adhesion|integrin-mediated signaling pathway|interspecies interaction between organisms|organ morphogenesis	integrin complex	collagen binding|identical protein binding|receptor activity			lung(1)	1		Lung NSC(810;3.11e-05)|Breast(144;0.014)|Prostate(461;0.0181)																---	---	---	---
Unknown	0	broad.mit.edu	37	5	52781991	52781991	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:52781991delA								FST (89 upstream) : NDUFS4 (74474 downstream)																																			---	---	---	---
NDUFS4	4724	broad.mit.edu	37	5	52884815	52884815	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:52884815delA	uc003jpe.2	+							NM_002495	NP_002486			NADH dehydrogenase (ubiquinone) Fe-S protein 4						brain development|cAMP-mediated signaling|mitochondrial electron transport, NADH to ubiquinone|mitochondrial respiratory chain complex I assembly|positive regulation of fibroblast proliferation|reactive oxygen species metabolic process|regulation of protein phosphorylation|response to cAMP|transport	mitochondrial respiratory chain complex I	NADH dehydrogenase (ubiquinone) activity			central_nervous_system(1)	1		Lung NSC(810;8.27e-05)|Breast(144;0.0848)			NADH(DB00157)													---	---	---	---
ARL15	54622	broad.mit.edu	37	5	53319364	53319364	+	Intron	DEL	A	-	-	rs71598892		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:53319364delA	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)																---	---	---	---
DHX29	54505	broad.mit.edu	37	5	54586202	54586202	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54586202delA	uc003jpx.2	-						DHX29_uc010ivw.2_Intron	NM_019030	NP_061903			DEAH (Asp-Glu-Ala-His) box polypeptide 29								ATP binding|ATP-dependent helicase activity|translation initiation factor activity			ovary(2)|central_nervous_system(1)|skin(1)	4		Lung NSC(810;4.08e-05)|Breast(144;0.0544)|Prostate(74;0.183)																---	---	---	---
SKIV2L2	23517	broad.mit.edu	37	5	54662536	54662536	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54662536delT	uc003jpy.3	+						SKIV2L2_uc011cqi.1_Intron	NM_015360	NP_056175			superkiller viralicidic activity 2-like 2						maturation of 5.8S rRNA	catalytic step 2 spliceosome|nucleolus	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			ovary(1)|skin(1)	2		Lung NSC(810;0.000744)|Breast(144;0.181)|Prostate(74;0.194)																---	---	---	---
SLC38A9	153129	broad.mit.edu	37	5	54923109	54923109	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54923109delA	uc003jqf.2	-						SLC38A9_uc003jqd.2_Intron|SLC38A9_uc010ivx.2_Intron|SLC38A9_uc003jqe.2_Intron|SLC38A9_uc010ivy.2_Intron	NM_173514	NP_775785			solute carrier family 38, member 9						amino acid transport|sodium ion transport	integral to membrane					0		Lung NSC(810;0.00122)|Prostate(74;0.0376)|Breast(144;0.181)																---	---	---	---
DDX4	54514	broad.mit.edu	37	5	55108421	55108422	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:55108421_55108422delAA	uc003jqg.3	+						DDX4_uc010ivz.2_Intron|DDX4_uc003jqh.3_Intron|DDX4_uc003jqj.2_Intron	NM_001136034	NP_001129506			DEAD (Asp-Glu-Ala-Asp) box polypeptide 4 isoform						multicellular organismal development|sperm motility	perinuclear region of cytoplasm|pi-body|piP-body	ATP binding|ATP-dependent helicase activity|nucleic acid binding			ovary(1)|skin(1)	2		Lung NSC(810;6.93e-05)|all_neural(839;0.00409)|Prostate(74;0.0107)|Breast(144;0.0544)|Ovarian(174;0.223)																---	---	---	---
Unknown	0	broad.mit.edu	37	5	55342420	55342420	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:55342420delT								IL6ST (51657 upstream) : ANKRD55 (53088 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	55754787	55754794	+	IGR	DEL	TTCCCTCC	-	-	rs138715660		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:55754787_55754794delTTCCCTCC								ANKRD55 (225601 upstream) : MAP3K1 (356106 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	56293871	56293872	+	IGR	DEL	AC	-	-	rs112687839		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56293871_56293872delAC								MIER3 (26370 upstream) : GPBP1 (175903 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	56399829	56399829	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56399829delA								MIER3 (132328 upstream) : GPBP1 (69946 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	56401157	56401158	+	IGR	DEL	TC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56401157_56401158delTC								MIER3 (133656 upstream) : GPBP1 (68617 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	56824229	56824229	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56824229delT								ACTBL2 (45593 upstream) : PLK2 (925583 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	57283040	57283040	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:57283040delT								ACTBL2 (504404 upstream) : PLK2 (466772 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	57475724	57475724	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:57475724delA								ACTBL2 (697088 upstream) : PLK2 (274088 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	57507655	57507658	+	IGR	DEL	AAAG	-	-	rs10608750		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:57507655_57507658delAAAG								ACTBL2 (729019 upstream) : PLK2 (242154 downstream)																																			---	---	---	---
PDE4D	5144	broad.mit.edu	37	5	59015997	59015997	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:59015997delT	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	59311839	59311840	+	Intron	DEL	TC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:59311839_59311840delTC	uc003jsb.2	-						PDE4D_uc010iwj.1_Intron|PDE4D_uc003jse.1_Intron	NM_006203	NP_006194			phosphodiesterase 4D isoform 2						signal transduction	cytosol|insoluble fraction|membrane|microtubule organizing center|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			breast(1)|central_nervous_system(1)	2		all_cancers(5;6.5e-58)|all_epithelial(5;1.75e-57)|all_lung(5;6.84e-18)|Lung NSC(5;1.29e-17)|Melanoma(5;0.00168)|Prostate(74;0.00234)|Colorectal(97;0.00629)|Ovarian(174;0.00832)|Breast(144;0.00996)|all_hematologic(6;0.0344)|Hepatocellular(6;0.0742)|Esophageal squamous(6;0.0954)		Epithelial(2;2.6e-55)|all cancers(2;2.66e-49)|OV - Ovarian serous cystadenocarcinoma(10;1.48e-39)|Colorectal(2;8.29e-08)|Lung(2;4.47e-07)|STAD - Stomach adenocarcinoma(2;1.11e-05)|COAD - Colon adenocarcinoma(2;0.00012)|LUSC - Lung squamous cell carcinoma(2;0.000775)|LUAD - Lung adenocarcinoma(3;0.0173)|READ - Rectum adenocarcinoma(2;0.0276)	Adenosine monophosphate(DB00131)|Dyphylline(DB00651)													---	---	---	---
Unknown	0	broad.mit.edu	37	5	60605744	60605744	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:60605744delA								C5orf43 (147442 upstream) : ZSWIM6 (22356 downstream)																																			---	---	---	---
ZSWIM6	57688	broad.mit.edu	37	5	60656060	60656060	+	Intron	DEL	A	-	-	rs66597914		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:60656060delA	uc003jsr.2	+							NM_020928	NP_065979			zinc finger, SWIM-type containing 6								zinc ion binding				0																		---	---	---	---
ZSWIM6	57688	broad.mit.edu	37	5	60693379	60693379	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:60693379delT	uc003jsr.2	+							NM_020928	NP_065979			zinc finger, SWIM-type containing 6								zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	61533523	61533526	+	IGR	DEL	ACAC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61533523_61533526delACAC								FLJ37543 (531161 upstream) : KIF2A (68463 downstream)																																			---	---	---	---
KIF2A	3796	broad.mit.edu	37	5	61613756	61613757	+	Intron	INS	-	A	A	rs138499765	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61613756_61613757insA	uc003jsy.3	+						KIF2A_uc003jsz.3_Intron|KIF2A_uc010iwp.2_Intron|KIF2A_uc003jsx.3_Intron	NM_004520	NP_004511			kinesin heavy chain member 2 isoform 1						blood coagulation|cell differentiation|cell division|microtubule-based movement|mitotic prometaphase|mitotic spindle organization|nervous system development	centrosome|cytosol|microtubule|spindle pole	ATP binding|microtubule motor activity|protein binding				0		Lung NSC(810;8.94e-06)|Prostate(74;0.0132)|Ovarian(174;0.051)|Breast(144;0.077)		Lung(70;0.14)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	62121290	62121291	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:62121290_62121291delTT								ISCA1P1 (48120 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	63999812	63999812	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:63999812delA								RGS7BP (91693 upstream) : SFRS12IP1 (14168 downstream)																																			---	---	---	---
ADAMTS6	11174	broad.mit.edu	37	5	64698796	64698796	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64698796delT	uc003jtp.2	-						ADAMTS6_uc003jto.2_Intron|ADAMTS6_uc003jtq.2_Intron|ADAMTS6_uc003jtr.1_Intron	NM_197941	NP_922932			ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding				0		Lung NSC(167;2.44e-06)|Prostate(74;0.014)|Ovarian(174;0.0549)|Breast(144;0.111)|Colorectal(97;0.235)		Lung(70;0.00942)														---	---	---	---
ADAMTS6	11174	broad.mit.edu	37	5	64773953	64773954	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64773953_64773954insA	uc003jtp.2	-						ADAMTS6_uc003jtq.2_Intron	NM_197941	NP_922932			ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding				0		Lung NSC(167;2.44e-06)|Prostate(74;0.014)|Ovarian(174;0.0549)|Breast(144;0.111)|Colorectal(97;0.235)		Lung(70;0.00942)														---	---	---	---
NLN	57486	broad.mit.edu	37	5	65068562	65068563	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:65068562_65068563delTT	uc003juf.2	+						NLN_uc003jue.2_Intron	NM_020726	NP_065777			neurolysin precursor						proteolysis	mitochondrial intermembrane space	metal ion binding|metalloendopeptidase activity			central_nervous_system(1)	1		Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0743)|Lung(70;0.00616)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	65173033	65173033	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:65173033delT								NLN (53646 upstream) : ERBB2IP (49351 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	65495568	65495568	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:65495568delA								SFRS12 (18856 upstream) : MAST4 (396608 downstream)																																			---	---	---	---
MAST4	375449	broad.mit.edu	37	5	66300755	66300755	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:66300755delT	uc003jut.1	+						MAST4_uc003jus.2_Intron|MAST4_uc003juu.1_Intron|MAST4_uc011cra.1_Intron|MAST4_uc010ixa.2_RNA|MAST4_uc003juv.2_5'UTR|MAST4_uc003juw.2_5'Flank	NM_015183	NP_055998			microtubule associated serine/threonine kinase							cytoplasm	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			lung(6)|ovary(2)|kidney(2)|breast(2)|central_nervous_system(1)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)														---	---	---	---
MAST4	375449	broad.mit.edu	37	5	66444870	66444870	+	Intron	DEL	G	-	-	rs150520121	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:66444870delG	uc003jut.1	+						MAST4_uc003juu.1_Intron|MAST4_uc011cra.1_Intron|MAST4_uc003juv.2_Intron|MAST4_uc003juw.2_Intron	NM_015183	NP_055998			microtubule associated serine/threonine kinase							cytoplasm	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			lung(6)|ovary(2)|kidney(2)|breast(2)|central_nervous_system(1)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	67105675	67105675	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:67105675delT								CD180 (613058 upstream) : PIK3R1 (405929 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	68086184	68086185	+	IGR	DEL	AG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:68086184_68086185delAG								PIK3R1 (488537 upstream) : SLC30A5 (303633 downstream)																																			---	---	---	---
SLC30A5	64924	broad.mit.edu	37	5	68420060	68420060	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:68420060delA	uc003jvh.2	+						SLC30A5_uc003jvj.2_Intron|SLC30A5_uc003jvk.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)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	68632608	68632608	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:68632608delA								CCDC125 (3988 upstream) : TAF9 (14947 downstream)																																			---	---	---	---
MCCC2	64087	broad.mit.edu	37	5	70939896	70939899	+	Intron	DEL	GTGC	-	-	rs71859051		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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)													---	---	---	---
MAP1B	4131	broad.mit.edu	37	5	71439688	71439689	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:71439688_71439689insT	uc003kbw.3	+						MAP1B_uc010iyw.1_Intron|MAP1B_uc010iyx.1_Intron	NM_005909	NP_005900			microtubule-associated protein 1B							microtubule|microtubule associated complex	structural molecule activity			large_intestine(2)|ovary(1)|central_nervous_system(1)|pancreas(1)	5		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)														---	---	---	---
PTCD2	79810	broad.mit.edu	37	5	71624447	71624447	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:71624447delT	uc003kcb.2	+						PTCD2_uc011csf.1_Intron|PTCD2_uc003kcc.2_Intron|PTCD2_uc011csg.1_Intron|PTCD2_uc011csh.1_Intron|PTCD2_uc003kcd.2_Intron	NM_024754	NP_079030			pentatricopeptide repeat domain 2												0		Lung NSC(167;0.00237)|Ovarian(174;0.0175)|Prostate(461;0.141)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;1.73e-53)														---	---	---	---
TNPO1	3842	broad.mit.edu	37	5	72182221	72182221	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72182221delT	uc003kck.3	+						TNPO1_uc011csj.1_Intron|TNPO1_uc003kch.2_Intron|TNPO1_uc003kci.3_Intron|TNPO1_uc003kcg.3_Intron	NM_002270	NP_002261			transportin 1 isoform 1						interspecies interaction between organisms|mRNA metabolic process|protein import into nucleus, translocation	cytosol|nucleus	nuclear localization sequence binding|protein binding|protein transporter activity			skin(3)|urinary_tract(1)|ovary(1)|kidney(1)|central_nervous_system(1)	7		Lung NSC(167;0.0053)|Ovarian(174;0.0175)		OV - Ovarian serous cystadenocarcinoma(47;6.14e-54)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	72215425	72215425	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72215425delA								TNPO1 (5211 upstream) : FCHO2 (36383 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	72246310	72246310	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72246310delA								TNPO1 (36096 upstream) : FCHO2 (5498 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	72600664	72600664	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72600664delT								TMEM174 (129696 upstream) : FOXD1 (141423 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	72603478	72603478	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72603478delT								TMEM174 (132510 upstream) : FOXD1 (138609 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	72770530	72770531	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72770530_72770531delTT								FOXD1 (26178 upstream) : BTF3 (23719 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	72884250	72884250	+	IGR	DEL	A	-	-	rs35594737		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72884250delA								UTP15 (6456 upstream) : RGNEF (37733 downstream)																																			---	---	---	---
RGNEF	64283	broad.mit.edu	37	5	73165740	73165740	+	Intron	DEL	C	-	-	rs66675411	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:73165740delC	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	73400411	73400412	+	IGR	INS	-	AC	AC	rs141408900	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:73400411_73400412insAC								RGNEF (162998 upstream) : ENC1 (522823 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	73521518	73521540	+	IGR	DEL	TCCTTTCCTTCCTTTCCCTCCTG	-	-	rs28553575		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:73521518_73521540delTCCTTTCCTTCCTTTCCCTCCTG								RGNEF (284105 upstream) : ENC1 (401695 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	73836358	73836358	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:73836358delA								RGNEF (598945 upstream) : ENC1 (86877 downstream)																																			---	---	---	---
COL4A3BP	10087	broad.mit.edu	37	5	74780133	74780133	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74780133delA	uc011csu.1	-						COL4A3BP_uc003kds.2_Intron|COL4A3BP_uc003kdt.2_Intron|COL4A3BP_uc003kdu.2_Intron	NM_005713	NP_005704			alpha 3 type IV collagen binding protein isoform						ER to Golgi ceramide transport|immune response	cytosol|endoplasmic reticulum membrane|Golgi apparatus	ceramide binding|phosphatidylinositol-4-phosphate binding|protein binding|protein kinase activity			skin(1)	1		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Prostate(461;0.174)		OV - Ovarian serous cystadenocarcinoma(47;1e-53)														---	---	---	---
AP3B1	8546	broad.mit.edu	37	5	77527352	77527352	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:77527352delA	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	77533638	77533638	+	Intron	DEL	A	-	-	rs76769186		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:77533638delA	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				---	---	---	---
ARSB	411	broad.mit.edu	37	5	78155542	78155542	+	Intron	DEL	A	-	-	rs146734031		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78155542delA	uc003kfq.2	-						ARSB_uc003kfr.3_Intron	NM_000046	NP_000037			arylsulfatase B isoform 1 precursor						lysosomal transport|lysosome organization	lysosome	arylsulfatase activity|metal ion binding|N-acetylgalactosamine-4-sulfatase activity			upper_aerodigestive_tract(1)	1		all_lung(232;0.000637)|Lung NSC(167;0.00173)|Ovarian(174;0.0105)|Prostate(461;0.192)		OV - Ovarian serous cystadenocarcinoma(54;4.24e-44)|Epithelial(54;3.12e-39)|all cancers(79;3.02e-34)														---	---	---	---
ARSB	411	broad.mit.edu	37	5	78217193	78217196	+	Intron	DEL	GTGT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78217193_78217196delGTGT	uc003kfq.2	-						ARSB_uc003kfr.3_Intron	NM_000046	NP_000037			arylsulfatase B isoform 1 precursor						lysosomal transport|lysosome organization	lysosome	arylsulfatase activity|metal ion binding|N-acetylgalactosamine-4-sulfatase activity			upper_aerodigestive_tract(1)	1		all_lung(232;0.000637)|Lung NSC(167;0.00173)|Ovarian(174;0.0105)|Prostate(461;0.192)		OV - Ovarian serous cystadenocarcinoma(54;4.24e-44)|Epithelial(54;3.12e-39)|all cancers(79;3.02e-34)														---	---	---	---
BHMT2	23743	broad.mit.edu	37	5	78378959	78378959	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78378959delA	uc003kft.2	+						BHMT2_uc011cth.1_Intron	NM_017614	NP_060084			betaine-homocysteine methyltransferase 2						methionine biosynthetic process	cytoplasm	betaine-homocysteine S-methyltransferase activity|homocysteine S-methyltransferase activity|zinc ion binding			ovary(1)	1		all_lung(232;0.00063)|Lung NSC(167;0.00171)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;2.09e-45)|Epithelial(54;9.3e-41)|all cancers(79;4.09e-36)	L-Methionine(DB00134)													---	---	---	---
SPZ1	84654	broad.mit.edu	37	5	79617569	79617569	+	3'UTR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79617569delT	uc003kgn.2	+	1					uc011ctk.1_RNA	NM_032567	NP_115956			spermatogenic leucine zipper 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding			ovary(1)	1		Lung NSC(167;0.0393)|all_lung(232;0.0428)|Ovarian(174;0.113)		OV - Ovarian serous cystadenocarcinoma(54;3.43e-47)|Epithelial(54;2.25e-41)|all cancers(79;4.19e-36)														---	---	---	---
MSH3	4437	broad.mit.edu	37	5	80045867	80045867	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80045867delT	uc003kgz.2	+							NM_002439	NP_002430			mutS homolog 3						maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments	MutSbeta complex|nuclear chromosome	ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding			lung(2)|ovary(1)|breast(1)	4		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)									MMR					---	---	---	---
RASGRF2	5924	broad.mit.edu	37	5	80317379	80317380	+	Intron	DEL	GT	-	-	rs34148067		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80317379_80317380delGT	uc003kha.1	+						RASGRF2_uc011ctn.1_Intron	NM_006909	NP_008840			Ras protein-specific guanine						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|synaptic transmission	cytosol|endoplasmic reticulum membrane|plasma membrane	protein binding|Rho guanyl-nucleotide exchange factor activity			breast(5)|ovary(3)|large_intestine(2)|central_nervous_system(1)|skin(1)	12		Lung NSC(167;0.00498)|all_lung(232;0.00531)|Ovarian(174;0.0357)		OV - Ovarian serous cystadenocarcinoma(54;4.22e-42)|Epithelial(54;4.04e-35)|all cancers(79;2.52e-29)														---	---	---	---
RNU5E	26829	broad.mit.edu	37	5	80582042	80582042	+	Intron	DEL	C	-	-	rs34551509		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80582042delC	uc011cto.1	+						uc003khe.1_Intron|uc003khf.1_Intron|uc003khg.1_Intron	NR_002754				Homo sapiens RNA, U5E small nuclear (RNU5E), non-coding RNA.												0																		---	---	---	---
XRCC4	7518	broad.mit.edu	37	5	82400057	82400057	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:82400057delT	uc003kib.2	+						XRCC4_uc003kia.1_Intron|XRCC4_uc003kid.2_Intron|XRCC4_uc003kic.2_Intron|XRCC4_uc003kie.2_Intron|XRCC4_uc003kif.1_5'Flank	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					---	---	---	---
XRCC4	7518	broad.mit.edu	37	5	82529884	82529884	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:82529884delT	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					---	---	---	---
HAPLN1	1404	broad.mit.edu	37	5	83014165	83014166	+	Intron	DEL	AG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:83014165_83014166delAG	uc003kin.2	-							NM_001884	NP_001875			hyaluronan and proteoglycan link protein 1						cell adhesion	proteinaceous extracellular matrix	hyaluronic acid binding			large_intestine(3)|ovary(1)|skin(1)	5		Lung NSC(167;0.0484)|all_lung(232;0.0522)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;7.82e-42)|Epithelial(54;5.88e-35)|all cancers(79;1.14e-29)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	83075237	83075238	+	IGR	INS	-	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:83075237_83075238insG								HAPLN1 (58341 upstream) : EDIL3 (162888 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	83138897	83138897	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:83138897delT								HAPLN1 (122001 upstream) : EDIL3 (99229 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	83730939	83730940	+	IGR	DEL	TG	-	-	rs148750287	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:83730939_83730940delTG								EDIL3 (50328 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	84790765	84790766	+	IGR	INS	-	AA	AA			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:84790765_84790766insAA								None (None upstream) : NBPF22P (787496 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	85519512	85519513	+	IGR	INS	-	C	C	rs146802232	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:85519512_85519513insC								None (None upstream) : NBPF22P (58749 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	86715331	86715331	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:86715331delC								CCNH (6495 upstream) : TMEM161B (775693 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	87152377	87152377	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87152377delC								CCNH (443541 upstream) : TMEM161B (338647 downstream)																																			---	---	---	---
LOC645323	645323	broad.mit.edu	37	5	87885191	87885191	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87885191delA	uc011cua.1	-							NR_015436				Homo sapiens cDNA FLJ34037 fis, clone FCBBF2005439.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	88417522	88417522	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:88417522delA								MEF2C (217653 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	88466140	88466140	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:88466140delA								MEF2C (266271 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	88713342	88713343	+	IGR	INS	-	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:88713342_88713343insG								MEF2C (513473 upstream) : CETN3 (976188 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	88893585	88893585	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:88893585delC								MEF2C (693716 upstream) : CETN3 (795946 downstream)																																			---	---	---	---
GPR98	84059	broad.mit.edu	37	5	90075086	90075086	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:90075086delT	uc003kju.2	+						GPR98_uc003kjt.2_Intron|GPR98_uc003kjw.2_5'Flank	NM_032119	NP_115495			G protein-coupled receptor 98 precursor						cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	90475765	90475772	+	IGR	DEL	GAAGGAAG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:90475765_90475772delGAAGGAAG								GPR98 (15733 upstream) : ARRDC3 (188769 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	90630406	90630406	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:90630406delT								GPR98 (170374 upstream) : ARRDC3 (34135 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	91805513	91805513	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:91805513delT								None (None upstream) : FLJ42709 (939552 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	91911973	91911975	+	IGR	DEL	TTC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:91911973_91911975delTTC								None (None upstream) : FLJ42709 (833090 downstream)																																			---	---	---	---
FAM172A	83989	broad.mit.edu	37	5	93338155	93338155	+	Intron	DEL	T	-	-	rs112863655		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:93338155delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	95039768	95039769	+	IGR	INS	-	AC	AC	rs151126784	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:95039768_95039769insAC								SPATA9 (21054 upstream) : RHOBTB3 (13568 downstream)																																			---	---	---	---
ELL2	22936	broad.mit.edu	37	5	95261881	95261884	+	Intron	DEL	AAAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:95261881_95261884delAAAA	uc003klr.3	-							NM_012081	NP_036213			elongation factor, RNA polymerase II, 2						regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter	transcription elongation factor complex				central_nervous_system(1)	1		all_cancers(142;2.04e-06)|all_epithelial(76;3.1e-09)|all_lung(232;0.00309)|Lung NSC(167;0.00454)|Ovarian(225;0.0165)|Colorectal(57;0.0343)|Breast(839;0.198)		all cancers(79;2.16e-15)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	95494017	95494018	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:95494017_95494018insT								MIR583 (79101 upstream) : PCSK1 (232101 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	95495849	95495850	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:95495849_95495850delAA								MIR583 (80933 upstream) : PCSK1 (230269 downstream)																																			---	---	---	---
PCSK1	5122	broad.mit.edu	37	5	95734920	95734920	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:95734920delA	uc003kls.1	-						PCSK1_uc010jbi.1_Intron	NM_000439	NP_000430			proprotein convertase subtilisin/kexin type 1						cell-cell signaling|cellular nitrogen compound metabolic process|energy reserve metabolic process|hormone biosynthetic process|peptide biosynthetic process|peptide hormone processing|regulation of insulin secretion	extracellular space|stored secretory granule|transport vesicle	serine-type endopeptidase activity			ovary(2)	2		all_cancers(142;2.67e-06)|all_epithelial(76;6.92e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0112)|Colorectal(57;0.0341)|Breast(839;0.244)		all cancers(79;3.44e-16)	Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)													---	---	---	---
Unknown	0	broad.mit.edu	37	5	96579686	96579687	+	IGR	DEL	TT	-	-	rs11303031		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96579686_96579687delTT								RIOK2 (60681 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	97707525	97707526	+	IGR	DEL	CA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:97707525_97707526delCA								None (None upstream) : RGMB (397473 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	97804879	97804879	+	IGR	DEL	A	-	-	rs111497651		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:97804879delA								None (None upstream) : RGMB (300120 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	97969721	97969721	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:97969721delA								None (None upstream) : RGMB (135278 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	98094751	98094751	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:98094751delT								None (None upstream) : RGMB (10248 downstream)																																			---	---	---	---
CHD1	1105	broad.mit.edu	37	5	98199049	98199051	+	Intron	DEL	AAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:98199049_98199051delAAA	uc003knf.2	-						CHD1_uc010jbn.2_Intron	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	98300195	98300195	+	IGR	DEL	A	-	-	rs114220345	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:98300195delA								CHD1 (37957 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	99050355	99050356	+	IGR	DEL	AA	-	-	rs35529645		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:99050355_99050356delAA								CHD1 (788117 upstream) : LOC100133050 (664853 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	99064740	99064741	+	IGR	DEL	TT	-	-	rs150539745	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:99064740_99064741delTT								CHD1 (802502 upstream) : LOC100133050 (650468 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	99446310	99446310	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:99446310delT								None (None upstream) : LOC100133050 (268899 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	101935326	101935326	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:101935326delT								SLCO6A1 (100606 upstream) : PAM (266201 downstream)																																			---	---	---	---
C5orf30	90355	broad.mit.edu	37	5	102609719	102609719	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:102609719delT	uc003kog.1	+						C5orf30_uc003koh.1_Intron	NM_033211	NP_149988			hypothetical protein LOC90355												0		all_cancers(142;2.22e-05)|all_epithelial(76;9.54e-08)|Prostate(80;0.0174)|Colorectal(57;0.0551)|Ovarian(225;0.11)|Lung NSC(167;0.136)|all_lung(232;0.18)		Epithelial(69;2.84e-14)|COAD - Colon adenocarcinoma(37;0.00762)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	104631526	104631526	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:104631526delA								RAB9BP1 (195728 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	105235730	105235730	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:105235730delA								RAB9BP1 (799932 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	105457040	105457040	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:105457040delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	105608471	105608473	+	IGR	DEL	AAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:105608471_105608473delAAA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	106288681	106288683	+	IGR	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:106288681_106288683delTTT								None (None upstream) : EFNA5 (423908 downstream)																																			---	---	---	---
EFNA5	1946	broad.mit.edu	37	5	106940854	106940854	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:106940854delG	uc003kol.2	-						EFNA5_uc010jbr.1_Intron	NM_001962	NP_001953			ephrin-A5 precursor						cell-cell signaling	anchored to plasma membrane|caveola|extracellular space	ephrin receptor binding				0		all_cancers(142;5.15e-06)|all_epithelial(76;4.39e-07)|Prostate(80;0.00726)|Lung NSC(167;0.0736)|Ovarian(225;0.0797)|all_lung(232;0.0854)|Colorectal(57;0.241)		Epithelial(69;1.25e-12)|OV - Ovarian serous cystadenocarcinoma(64;1.32e-11)|BRCA - Breast invasive adenocarcinoma(61;0.0376)|COAD - Colon adenocarcinoma(37;0.109)														---	---	---	---
FBXL17	64839	broad.mit.edu	37	5	107318712	107318712	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:107318712delT	uc011cvc.1	-						FBXL17_uc003kon.3_Intron	NM_001163315	NP_001156787			F-box and leucine-rich repeat protein 17												0		all_cancers(142;0.00273)|all_epithelial(76;0.000362)|Prostate(80;0.0115)|Myeloproliferative disorder(839;0.0393)|Ovarian(225;0.232)		OV - Ovarian serous cystadenocarcinoma(64;9.63e-11)|Epithelial(69;4.02e-10)														---	---	---	---
FBXL17	64839	broad.mit.edu	37	5	107714042	107714042	+	Intron	DEL	G	-	-	rs35486124		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:107714042delG	uc011cvc.1	-							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)														---	---	---	---
FER	2241	broad.mit.edu	37	5	108114712	108114714	+	Intron	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:108114712_108114714delTTT	uc003kop.1	+						FER_uc011cve.1_Intron|FER_uc011cvf.1_Intron|FER_uc003koq.2_Intron|FER_uc011cvg.1_Intron	NM_005246	NP_005237			fer (fps/fes related) tyrosine kinase						intracellular signal transduction|peptidyl-tyrosine phosphorylation	cytoplasm|nucleus	ATP binding|non-membrane spanning protein tyrosine kinase activity			lung(2)|stomach(1)|ovary(1)|kidney(1)	5		all_cancers(142;2.86e-06)|all_epithelial(76;9.81e-08)|Prostate(80;0.00972)|Lung NSC(167;0.039)|Ovarian(225;0.0448)|all_lung(232;0.0496)|Colorectal(57;0.0986)|Breast(839;0.152)		OV - Ovarian serous cystadenocarcinoma(64;6.77e-10)|Epithelial(69;4.13e-08)|COAD - Colon adenocarcinoma(37;0.0174)														---	---	---	---
FER	2241	broad.mit.edu	37	5	108371448	108371448	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:108371448delA	uc003kop.1	+						FER_uc011cvg.1_Intron	NM_005246	NP_005237			fer (fps/fes related) tyrosine kinase						intracellular signal transduction|peptidyl-tyrosine phosphorylation	cytoplasm|nucleus	ATP binding|non-membrane spanning protein tyrosine kinase activity			lung(2)|stomach(1)|ovary(1)|kidney(1)	5		all_cancers(142;2.86e-06)|all_epithelial(76;9.81e-08)|Prostate(80;0.00972)|Lung NSC(167;0.039)|Ovarian(225;0.0448)|all_lung(232;0.0496)|Colorectal(57;0.0986)|Breast(839;0.152)		OV - Ovarian serous cystadenocarcinoma(64;6.77e-10)|Epithelial(69;4.13e-08)|COAD - Colon adenocarcinoma(37;0.0174)														---	---	---	---
FER	2241	broad.mit.edu	37	5	108503723	108503726	+	Intron	DEL	GAAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:108503723_108503726delGAAA	uc003kop.1	+						FER_uc011cvg.1_Intron	NM_005246	NP_005237			fer (fps/fes related) tyrosine kinase						intracellular signal transduction|peptidyl-tyrosine phosphorylation	cytoplasm|nucleus	ATP binding|non-membrane spanning protein tyrosine kinase activity			lung(2)|stomach(1)|ovary(1)|kidney(1)	5		all_cancers(142;2.86e-06)|all_epithelial(76;9.81e-08)|Prostate(80;0.00972)|Lung NSC(167;0.039)|Ovarian(225;0.0448)|all_lung(232;0.0496)|Colorectal(57;0.0986)|Breast(839;0.152)		OV - Ovarian serous cystadenocarcinoma(64;6.77e-10)|Epithelial(69;4.13e-08)|COAD - Colon adenocarcinoma(37;0.0174)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	108754965	108754965	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:108754965delT								PJA2 (9290 upstream) : MAN2A1 (270191 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	108914274	108914274	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:108914274delT								PJA2 (168599 upstream) : MAN2A1 (110882 downstream)																																			---	---	---	---
TMEM232	642987	broad.mit.edu	37	5	109754869	109754869	+	Intron	DEL	T	-	-	rs79497254		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:109754869delT	uc003kow.1	-						TMEM232_uc003kov.1_Intron|TMEM232_uc003kox.2_Intron	NM_001039763	NP_001034852			transmembrane protein 232							integral to membrane					0																		---	---	---	---
TMEM232	642987	broad.mit.edu	37	5	109822757	109822757	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:109822757delT	uc011cvh.1	-						TMEM232_uc003kow.1_Intron|TMEM232_uc003kox.2_Intron|TMEM232_uc010jbs.2_Intron|TMEM232_uc003koy.3_Intron					SubName: Full=cDNA FLJ54480;							integral to membrane					0																		---	---	---	---
EPB41L4A	64097	broad.mit.edu	37	5	111523915	111523915	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:111523915delT	uc003kpv.1	-						EPB41L4A_uc003kpp.1_Intron	NM_022140	NP_071423			erythrocyte protein band 4.1-like 4							cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding			ovary(1)	1		all_cancers(142;4.93e-06)|all_epithelial(76;2.28e-08)|Prostate(80;0.000244)|Colorectal(10;0.000788)|Ovarian(225;0.0448)|Lung NSC(167;0.126)|all_lung(232;0.135)		OV - Ovarian serous cystadenocarcinoma(64;6.24e-09)|Epithelial(69;1.43e-07)|all cancers(49;2.78e-05)|COAD - Colon adenocarcinoma(37;0.0467)|Colorectal(14;0.0791)														---	---	---	---
EPB41L4A	64097	broad.mit.edu	37	5	111592985	111592986	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:111592985_111592986insA	uc003kpv.1	-							NM_022140	NP_071423			erythrocyte protein band 4.1-like 4							cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding			ovary(1)	1		all_cancers(142;4.93e-06)|all_epithelial(76;2.28e-08)|Prostate(80;0.000244)|Colorectal(10;0.000788)|Ovarian(225;0.0448)|Lung NSC(167;0.126)|all_lung(232;0.135)		OV - Ovarian serous cystadenocarcinoma(64;6.24e-09)|Epithelial(69;1.43e-07)|all cancers(49;2.78e-05)|COAD - Colon adenocarcinoma(37;0.0467)|Colorectal(14;0.0791)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	111900937	111900937	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:111900937delA								FLJ11235 (144264 upstream) : APC (142281 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	111962758	111962758	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:111962758delT								FLJ11235 (206085 upstream) : APC (80460 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	111982616	111982617	+	IGR	INS	-	T	T	rs146372813	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:111982616_111982617insT								FLJ11235 (225943 upstream) : APC (60601 downstream)																																			---	---	---	---
DCP2	167227	broad.mit.edu	37	5	112336117	112336118	+	Intron	INS	-	CC	CC	rs138314846	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112336117_112336118insCC	uc003kqh.2	+						DCP2_uc011cwa.1_Intron|DCP2_uc010jcc.2_Intron	NM_152624	NP_689837			DCP2 decapping enzyme						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|histone mRNA catabolic process|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	cytoplasmic mRNA processing body|cytosol|nucleus|RNA-induced silencing complex	exoribonuclease activity, producing 5'-phosphomonoesters|manganese ion binding|protein binding|protein binding|RNA 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)		OV - Ovarian serous cystadenocarcinoma(64;6.98e-08)|Epithelial(69;7.87e-08)|all cancers(49;1.06e-05)|COAD - Colon adenocarcinoma(37;0.0123)|Colorectal(14;0.0171)														---	---	---	---
MCC	4163	broad.mit.edu	37	5	112437238	112437238	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112437238delT	uc003kqj.3	-						MCC_uc003kqk.3_Intron|MCC_uc003kql.3_Intron|MCC_uc011cwb.1_Intron|MCC_uc010jcd.1_Intron	NM_002387	NP_002378			mutated in colorectal cancers isoform 2						negative regulation of canonical Wnt receptor signaling pathway|negative regulation of epithelial cell migration|negative regulation of epithelial cell proliferation|Wnt receptor signaling pathway	cytoplasm|nucleus|plasma membrane	protein binding|receptor activity			ovary(1)	1		all_cancers(142;5.89e-08)|all_epithelial(76;3.57e-11)|all_lung(232;0.000605)|Lung NSC(810;0.000697)|Colorectal(10;0.00146)|Prostate(80;0.00174)|Ovarian(225;0.0175)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(64;2.04e-54)|Epithelial(69;9.69e-49)|all cancers(49;6.25e-44)|COAD - Colon adenocarcinoma(37;0.0432)|Colorectal(14;0.0766)														---	---	---	---
MCC	4163	broad.mit.edu	37	5	112601936	112601937	+	Intron	DEL	AC	-	-	rs72346279		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112601936_112601937delAC	uc003kqj.3	-						MCC_uc003kqk.3_Intron|MCC_uc003kql.3_Intron|MCC_uc011cwb.1_Intron|MCC_uc010jcd.1_Intron	NM_002387	NP_002378			mutated in colorectal cancers isoform 2						negative regulation of canonical Wnt receptor signaling pathway|negative regulation of epithelial cell migration|negative regulation of epithelial cell proliferation|Wnt receptor signaling pathway	cytoplasm|nucleus|plasma membrane	protein binding|receptor activity			ovary(1)	1		all_cancers(142;5.89e-08)|all_epithelial(76;3.57e-11)|all_lung(232;0.000605)|Lung NSC(810;0.000697)|Colorectal(10;0.00146)|Prostate(80;0.00174)|Ovarian(225;0.0175)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(64;2.04e-54)|Epithelial(69;9.69e-49)|all cancers(49;6.25e-44)|COAD - Colon adenocarcinoma(37;0.0432)|Colorectal(14;0.0766)														---	---	---	---
TRIM36	55521	broad.mit.edu	37	5	114509220	114509221	+	Intron	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:114509220_114509221delTG	uc003kqs.2	-						TRIM36_uc003kqt.2_Intron|TRIM36_uc003kqu.2_Intron	NM_018700	NP_061170			tripartite motif-containing 36 isoform 1							acrosomal vesicle|cytoskeleton	ligase activity|zinc ion binding			ovary(4)|lung(2)|breast(2)	8		all_cancers(142;0.00133)|all_epithelial(76;2.41e-05)|Prostate(80;0.00955)|Ovarian(225;0.0443)|Breast(839;0.195)		OV - Ovarian serous cystadenocarcinoma(64;3.62e-08)|Epithelial(69;7.69e-08)|all cancers(49;9.33e-06)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	114719822	114719822	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:114719822delA								CCDC112 (87364 upstream) : FEM1C (136786 downstream)																																			---	---	---	---
AP3S1	1176	broad.mit.edu	37	5	115195023	115195023	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115195023delT	uc003krl.2	+						AP3S1_uc003krk.2_Intron|AP3S1_uc003krm.2_Intron	NM_001284	NP_001275			adaptor-related protein complex 3, sigma 1						insulin receptor signaling pathway|intracellular protein transport|vesicle-mediated transport	AP-type membrane coat adaptor complex|cytoplasmic vesicle membrane|Golgi apparatus|transport vesicle	protein binding|protein transporter activity				0		all_cancers(142;0.00377)|all_epithelial(76;0.000129)|Prostate(80;0.0132)|Ovarian(225;0.0776)|Lung NSC(810;0.245)		OV - Ovarian serous cystadenocarcinoma(64;1.08e-07)|Epithelial(69;1.11e-06)|all cancers(49;5.2e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	115712492	115712492	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115712492delT								COMMD10 (83514 upstream) : SEMA6A (66760 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	116024079	116024082	+	IGR	DEL	CTAC	-	-	rs2933613		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:116024079_116024082delCTAC								SEMA6A (113528 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	116099604	116099604	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:116099604delT								SEMA6A (189053 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	116142470	116142470	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:116142470delA								SEMA6A (231919 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	116872063	116872064	+	Intron	DEL	TC	-	-	rs72365266		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:116872063_116872064delTC	uc003kry.2	+											Homo sapiens cDNA clone IMAGE:5297581.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	117900806	117900807	+	IGR	DEL	AC	-	-	rs112558032		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:117900806_117900807delAC								None (None upstream) : DTWD2 (271764 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	119014150	119014150	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:119014150delT								FAM170A (42634 upstream) : PRR16 (785869 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	119044445	119044445	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:119044445delG								FAM170A (72929 upstream) : PRR16 (755574 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	119475226	119475226	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:119475226delC								FAM170A (503710 upstream) : PRR16 (324793 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	119579245	119579245	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:119579245delC								FAM170A (607729 upstream) : PRR16 (220774 downstream)																																			---	---	---	---
PRR16	51334	broad.mit.edu	37	5	119839337	119839338	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:119839337_119839338delTT	uc003ksq.2	+						PRR16_uc003ksp.2_Intron	NM_016644	NP_057728			proline rich 16											pancreas(2)|ovary(1)	3		all_cancers(142;0.0464)|Prostate(80;0.00446)	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.000126)|Epithelial(69;0.000331)|all cancers(49;0.00169)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	120882034	120882037	+	IGR	DEL	TTTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:120882034_120882037delTTTT								PRR16 (859072 upstream) : FTMT (305613 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	121547499	121547499	+	IGR	DEL	A	-	-	rs113136044		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:121547499delA								ZNF474 (58242 upstream) : SNCAIP (99887 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	121836843	121836843	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:121836843delT								SNCAIP (37049 upstream) : SNX2 (273907 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	122077550	122077550	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122077550delC								SNCAIP (277756 upstream) : SNX2 (33200 downstream)																																			---	---	---	---
CEP120	153241	broad.mit.edu	37	5	122722368	122722368	+	Intron	DEL	T	-	-	rs34328840		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122722368delT	uc003ktk.2	-						CEP120_uc011cwq.1_Intron|CEP120_uc010jcz.1_Intron	NM_153223	NP_694955			coiled-coil domain containing 100							centrosome				ovary(1)	1																		---	---	---	---
CSNK1G3	1456	broad.mit.edu	37	5	122864736	122864736	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122864736delC	uc003ktm.2	+						CSNK1G3_uc003ktl.2_Intron|CSNK1G3_uc003ktn.2_Intron|CSNK1G3_uc003kto.2_Intron|CSNK1G3_uc011cwr.1_Intron|CSNK1G3_uc011cws.1_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)														---	---	---	---
CSNK1G3	1456	broad.mit.edu	37	5	122929252	122929252	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122929252delC	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	123771996	123771997	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:123771996_123771997delAA								CSNK1G3 (819534 upstream) : ZNF608 (200613 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	123802900	123802900	+	IGR	DEL	A	-	-	rs78019088		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:123802900delA								CSNK1G3 (850438 upstream) : ZNF608 (169710 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	124968704	124968704	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:124968704delT								ZNF608 (884204 upstream) : GRAMD3 (727084 downstream)																																			---	---	---	---
PHAX	51808	broad.mit.edu	37	5	125949468	125949468	+	Intron	DEL	T	-	-	rs77157717		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:125949468delT	uc003kua.1	+							NM_032177	NP_115553			RNA U, small nuclear RNA export adaptor						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	126188917	126188918	+	3'UTR	INS	-	T	T	rs145868030	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:126188917_126188918insT	uc003kue.1	+	1										Homo sapiens cDNA FLJ36242 fis, clone THYMU2001727.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	126900763	126900763	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:126900763delA								PRRC1 (9985 upstream) : CTXN3 (83950 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	128661182	128661184	+	IGR	DEL	TCT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:128661182_128661184delTCT								ISOC1 (211465 upstream) : ADAMTS19 (134919 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	129711139	129711139	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:129711139delT								CHSY3 (188813 upstream) : HINT1 (783736 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	130018962	130018962	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:130018962delC								CHSY3 (496636 upstream) : HINT1 (475913 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	130102266	130102267	+	IGR	DEL	AA	-	-	rs11401591		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:130102266_130102267delAA								CHSY3 (579940 upstream) : HINT1 (392608 downstream)																																			---	---	---	---
CDC42SE2	56990	broad.mit.edu	37	5	130611795	130611796	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:130611795_130611796delTT	uc003kvh.2	+						CDC42SE2_uc003kvi.2_Intron|CDC42SE2_uc003kvj.2_Intron|CDC42SE2_uc003kvk.2_Intron	NM_020240	NP_064625			CDC42 small effector 2						phagocytosis|regulation of cell shape|regulation of signal transduction	cell projection|cytoplasm|cytoskeleton|phagocytic cup	protein binding|structural molecule activity				0		all_cancers(142;0.0525)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)															---	---	---	---
RAPGEF6	51735	broad.mit.edu	37	5	130806636	130806636	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:130806636delG	uc003kvn.1	-						RAPGEF6_uc003kvp.1_Intron|RAPGEF6_uc003kvo.1_Intron|RAPGEF6_uc010jdi.1_Intron|RAPGEF6_uc010jdj.1_Intron|RAPGEF6_uc003kvq.2_Intron|RAPGEF6_uc003kvr.2_Intron|RAPGEF6_uc011cxe.1_Intron|RAPGEF6_uc010jdk.2_Intron	NM_016340	NP_057424			PDZ domain-containing guanine nucleotide						Ras protein signal transduction|regulation of GTPase activity|regulation of small GTPase mediated signal transduction	cytoplasm|plasma membrane	GTP-dependent protein binding|guanyl-nucleotide exchange factor activity|Ras GTPase binding			ovary(1)|lung(1)|central_nervous_system(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)														---	---	---	---
RAPGEF6	51735	broad.mit.edu	37	5	130860303	130860312	+	Intron	DEL	GAGAGAGAGA	-	-	rs10537194		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:130860303_130860312delGAGAGAGAGA	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	131017456	131017456	+	Intron	DEL	A	-	-	rs71643734		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131017456delA	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	132323853	132323854	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132323853_132323854insT								AFF4 (24499 upstream) : ZCCHC10 (8826 downstream)																																			---	---	---	---
HSPA4	3308	broad.mit.edu	37	5	132385767	132385772	+	5'Flank	DEL	AAACTG	-	-	rs11276809		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132385767_132385772delAAACTG	uc003kyj.2	+							NM_002154	NP_002145			heat shock 70kDa protein 4						cellular chaperone-mediated protein complex assembly|protein import into mitochondrial outer membrane|response to unfolded protein	cytoplasm|nucleus	ATP binding			lung(1)|breast(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)															---	---	---	---
HSPA4	3308	broad.mit.edu	37	5	132395140	132395143	+	Intron	DEL	AAAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132395140_132395143delAAAA	uc003kyj.2	+							NM_002154	NP_002145			heat shock 70kDa protein 4						cellular chaperone-mediated protein complex assembly|protein import into mitochondrial outer membrane|response to unfolded protein	cytoplasm|nucleus	ATP binding			lung(1)|breast(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)															---	---	---	---
CDKL3	51265	broad.mit.edu	37	5	133542939	133542939	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133542939delA	uc011cxm.1	-						CDKL3_uc011cxn.1_Intron|PPP2CA_uc003kze.2_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	133971543	133971543	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133971543delA								SAR1B (3016 upstream) : SEC24A (12936 downstream)																																			---	---	---	---
DDX46	9879	broad.mit.edu	37	5	134112082	134112082	+	Intron	DEL	A	-	-	rs74390283		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134112082delA	uc003kzw.2	+						DDX46_uc003kzv.1_Intron	NM_014829	NP_055644			DEAD (Asp-Glu-Ala-Asp) box polypeptide 46						mRNA processing|RNA splicing	Cajal body|nuclear speck	ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)															---	---	---	---
CXCL14	9547	broad.mit.edu	37	5	134908732	134908732	+	Intron	DEL	A	-	-	rs111277613		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	135132673	135132673	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:135132673delC								LOC340074 (143049 upstream) : LOC153328 (37692 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	135333410	135333410	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:135333410delT								LECT2 (42687 upstream) : TGFBI (31174 downstream)																																			---	---	---	---
SMAD5	4090	broad.mit.edu	37	5	135487494	135487494	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:135487494delT	uc003lbj.1	+						SMAD5_uc003lbk.1_Intron|SMAD5_uc003lbl.1_Intron	NM_001001419	NP_001001419			SMAD family member 5						BMP signaling pathway|embryonic pattern specification|positive regulation of transcription, DNA-dependent|transforming growth factor beta receptor signaling pathway	cytosol|integral to membrane|transcription factor complex	sequence-specific DNA binding transcription factor activity|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity|ubiquitin protein ligase binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)															---	---	---	---
TRPC7	57113	broad.mit.edu	37	5	135582913	135582913	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:135582913delT	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	135793513	135793513	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:135793513delA								TRPC7 (100440 upstream) : SPOCK1 (517475 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	136213874	136213875	+	IGR	INS	-	A	A	rs146219650	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:136213874_136213875insA								TRPC7 (520801 upstream) : SPOCK1 (97113 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	136274628	136274629	+	IGR	INS	-	A	A	rs148444887	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:136274628_136274629insA								TRPC7 (581555 upstream) : SPOCK1 (36359 downstream)																																			---	---	---	---
FAM13B	51306	broad.mit.edu	37	5	137311670	137311671	+	Intron	DEL	TT	-	-	rs72408638		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137311670_137311671delTT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	138057061	138057062	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138057061_138057062delTT								HSPA9 (145946 upstream) : CTNNA1 (32045 downstream)																																			---	---	---	---
CTNNA1	1495	broad.mit.edu	37	5	138145546	138145547	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138145546_138145547insT	uc003ldh.2	+						CTNNA1_uc011cyx.1_Intron|CTNNA1_uc011cyy.1_Intron|CTNNA1_uc003ldi.2_Intron|CTNNA1_uc003ldj.2_Intron	NM_001903	NP_001894			catenin, alpha 1						adherens junction organization|apical junction assembly|cell adhesion|cellular response to indole-3-methanol|muscle cell differentiation|positive regulation of muscle cell differentiation	actin cytoskeleton|catenin complex|cytosol	beta-catenin binding|cadherin binding|gamma-catenin binding|structural molecule activity|vinculin binding			breast(6)|ovary(2)|large_intestine(2)|kidney(1)	11			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	139094475	139094476	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139094475_139094476delTT								CXXC5 (31795 upstream) : PSD2 (80930 downstream)																																			---	---	---	---
PSD2	84249	broad.mit.edu	37	5	139193288	139193288	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139193288delG	uc003leu.1	+	3	971	c.766delG	c.(766-768)GGGfs	p.G256fs		NM_032289	NP_115665	Q9BQI7	PSD2_HUMAN	pleckstrin and Sec7 domain containing 2	256					regulation of ARF protein signal transduction	cytoplasm|integral to membrane	ARF guanyl-nucleotide exchange factor activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	139432068	139432068	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139432068delA								NRG2 (9189 upstream) : PURA (61640 downstream)																																			---	---	---	---
C5orf32	84418	broad.mit.edu	37	5	139606352	139606352	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139606352delA	uc003lfd.2	+						C5orf32_uc010jfi.2_Intron	NM_032412	NP_115788			hypothetical protein LOC84418												0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
ANKHD1-EIF4EBP3	404734	broad.mit.edu	37	5	139912683	139912683	+	Intron	DEL	A	-	-	rs113564152		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139912683delA	uc003lfs.1	+						ANKHD1_uc003lfr.2_Intron|ANKHD1-EIF4EBP3_uc011czh.1_Intron|ANKHD1_uc003lfw.2_Intron|ANKHD1_uc010jfl.2_Intron|ANKHD1-EIF4EBP3_uc003lfx.1_Intron	NM_020690	NP_065741			ANKHD1-EIF4EBP3 protein							cytoplasm|nucleus	RNA binding			ovary(6)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
IK	3550	broad.mit.edu	37	5	140039476	140039476	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140039476delC	uc003lgq.2	+							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)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	140113265	140113265	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140113265delT								VTRNA1-3 (7434 upstream) : PCDHA1 (52611 downstream)																																			---	---	---	---
PCDHGA11	56105	broad.mit.edu	37	5	140803318	140803318	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140803318delG	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)															---	---	---	---
DIAPH1	1729	broad.mit.edu	37	5	140895486	140895486	+	3'UTR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140895486delT	uc003llb.3	-	29					DIAPH1_uc011dbd.1_3'UTR|DIAPH1_uc003llc.3_3'UTR	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)															---	---	---	---
KIAA0141	9812	broad.mit.edu	37	5	141304316	141304317	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141304316_141304317delTT	uc003lls.2	+						KIAA0141_uc003llt.2_Intron	NM_001142603	NP_001136075			hypothetical protein LOC9812 precursor						apoptosis|regulation of caspase activity	mitochondrion	protein binding			skin(1)	1		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	141862013	141862013	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141862013delG								SPRY4 (157393 upstream) : FGF1 (109731 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	141949123	141949123	+	IGR	DEL	A	-	-	rs11744900	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141949123delA								SPRY4 (244503 upstream) : FGF1 (22621 downstream)																																			---	---	---	---
FGF1	2246	broad.mit.edu	37	5	141982284	141982284	+	Intron	DEL	T	-	-	rs79833552		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141982284delT	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	142315674	142315677	+	Intron	DEL	ACAC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142315674_142315677delACAC	uc011dbj.1	+						ARHGAP26_uc003lmt.2_Intron|ARHGAP26_uc003lmw.2_Intron	NM_015071	NP_055886			GTPase regulator associated with the focal						actin cytoskeleton organization|filopodium assembly|nervous system development|small GTPase mediated signal transduction	cytoskeleton|cytosol|focal adhesion	cytoskeletal adaptor activity|Rho GTPase activator activity|SH3 domain binding			ovary(1)	1		all_hematologic(541;0.0416)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
NR3C1	2908	broad.mit.edu	37	5	142661045	142661045	+	3'UTR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142661045delG	uc003lmz.2	-	9					NR3C1_uc003lmy.2_3'UTR|NR3C1_uc003lna.2_Intron|NR3C1_uc003lnb.2_3'UTR|NR3C1_uc011dbk.1_3'UTR|NR3C1_uc003lnc.2_3'UTR|NR3C1_uc003lnd.2_3'UTR|NR3C1_uc003lne.2_3'UTR|NR3C1_uc003lnf.2_3'UTR	NM_000176	NP_000167			glucocorticoid receptor isoform alpha						chromatin modification|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to protein stimulus|transcription from RNA polymerase II promoter	mitochondrial matrix|nucleoplasm	glucocorticoid receptor activity|protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid binding|zinc ion binding			ovary(2)	2		Acute lymphoblastic leukemia(2;3.2e-05)|all_hematologic(2;0.000361)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)		Amcinonide(DB00288)|Betamethasone(DB00443)|Budesonide(DB01222)|Dexamethasone(DB01234)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluticasone Propionate(DB00588)|Hydrocortamate(DB00769)|Hydrocortisone(DB00741)|Loteprednol Etabonate(DB00873)|Methylprednisolone(DB00959)|Mifepristone(DB00834)|Mometasone(DB00764)|Prednisone(DB00635)													---	---	---	---
Unknown	0	broad.mit.edu	37	5	143057283	143057287	+	IGR	DEL	CTTTT	-	-	rs146946594		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:143057283_143057287delCTTTT								NR3C1 (242206 upstream) : HMHB1 (134439 downstream)																																			---	---	---	---
YIPF5	81555	broad.mit.edu	37	5	143540266	143540266	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:143540266delT	uc003lnk.3	-						YIPF5_uc003lnl.3_Intron|YIPF5_uc010jgl.2_Intron	NM_001024947	NP_001020118			Yip1 domain family, member 5						protein transport|vesicle-mediated transport	endoplasmic reticulum membrane|ER to Golgi transport vesicle|Golgi cisterna membrane|integral to membrane				ovary(1)|skin(1)	2		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)															---	---	---	---
KCTD16	57528	broad.mit.edu	37	5	143650194	143650194	+	Intron	DEL	A	-	-	rs144140440		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:143650194delA	uc003lnm.1	+						KCTD16_uc003lnn.1_Intron	NM_020768	NP_065819			potassium channel tetramerisation domain							cell junction|postsynaptic membrane|presynaptic membrane|voltage-gated potassium channel complex	voltage-gated potassium channel activity			large_intestine(2)|ovary(1)|skin(1)	4		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)															---	---	---	---
KCTD16	57528	broad.mit.edu	37	5	143656465	143656467	+	Intron	DEL	AAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:143656465_143656467delAAA	uc003lnm.1	+						KCTD16_uc003lnn.1_Intron	NM_020768	NP_065819			potassium channel tetramerisation domain							cell junction|postsynaptic membrane|presynaptic membrane|voltage-gated potassium channel complex	voltage-gated potassium channel activity			large_intestine(2)|ovary(1)|skin(1)	4		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	144026911	144026912	+	IGR	DEL	GT	-	-	rs71971298		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:144026911_144026912delGT								KCTD16 (169967 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	144876435	144876435	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:144876435delT								None (None upstream) : PRELID2 (262147 downstream)																																			---	---	---	---
PRELID2	153768	broad.mit.edu	37	5	145144578	145144578	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145144578delA	uc003lnp.1	-						PRELID2_uc003lnq.1_Intron|PRELID2_uc003lno.1_Intron	NM_182960	NP_892005			PRELI domain containing 2 isoform a												0			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
STK32A	202374	broad.mit.edu	37	5	146742487	146742488	+	Intron	INS	-	T	T	rs143439919	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:146742487_146742488insT	uc010jgn.1	+						STK32A_uc003lom.2_Intron|STK32A_uc011dbw.1_Intron	NM_001112724	NP_001106195			serine/threonine kinase 32A isoform 1								ATP binding|metal ion binding|protein serine/threonine kinase activity			lung(2)|skin(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
JAKMIP2	9832	broad.mit.edu	37	5	147081897	147081898	+	Intron	INS	-	ACTAC	ACTAC	rs148992180	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147081897_147081898insACTAC	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	147714275	147714276	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147714275_147714276delAA	uc003lpb.1	-						SPINK9_uc003lpe.1_5'Flank					Homo sapiens cDNA FLJ30191 fis, clone BRACE2001313.																														---	---	---	---
HTR4	3360	broad.mit.edu	37	5	147993977	147993977	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147993977delA	uc003lpn.2	-						HTR4_uc010jgu.1_Intron|HTR4_uc003lpi.1_Intron|HTR4_uc003lpj.1_Intron|HTR4_uc003lpk.2_Intron|HTR4_uc011dby.1_Intron|HTR4_uc003lpl.2_Intron|HTR4_uc003lpm.2_Intron|HTR4_uc010jgv.2_Intron|HTR4_uc003lpo.1_Intron|SH3TC2_uc003lpp.1_Intron	NM_000870	NP_000861			serotonin 5-HT4 receptor isoform b						G-protein signaling, coupled to cyclic nucleotide second messenger|positive regulation of cell proliferation	endosome|integral to plasma membrane|membrane fraction	serotonin receptor activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Cisapride(DB00604)|Rizatriptan(DB00953)|Tegaserod(DB01079)|Zolmitriptan(DB00315)													---	---	---	---
SH3TC2	79628	broad.mit.edu	37	5	148085913	148085913	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148085913delA	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	148321603	148321604	+	Intron	INS	-	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148321603_148321604insG	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	148399677	148399678	+	Intron	DEL	AC	-	-	rs62378236		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148399677_148399678delAC	uc003lpu.2	-						SH3TC2_uc003lpp.1_Intron|SH3TC2_uc010jgw.2_Intron|SH3TC2_uc003lps.2_Intron|SH3TC2_uc003lpt.2_Intron|SH3TC2_uc010jgx.2_Intron	NM_024577	NP_078853			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	148438130	148438130	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148438130delT	uc003lpu.2	-						SH3TC2_uc003lpp.1_Intron|SH3TC2_uc003lpt.2_Intron|SH3TC2_uc010jgx.2_Intron|SH3TC2_uc003lpv.1_Intron|SH3TC2_uc011dbz.1_Intron|SH3TC2_uc003lpw.1_Intron	NM_024577	NP_078853			SH3 domain and tetratricopeptide repeats 2								binding			ovary(2)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
CSNK1A1	1452	broad.mit.edu	37	5	148884875	148884875	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148884875delT	uc003lqx.1	-						CSNK1A1_uc011dcb.1_Intron|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	148924822	148924822	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148924822delT	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)														---	---	---	---
ARHGEF37	389337	broad.mit.edu	37	5	148987018	148987018	+	Intron	DEL	A	-	-	rs73798249	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148987018delA	uc003lra.1	+							NM_001001669	NP_001001669			hypothetical protein LOC389337						regulation of Rho protein signal transduction	cytoplasm	Rho guanyl-nucleotide exchange factor activity				0																		---	---	---	---
PDE6A	5145	broad.mit.edu	37	5	149323596	149323596	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149323596delT	uc003lrg.3	-							NM_000440	NP_000431			phosphodiesterase 6A						cytosolic calcium ion homeostasis|GMP metabolic process|platelet activation|signal transduction|visual perception	cytosol|plasma membrane	3',5'-cyclic-GMP phosphodiesterase activity|metal ion binding			ovary(1)|pancreas(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	149809499	149809499	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149809499delG								CD74 (17167 upstream) : RPS14 (14295 downstream)																																			---	---	---	---
ANXA6	309	broad.mit.edu	37	5	150503138	150503138	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150503138delT	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)															---	---	---	---
GM2A	2760	broad.mit.edu	37	5	150785902	150785902	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150785902delA	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)															---	---	---	---
ATOX1	475	broad.mit.edu	37	5	151123327	151123327	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:151123327delT	uc003luk.2	-							NM_004045	NP_004036			antioxidant protein 1						cellular copper ion homeostasis|copper ion transport|response to oxidative stress	cytosol	copper chaperone activity|copper-dependent protein binding				0		Medulloblastoma(196;0.091)|all_hematologic(541;0.103)	Kidney(363;0.000171)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)															---	---	---	---
G3BP1	10146	broad.mit.edu	37	5	151153905	151153905	+	Intron	DEL	T	-	-	rs77366512		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:151153905delT	uc003lun.2	+						G3BP1_uc010jhy.1_Intron|G3BP1_uc003lum.2_Intron|G3BP1_uc011dcu.1_Intron|G3BP1_uc010jhz.2_Intron	NM_005754	NP_005745			Ras-GTPase-activating protein SH3-domain-binding						Ras protein signal transduction|transport	cytosol|nucleus|plasma membrane	ATP binding|ATP-dependent DNA helicase activity|ATP-dependent RNA helicase activity|DNA binding|endonuclease activity|protein binding|RNA binding			skin(3)|ovary(1)	4		all_hematologic(541;0.0338)|Medulloblastoma(196;0.091)	Kidney(363;0.000171)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)															---	---	---	---
GLRA1	2741	broad.mit.edu	37	5	151288218	151288218	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:151288218delT	uc003lut.2	-						GLRA1_uc003lur.2_Intron|GLRA1_uc003lus.2_Intron	NM_001146040	NP_001139512			glycine receptor, alpha 1 isoform 1 precursor						muscle contraction|negative regulation of transmission of nerve impulse|neuropeptide signaling pathway|positive regulation of acrosome reaction|regulation of membrane potential|startle response	cell junction|chloride channel complex|integral to plasma membrane|intracellular membrane-bounded organelle|postsynaptic membrane	extracellular-glycine-gated chloride channel activity|glycine binding|protein binding|receptor activity|taurine binding|transmitter-gated ion channel activity			ovary(1)|central_nervous_system(1)	2		all_hematologic(541;0.0341)|Medulloblastoma(196;0.0912)	Kidney(363;0.000171)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Desflurane(DB01189)|Enflurane(DB00228)|Ethanol(DB00898)|Glycine(DB00145)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)													---	---	---	---
Unknown	0	broad.mit.edu	37	5	151728108	151728109	+	IGR	INS	-	CA	CA	rs145347475	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:151728108_151728109insCA								GLRA1 (423711 upstream) : NMUR2 (42993 downstream)																																			---	---	---	---
SAP30L	79685	broad.mit.edu	37	5	153832303	153832304	+	Intron	INS	-	GCCCTTCCCACT	GCCCTTCCCACT	rs112253650		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153832303_153832304insGCCCTTCCCACT	uc003lvk.2	+						SAP30L_uc003lvm.3_Intron|SAP30L_uc011ddc.1_Intron|SAP30L_uc011ddd.1_Intron	NM_024632	NP_078908			SAP30-like isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	DNA binding|metal ion binding				0	Renal(175;0.00488)	Medulloblastoma(196;0.0523)	Kidney(363;8.21e-05)|KIRC - Kidney renal clear cell carcinoma(527;0.000577)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	154028242	154028243	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154028242_154028243delAA								HAND1 (170418 upstream) : MIR1303 (37093 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	154069623	154069623	+	IGR	DEL	A	-	-	rs36087779		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154069623delA								MIR1303 (4202 upstream) : LARP1 (22839 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	154650995	154650995	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154650995delA								KIF4B (253310 upstream) : SGCD (484068 downstream)																																			---	---	---	---
TIMD4	91937	broad.mit.edu	37	5	156376457	156376467	+	Intron	DEL	CCTCCTCCTTC	-	-	rs138233412	by1000genomes;by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156376457_156376467delCCTCCTCCTTC	uc003lwh.2	-						TIMD4_uc010jii.2_Intron	NM_138379	NP_612388			T-cell immunoglobulin and mucin domain							integral to membrane				ovary(2)	2	Renal(175;0.00488)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)															---	---	---	---
TIMD4	91937	broad.mit.edu	37	5	156379301	156379303	+	Intron	DEL	AAA	-	-	rs77759806		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156379301_156379303delAAA	uc003lwh.2	-						TIMD4_uc010jii.2_Intron	NM_138379	NP_612388			T-cell immunoglobulin and mucin domain							integral to membrane				ovary(2)	2	Renal(175;0.00488)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)															---	---	---	---
CYFIP2	26999	broad.mit.edu	37	5	156768572	156768572	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156768572delA	uc003lwq.2	+						CYFIP2_uc011ddn.1_Intron|CYFIP2_uc011ddo.1_Intron|CYFIP2_uc003lwr.2_Intron|CYFIP2_uc003lws.2_Intron|CYFIP2_uc003lwt.2_Intron|CYFIP2_uc011ddp.1_Intron	NM_001037333	NP_001032410			cytoplasmic FMR1 interacting protein 2						apoptosis|cell-cell adhesion	cell junction|perinuclear region of cytoplasm|synapse|synaptosome	protein binding				0	Renal(175;0.00212)	Medulloblastoma(196;0.0306)|all_neural(177;0.0897)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)															---	---	---	---
ADAM19	8728	broad.mit.edu	37	5	156904863	156904864	+	3'UTR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156904863_156904864insA	uc003lwz.2	-	23					ADAM19_uc003lww.1_Intron|ADAM19_uc003lwy.2_Intron	NM_033274	NP_150377			ADAM metallopeptidase domain 19 preproprotein						proteolysis	integral to membrane	metalloendopeptidase activity|SH3 domain binding|zinc ion binding			ovary(3)|large_intestine(2)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	8	Renal(175;0.00488)	Medulloblastoma(196;0.0359)|all_neural(177;0.14)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	157462044	157462044	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:157462044delT								CLINT1 (175876 upstream) : EBF1 (660880 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	157827180	157827180	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:157827180delG								CLINT1 (541012 upstream) : EBF1 (295744 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	157836097	157836097	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:157836097delT								CLINT1 (549929 upstream) : EBF1 (286827 downstream)																																			---	---	---	---
EBF1	1879	broad.mit.edu	37	5	158458182	158458182	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:158458182delA	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								---	---	---	---
Unknown	0	broad.mit.edu	37	5	158657353	158657353	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:158657353delA								RNF145 (20292 upstream) : UBLCP1 (32736 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	159553263	159553264	+	IGR	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159553263_159553264delTG								PWWP2A (6811 upstream) : FABP6 (61110 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	159605022	159605022	+	IGR	DEL	T	-	-	rs78560760		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159605022delT								PWWP2A (58570 upstream) : FABP6 (9352 downstream)																																			---	---	---	---
FABP6	2172	broad.mit.edu	37	5	159650440	159650441	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159650440_159650441insT	uc003lxx.1	+						FABP6_uc003lxz.1_Intron	NM_001130958	NP_001124430			gastrotropin isoform 1						bile acid and bile salt transport|bile acid metabolic process|negative regulation of cell proliferation	cytosol	transporter activity				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)															---	---	---	---
ATP10B	23120	broad.mit.edu	37	5	160017570	160017570	+	Intron	DEL	T	-	-	rs67835553		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160017570delT	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	160108630	160108631	+	Intron	INS	-	AA	AA			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160108630_160108631insAA	uc003lym.1	-						ATP10B_uc003lyp.2_Intron|ATP10B_uc011deg.1_Intron|ATP10B_uc003lyo.2_Intron	NM_025153	NP_079429			ATPase, class V, type 10B						ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(3)|central_nervous_system(1)|pancreas(1)	5	Renal(175;0.00196)	Medulloblastoma(196;0.0377)|all_neural(177;0.121)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	160309955	160309955	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160309955delA								ATP10B (30736 upstream) : LOC285629 (48833 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	160358346	160358346	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160358346delC								ATP10B (79127 upstream) : LOC285629 (442 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	161647467	161647467	+	IGR	DEL	A	-	-	rs35391432		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:161647467delA								GABRG2 (64923 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	162089292	162089292	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:162089292delT								GABRG2 (506748 upstream) : CCNG1 (775285 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	163223064	163223064	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:163223064delT								MAT2B (276731 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	163304250	163304250	+	IGR	DEL	G	-	-	rs290135	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:163304250delG								MAT2B (357917 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	164128236	164128237	+	IGR	INS	-	A	A	rs34372588		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:164128236_164128237insA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	164219373	164219374	+	IGR	DEL	TG	-	-	rs62383687		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:164219373_164219374delTG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	164318467	164318467	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:164318467delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	164861220	164861221	+	IGR	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:164861220_164861221delTG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	165174870	165174871	+	IGR	INS	-	A	A	rs33917576		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:165174870_165174871insA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	165327235	165327236	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:165327235_165327236delTT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	165418665	165418666	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:165418665_165418666delTT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	165642996	165642996	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:165642996delT								None (None upstream) : None (None downstream)																																			---	---	---	---
ODZ2	57451	broad.mit.edu	37	5	166873619	166873619	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:166873619delT	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	167342232	167342232	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167342232delA	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	167488974	167488974	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167488974delA	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	167550629	167550629	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167550629delC	uc010jjd.2	+						ODZ2_uc003lzr.3_Intron|ODZ2_uc003lzt.3_Intron|ODZ2_uc010jje.2_5'Flank|uc003lzs.1_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)														---	---	---	---
RARS	5917	broad.mit.edu	37	5	167944139	167944139	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167944139delT	uc003lzx.2	+						RARS_uc011deo.1_Intron	NM_002887	NP_002878			arginyl-tRNA synthetase						arginyl-tRNA aminoacylation	cytosol|nucleus|soluble fraction	arginine-tRNA ligase activity|ATP binding|protein binding			ovary(2)|skin(1)	3	Renal(175;0.000159)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0208)|all_neural(177;0.0227)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0693)|Epithelial(171;0.131)|OV - Ovarian serous cystadenocarcinoma(192;0.156)														---	---	---	---
SLIT3	6586	broad.mit.edu	37	5	168324422	168324423	+	Intron	DEL	GA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168324422_168324423delGA	uc003mab.2	-						SLIT3_uc010jjg.2_Intron|SLIT3_uc010jji.2_Intron	NM_003062	NP_003053			slit homolog 3 precursor						apoptosis involved in luteolysis|axon extension involved in axon guidance|cellular response to hormone stimulus|negative chemotaxis|negative regulation of cell growth|negative regulation of chemokine-mediated signaling pathway|response to cortisol stimulus|Roundabout signaling pathway	extracellular space|mitochondrion	calcium ion binding|Roundabout binding			ovary(3)|skin(1)	4	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)															---	---	---	---
KCNMB1	3779	broad.mit.edu	37	5	169809945	169809948	+	Intron	DEL	AAGG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169809945_169809948delAAGG	uc003maq.1	-						KCNIP1_uc003map.2_Intron|KCNMB1_uc003mar.2_3'UTR	NM_004137	NP_004128			potassium large conductance calcium-activated						platelet activation|synaptic transmission		calcium-activated potassium channel activity|potassium channel regulator activity			ovary(2)	2	Renal(175;0.000159)|Lung NSC(126;0.0165)|all_lung(126;0.026)	Medulloblastoma(196;0.0109)|all_neural(177;0.0146)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.175)														---	---	---	---
KCNIP1	30820	broad.mit.edu	37	5	169977014	169977015	+	Intron	INS	-	T	T	rs147960731	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169977014_169977015insT	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)															---	---	---	---
GABRP	2568	broad.mit.edu	37	5	170235947	170235947	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170235947delT	uc003mau.2	+						GABRP_uc011dev.1_Intron	NM_014211	NP_055026			gamma-aminobutyric acid (GABA) A receptor, pi							cell junction|chloride channel complex|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			breast(1)	1	Renal(175;0.000159)|Lung NSC(126;0.0122)|all_lung(126;0.0193)	Medulloblastoma(196;0.0109)|all_neural(177;0.0298)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	170264230	170264230	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170264230delT								GABRP (23182 upstream) : RANBP17 (24792 downstream)																																			---	---	---	---
RANBP17	64901	broad.mit.edu	37	5	170595849	170595850	+	Intron	DEL	TC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170595849_170595850delTC	uc003mba.2	+						RANBP17_uc003max.1_Intron|RANBP17_uc003may.1_Intron|RANBP17_uc003maz.1_Intron|RANBP17_uc010jjr.1_Intron|RANBP17_uc003mbb.2_Intron	NM_022897	NP_075048			RAN binding protein 17						mRNA transport|protein import into nucleus|transmembrane transport	cytoplasm|nuclear pore	GTP binding|protein transporter activity			ovary(2)|central_nervous_system(1)	3	Renal(175;0.000159)|Lung NSC(126;0.00751)|all_lung(126;0.0123)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)					T	TRD@	ALL								---	---	---	---
Unknown	0	broad.mit.edu	37	5	171054459	171054459	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171054459delT								FGF18 (170297 upstream) : FBXW11 (234097 downstream)																																			---	---	---	---
FBXW11	23291	broad.mit.edu	37	5	171300935	171300935	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171300935delT	uc003mbm.1	-						FBXW11_uc011dey.1_Intron|FBXW11_uc003mbl.1_Intron|FBXW11_uc003mbn.1_Intron	NM_012300	NP_036432			F-box and WD repeat domain containing 11 isoform						cell cycle|negative regulation of transcription, DNA-dependent|positive regulation of circadian rhythm|positive regulation of proteolysis|positive regulation of transcription, DNA-dependent|protein dephosphorylation|protein destabilization|protein polyubiquitination|rhythmic process|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway	centrosome|cytosol|nucleus|SCF ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity			ovary(1)|breast(1)	2	Renal(175;0.000159)|Lung NSC(126;0.00384)|all_lung(126;0.00659)	Medulloblastoma(196;0.00853)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)															---	---	---	---
STK10	6793	broad.mit.edu	37	5	171516398	171516401	+	Intron	DEL	ATGG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171516398_171516401delATGG	uc003mbo.1	-							NM_005990	NP_005981			serine/threonine kinase 10								ATP binding|protein serine/threonine kinase activity			ovary(3)|lung(2)|testis(1)|breast(1)|pancreas(1)	8	Renal(175;0.000159)|Lung NSC(126;0.0056)|all_lung(126;0.0094)	Medulloblastoma(196;0.00868)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)															---	---	---	---
STK10	6793	broad.mit.edu	37	5	171570380	171570380	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171570380delA	uc003mbo.1	-							NM_005990	NP_005981			serine/threonine kinase 10								ATP binding|protein serine/threonine kinase activity			ovary(3)|lung(2)|testis(1)|breast(1)|pancreas(1)	8	Renal(175;0.000159)|Lung NSC(126;0.0056)|all_lung(126;0.0094)	Medulloblastoma(196;0.00868)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)															---	---	---	---
STK10	6793	broad.mit.edu	37	5	171589438	171589439	+	Intron	INS	-	CT	CT			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171589438_171589439insCT	uc003mbo.1	-							NM_005990	NP_005981			serine/threonine kinase 10								ATP binding|protein serine/threonine kinase activity			ovary(3)|lung(2)|testis(1)|breast(1)|pancreas(1)	8	Renal(175;0.000159)|Lung NSC(126;0.0056)|all_lung(126;0.0094)	Medulloblastoma(196;0.00868)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)															---	---	---	---
UBTD2	92181	broad.mit.edu	37	5	171688634	171688635	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171688634_171688635insT	uc003mbp.1	-							NM_152277	NP_689490			dendritic cell-derived ubiquitin-like protein							cytoplasm					0	Renal(175;0.000159)|Lung NSC(126;0.00976)|all_lung(126;0.0156)	Medulloblastoma(196;0.00853)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	172175498	172175499	+	IGR	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172175498_172175499delAC								NEURL1B (56967 upstream) : DUSP1 (19603 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	172178243	172178244	+	IGR	INS	-	AAGG	AAGG	rs28532090		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172178243_172178244insAAGG								NEURL1B (59712 upstream) : DUSP1 (16858 downstream)																																			---	---	---	---
ERGIC1	57222	broad.mit.edu	37	5	172260089	172260090	+	5'Flank	INS	-	TGAATGAATGAA	TGAATGAATGAA	rs138167077	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172260089_172260090insTGAATGAATGAA	uc003mbw.3	+							NM_001031711	NP_001026881			endoplasmic reticulum-golgi intermediate						ER to Golgi vesicle-mediated transport	endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|Golgi membrane|integral to membrane	protein binding			skin(2)|ovary(1)	3	Renal(175;0.000159)|Lung NSC(126;0.00344)|all_lung(126;0.00594)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)															---	---	---	---
ATP6V0E1	8992	broad.mit.edu	37	5	172410147	172410148	+	5'Flank	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172410147_172410148delTT	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	172563230	172563231	+	3'UTR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172563230_172563231insA	uc003mch.2	+	9						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	172692898	172692898	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172692898delT								NKX2-5 (30636 upstream) : STC2 (48828 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	172736105	172736105	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172736105delC								NKX2-5 (73843 upstream) : STC2 (5621 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	173189288	173189289	+	IGR	INS	-	G	G	rs71611196	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173189288_173189289insG								BOD1 (145622 upstream) : CPEB4 (126042 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	173577983	173577983	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173577983delG								HMP19 (41802 upstream) : MSX2 (573592 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	173838587	173838590	+	IGR	DEL	AGGG	-	-	rs150170750		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173838587_173838590delAGGG								HMP19 (302406 upstream) : MSX2 (312985 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	173868363	173868364	+	IGR	INS	-	A	A	rs138886824	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173868363_173868364insA								HMP19 (332182 upstream) : MSX2 (283211 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	173985987	173986002	+	IGR	DEL	TCCCTCCCTCCTTCCT	-	-	rs62394620		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173985987_173986002delTCCCTCCCTCCTTCCT								HMP19 (449806 upstream) : MSX2 (165573 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	174057591	174057591	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174057591delT								HMP19 (521410 upstream) : MSX2 (93984 downstream)																																			---	---	---	---
MSX2	4488	broad.mit.edu	37	5	174149061	174149062	+	5'Flank	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174149061_174149062delAA	uc003mcy.2	+							NM_002449	NP_002440			msh homeobox 2						cranial suture morphogenesis|negative regulation of transcription, DNA-dependent|osteoblast differentiation	cytoplasm|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding				0	Renal(175;0.000159)|Lung NSC(126;0.0196)|all_lung(126;0.0303)	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	174243230	174243231	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174243230_174243231delTT								MSX2 (85329 upstream) : DRD1 (624445 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	174309726	174309726	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174309726delT								MSX2 (151825 upstream) : DRD1 (557950 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	174510631	174510631	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174510631delG								MSX2 (352730 upstream) : DRD1 (357045 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	174630466	174630466	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174630466delA								MSX2 (472565 upstream) : DRD1 (237210 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	174812028	174812047	+	IGR	DEL	AAGGAAAGAAGGAAGGAAGA	-	-	rs111559272		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174812028_174812047delAAGGAAAGAAGGAAGGAAGA								MSX2 (654127 upstream) : DRD1 (55629 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	175188084	175188084	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175188084delC								HRH2 (74841 upstream) : CPLX2 (35526 downstream)																																			---	---	---	---
FAF2	23197	broad.mit.edu	37	5	175882077	175882077	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175882077delA	uc003mej.3	+							NM_014613	NP_055428			UBX domain containing 8						response to unfolded protein	endoplasmic reticulum|lipid particle	protein binding			ovary(1)	1																		---	---	---	---
FAF2	23197	broad.mit.edu	37	5	175925822	175925823	+	Intron	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175925822_175925823delAC	uc003mej.3	+							NM_014613	NP_055428			UBX domain containing 8						response to unfolded protein	endoplasmic reticulum|lipid particle	protein binding			ovary(1)	1																		---	---	---	---
CDHR2	54825	broad.mit.edu	37	5	176019086	176019097	+	Intron	DEL	TGGTGGTGGTGA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176019086_176019097delTGGTGGTGGTGA	uc003mem.1	+						CDHR2_uc003men.1_Intron	NM_017675	NP_060145			protocadherin LKC precursor						homophilic cell adhesion|negative regulation of cell growth	apical plasma membrane|cell junction|integral to membrane	calcium ion binding|protein binding			ovary(2)	2																		---	---	---	---
UIMC1	51720	broad.mit.edu	37	5	176395374	176395375	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176395374_176395375delAA	uc011dfp.1	-						UIMC1_uc003mfc.1_Intron|UIMC1_uc003mfd.1_Intron|UIMC1_uc003mfg.1_Intron|UIMC1_uc003mff.1_Intron	NM_016290	NP_057374			ubiquitin interaction motif containing 1						double-strand break repair|G2/M transition DNA damage checkpoint|histone H2A K63-linked deubiquitination|negative regulation of transcription, DNA-dependent|positive regulation of DNA repair|response to ionizing radiation|transcription, DNA-dependent	BRCA1-A complex	histone binding|K63-linked polyubiquitin binding			ovary(3)|skin(1)	4	all_cancers(89;7.96e-05)|Renal(175;0.000269)|Lung NSC(126;0.00476)|all_lung(126;0.00806)	Medulloblastoma(196;0.0145)|all_neural(177;0.0325)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
ZNF346	23567	broad.mit.edu	37	5	176508089	176508091	+	3'UTR	DEL	AAG	-	-	rs147592965	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176508089_176508091delAAG	uc003mfk.1	+	9					ZNF346_uc011dft.1_3'UTR	NM_012279	NP_036411			zinc finger protein 346							cytoplasm|nucleolus	double-stranded RNA binding|zinc ion binding				0	all_cancers(89;6.3e-05)|Renal(175;0.000269)|Lung NSC(126;0.00476)|all_lung(126;0.00806)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
NSD1	64324	broad.mit.edu	37	5	176645502	176645502	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176645502delT	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)			---	---	---	---
F12	2161	broad.mit.edu	37	5	176831956	176831957	+	Intron	INS	-	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176831956_176831957insC	uc003mgo.3	-						F12_uc011dfy.1_5'Flank|F12_uc003mgn.3_5'Flank|F12_uc010jkl.2_Intron	NM_000505	NP_000496			coagulation factor XII precursor						Factor XII activation|fibrinolysis|innate immune response|positive regulation of blood coagulation|positive regulation of fibrinolysis|positive regulation of plasminogen activation|protein autoprocessing|response to misfolded protein|zymogen activation	extracellular space|plasma membrane	serine-type endopeptidase activity				0	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	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)											Hereditary_Angioedema				---	---	---	---
B4GALT7	11285	broad.mit.edu	37	5	177035488	177035489	+	Intron	INS	-	C	C	rs71585644		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177035488_177035489insC	uc003mhy.2	+						B4GALT7_uc003mhz.2_Intron	NM_007255	NP_009186			xylosylprotein beta 1,4-galactosyltransferase 7						fibril organization|glycosaminoglycan biosynthetic process|negative regulation of fibroblast proliferation|protein modification process|proteoglycan metabolic process	Golgi cisterna membrane|integral to membrane	metal ion binding|xylosylprotein 4-beta-galactosyltransferase activity			pancreas(1)	1	all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	177488315	177488316	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177488315_177488316delTT								FAM153C (12227 upstream) : N4BP3 (52240 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	177533063	177533063	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177533063delA								FAM153C (56975 upstream) : N4BP3 (7493 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	178108517	178108518	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178108517_178108518delAA								CLK4 (50901 upstream) : ZNF354A (30013 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	179514056	179514062	+	IGR	DEL	TTTTTTT	-	-	rs66681579		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179514056_179514062delTTTTTTT								RNF130 (14947 upstream) : RASGEF1C (13734 downstream)																																			---	---	---	---
MAPK9	5601	broad.mit.edu	37	5	179707339	179707339	+	Intron	DEL	T	-	-	rs138341304	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179707339delT	uc003mls.3	-						MAPK9_uc003mlt.3_Intron|MAPK9_uc010jlc.2_Intron|MAPK9_uc003mlv.3_Intron|MAPK9_uc011dgx.1_Intron	NM_002752	NP_002743			mitogen-activated protein kinase 9 isoform JNK2						innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of gene expression|positive regulation of macrophage derived foam cell differentiation|regulation of sequence-specific DNA binding transcription factor activity|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|JUN kinase activity|protein binding|protein binding			central_nervous_system(2)|upper_aerodigestive_tract(1)|large_intestine(1)	4	all_cancers(89;6.54e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137)	all_cancers(40;0.0236)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
CNOT6	57472	broad.mit.edu	37	5	179924325	179924326	+	Intron	INS	-	A	A	rs111362029		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179924325_179924326insA	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	179975421	179975421	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179975421delG	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	179975880	179975880	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179975880delT	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	179997806	179997807	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179997806_179997807insA	uc003mlx.2	+						CNOT6_uc010jld.2_Intron|CNOT6_uc010jle.2_Intron	NM_015455	NP_056270			CCR4-NOT transcription complex, subunit 6						nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleus	exonuclease activity|metal ion binding|protein binding|RNA binding				0	all_cancers(89;3.3e-05)|all_epithelial(37;7.38e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00543)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	OV - Ovarian serous cystadenocarcinoma(192;0.023)														---	---	---	---
FLT4	2324	broad.mit.edu	37	5	180049927	180049928	+	Intron	DEL	CA	-	-	rs113248876		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180049927_180049928delCA	uc003mma.3	-						FLT4_uc003mlz.3_Intron|FLT4_uc003mmb.1_Intron|FLT4_uc011dgy.1_Intron	NM_002020	NP_002011			fms-related tyrosine kinase 4 isoform 2						positive regulation of cell proliferation	integral to plasma membrane	ATP binding|protein phosphatase binding|vascular endothelial growth factor receptor activity			lung(7)|skin(2)|ovary(2)|stomach(1)|central_nervous_system(1)|breast(1)|kidney(1)	15	all_cancers(89;2.21e-05)|all_epithelial(37;5.29e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00245)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.134)	Sorafenib(DB00398)|Sunitinib(DB01268)									Congenital_Hereditary_Lymphedema				---	---	---	---
EXOC2	55770	broad.mit.edu	37	6	597182	597182	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:597182delT	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	834408	834411	+	IGR	DEL	CCTA	-	-	rs72349013		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:834408_834411delCCTA								EXOC2 (141299 upstream) : LOC285768 (126831 downstream)																																			---	---	---	---
GMDS	2762	broad.mit.edu	37	6	1764329	1764329	+	Intron	DEL	A	-	-	rs79507370		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:1764329delA	uc003mtq.2	-							NM_001500	NP_001491			GDP-mannose 4,6-dehydratase						'de novo' GDP-L-fucose biosynthetic process|GDP-mannose metabolic process|leukocyte cell-cell adhesion		coenzyme binding|GDP-mannose 4,6-dehydratase activity			central_nervous_system(1)	1	Ovarian(93;0.0733)	all_cancers(2;7.64e-19)|all_epithelial(2;3.05e-16)|Colorectal(2;0.00414)|all_hematologic(90;0.00997)|all_lung(73;0.0141)|Lung NSC(90;0.0802)		Epithelial(2;7.61e-06)|all cancers(2;0.000111)|STAD - Stomach adenocarcinoma(2;0.000231)|Colorectal(2;0.00445)|COAD - Colon adenocarcinoma(2;0.0125)|OV - Ovarian serous cystadenocarcinoma(45;0.0563)														---	---	---	---
GMDS	2762	broad.mit.edu	37	6	1927592	1927592	+	Intron	DEL	T	-	-	rs67316164		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:1927592delT	uc003mtq.2	-							NM_001500	NP_001491			GDP-mannose 4,6-dehydratase						'de novo' GDP-L-fucose biosynthetic process|GDP-mannose metabolic process|leukocyte cell-cell adhesion		coenzyme binding|GDP-mannose 4,6-dehydratase activity			central_nervous_system(1)	1	Ovarian(93;0.0733)	all_cancers(2;7.64e-19)|all_epithelial(2;3.05e-16)|Colorectal(2;0.00414)|all_hematologic(90;0.00997)|all_lung(73;0.0141)|Lung NSC(90;0.0802)		Epithelial(2;7.61e-06)|all cancers(2;0.000111)|STAD - Stomach adenocarcinoma(2;0.000231)|Colorectal(2;0.00445)|COAD - Colon adenocarcinoma(2;0.0125)|OV - Ovarian serous cystadenocarcinoma(45;0.0563)														---	---	---	---
GMDS	2762	broad.mit.edu	37	6	2223703	2223704	+	Intron	INS	-	A	A	rs142012313	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2223703_2223704insA	uc003mtq.2	-							NM_001500	NP_001491			GDP-mannose 4,6-dehydratase						'de novo' GDP-L-fucose biosynthetic process|GDP-mannose metabolic process|leukocyte cell-cell adhesion		coenzyme binding|GDP-mannose 4,6-dehydratase activity			central_nervous_system(1)	1	Ovarian(93;0.0733)	all_cancers(2;7.64e-19)|all_epithelial(2;3.05e-16)|Colorectal(2;0.00414)|all_hematologic(90;0.00997)|all_lung(73;0.0141)|Lung NSC(90;0.0802)		Epithelial(2;7.61e-06)|all cancers(2;0.000111)|STAD - Stomach adenocarcinoma(2;0.000231)|Colorectal(2;0.00445)|COAD - Colon adenocarcinoma(2;0.0125)|OV - Ovarian serous cystadenocarcinoma(45;0.0563)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	2296216	2296216	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2296216delT								GMDS (50370 upstream) : C6orf195 (326756 downstream)																																			---	---	---	---
RIPK1	8737	broad.mit.edu	37	6	3106972	3106972	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3106972delA	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)																---	---	---	---
BPHL	670	broad.mit.edu	37	6	3117089	3117089	+	5'Flank	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3117089delA	uc003mva.2	+						BPHL_uc003muz.2_5'Flank|BPHL_uc011dht.1_5'Flank|BPHL_uc003muy.2_5'Flank	NM_004332	NP_004323			biphenyl hydrolase-like precursor						cellular amino acid metabolic process|response to toxin	mitochondrion	hydrolase activity				0	Ovarian(93;0.0386)	all_hematologic(90;0.108)																---	---	---	---
BPHL	670	broad.mit.edu	37	6	3120380	3120380	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3120380delG	uc003mva.2	+						BPHL_uc003muz.2_Intron|BPHL_uc011dht.1_Intron|BPHL_uc003muy.2_Intron	NM_004332	NP_004323			biphenyl hydrolase-like precursor						cellular amino acid metabolic process|response to toxin	mitochondrion	hydrolase activity				0	Ovarian(93;0.0386)	all_hematologic(90;0.108)																---	---	---	---
Unknown	0	broad.mit.edu	37	6	3543003	3543004	+	IGR	DEL	GT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3543003_3543004delGT								SLC22A23 (86210 upstream) : C6orf145 (179832 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	3720134	3720136	+	IGR	DEL	TCC	-	-	rs147611617		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3720134_3720136delTCC								SLC22A23 (263341 upstream) : C6orf145 (2700 downstream)																																			---	---	---	---
PRPF4B	8899	broad.mit.edu	37	6	4059124	4059124	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:4059124delA	uc003mvv.2	+						PRPF4B_uc003mvw.2_Intron|C6orf146_uc010jnq.1_Intron|PRPF4B_uc011dhv.1_Intron	NM_003913	NP_003904			serine/threonine-protein kinase PRP4K							catalytic step 2 spliceosome	ATP binding|protein binding|protein serine/threonine kinase activity			breast(5)	5	Ovarian(93;0.0925)	all_hematologic(90;0.0895)																---	---	---	---
CDYL	9425	broad.mit.edu	37	6	4712579	4712579	+	Intron	DEL	C	-	-	rs74940182	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:4712579delC	uc003mwi.2	+							NM_001143971	NP_001137443			chromodomain protein, Y chromosome-like isoform						regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	nucleus	histone acetyltransferase activity				0	Ovarian(93;0.11)	all_hematologic(90;0.0901)|Lung NSC(90;0.244)		OV - Ovarian serous cystadenocarcinoma(45;0.182)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	6012170	6012173	+	IGR	DEL	ACAC	-	-	rs71879678		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:6012170_6012173delACAC								NRN1 (4537 upstream) : F13A1 (132139 downstream)																																			---	---	---	---
RREB1	6239	broad.mit.edu	37	6	7125814	7125814	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7125814delT	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	7172181	7172183	+	Intron	DEL	TTT	-	-	rs77143452		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7172181_7172183delTTT	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)																---	---	---	---
DSP	1832	broad.mit.edu	37	6	7562607	7562607	+	Intron	DEL	T	-	-	rs147191716		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7562607delT	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	7655233	7655234	+	IGR	INS	-	GT	GT	rs151206858	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7655233_7655234insGT								SNRNP48 (43034 upstream) : BMP6 (71777 downstream)																																			---	---	---	---
BMP6	654	broad.mit.edu	37	6	7871309	7871310	+	Intron	DEL	TG	-	-	rs3031042		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7871309_7871310delTG	uc003mxu.3	+							NM_001718	NP_001709			bone morphogenetic protein 6 preproprotein						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)																	---	---	---	---
TXNDC5	81567	broad.mit.edu	37	6	7940863	7940874	+	Intron	DEL	AGAGAGAAAGAA	-	-	rs57317250	by1000genomes;by1000genomes;by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7940863_7940874delAGAGAGAAAGAA	uc003mxw.2	-							NM_001145549	NP_001139021			thioredoxin domain containing 5 isoform 3						anti-apoptosis|cell redox homeostasis|cellular membrane organization|glycerol ether metabolic process|post-Golgi vesicle-mediated transport	endoplasmic reticulum lumen|lysosomal lumen	electron carrier activity|isomerase activity|protein disulfide oxidoreductase activity				0	Ovarian(93;0.0398)																	---	---	---	---
TXNDC5	81567	broad.mit.edu	37	6	8031099	8031099	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:8031099delA	uc003mxw.2	-						MUTED_uc003mxy.2_Intron|MUTED_uc010joc.2_Intron|MUTED_uc010job.2_Intron	NM_001145549	NP_001139021			thioredoxin domain containing 5 isoform 3						anti-apoptosis|cell redox homeostasis|cellular membrane organization|glycerol ether metabolic process|post-Golgi vesicle-mediated transport	endoplasmic reticulum lumen|lysosomal lumen	electron carrier activity|isomerase activity|protein disulfide oxidoreductase activity				0	Ovarian(93;0.0398)																	---	---	---	---
Unknown	0	broad.mit.edu	37	6	8323263	8323264	+	IGR	INS	-	TTCCTTCT	TTCCTTCT	rs139963481	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:8323263_8323264insTTCCTTCT								EEF1E1 (220435 upstream) : SLC35B3 (88469 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	9904232	9904233	+	Intron	INS	-	AC	AC	rs142690277	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:9904232_9904233insAC	uc003myg.1	-						uc010jog.1_Intron|uc003myh.1_Intron|uc003myi.2_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	9947197	9947200	+	Intron	DEL	AAAG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:9947197_9947200delAAAG	uc003myn.2	-						uc010joi.1_Intron|uc010joj.1_Intron|uc003myp.1_Intron					RecName: Full=Orofacial cleft 1 candidate gene 1 protein; AltName: Full=Orofacial clefting chromosomal breakpoint region candidate 1 protein;																														---	---	---	---
SYCP2L	221711	broad.mit.edu	37	6	10886475	10886475	+	5'Flank	DEL	A	-	-	rs78459488		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10886475delA	uc003mzo.2	+						SYCP2L_uc011dim.1_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	11493261	11493261	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:11493261delG	uc003mzz.1	+											Homo sapiens cDNA clone IMAGE:5269873.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	11793503	11793503	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:11793503delT								C6orf105 (14223 upstream) : HIVEP1 (219221 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	13343848	13343848	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13343848delA								TBC1D7 (15078 upstream) : GFOD1 (19971 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	13906937	13906937	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13906937delT								CCDC90A (92148 upstream) : RNF182 (18266 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	14703081	14703082	+	IGR	DEL	AG	-	-	rs66895879		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:14703081_14703082delAG								CD83 (565935 upstream) : JARID2 (542652 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	15771886	15771886	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:15771886delG								DTNBP1 (108615 upstream) : MYLIP (357431 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	18093897	18093898	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:18093897_18093898delTT								KIF13A (106098 upstream) : NHLRC1 (26820 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	18351367	18351367	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:18351367delA								DEK (86568 upstream) : RNF144B (36227 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	19552914	19552915	+	IGR	DEL	TC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:19552914_19552915delTC								MIR548A1 (980803 upstream) : ID4 (284702 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	19985459	19985459	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:19985459delT								ID4 (144545 upstream) : MBOAT1 (115476 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	20017190	20017192	+	IGR	DEL	AAC	-	-	rs66465759		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:20017190_20017192delAAC								ID4 (176276 upstream) : MBOAT1 (83743 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	20094608	20094608	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:20094608delT								ID4 (253694 upstream) : MBOAT1 (6327 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	20236717	20236717	+	IGR	DEL	A	-	-	rs35502765		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:20236717delA								MBOAT1 (24047 upstream) : E2F3 (165420 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	20369979	20369979	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:20369979delA								MBOAT1 (157309 upstream) : E2F3 (32158 downstream)																																			---	---	---	---
CDKAL1	54901	broad.mit.edu	37	6	20583853	20583853	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:20583853delT	uc003ndc.1	+						CDKAL1_uc003ndd.1_Intron|CDKAL1_uc003nde.1_Intron|CDKAL1_uc010jpo.1_Intron	NM_017774	NP_060244			CDK5 regulatory subunit associated protein						RNA modification	integral to membrane	4 iron, 4 sulfur cluster binding|metal ion binding|transferase activity			ovary(2)	2	all_epithelial(95;0.0708)|Breast(50;0.131)|Ovarian(93;0.227)		OV - Ovarian serous cystadenocarcinoma(7;0.0241)|all cancers(50;0.123)|Epithelial(50;0.248)															---	---	---	---
FLJ22536	401237	broad.mit.edu	37	6	21726383	21726384	+	Intron	DEL	CA	-	-	rs112787464		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:21726383_21726384delCA	uc010jpp.1	+						FLJ22536_uc003ndj.2_Intron|FLJ22536_uc011djk.1_Intron|FLJ22536_uc011djj.1_Intron					Homo sapiens cDNA FLJ12803 fis, clone NT2RP2002172.												0																		---	---	---	---
FLJ22536	401237	broad.mit.edu	37	6	21734110	21734110	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:21734110delA	uc010jpp.1	+						FLJ22536_uc003ndj.2_Intron|FLJ22536_uc011djk.1_Intron|FLJ22536_uc011djj.1_Intron					Homo sapiens cDNA FLJ12803 fis, clone NT2RP2002172.												0																		---	---	---	---
FLJ22536	401237	broad.mit.edu	37	6	21994551	21994552	+	Intron	INS	-	TAT	TAT	rs145492001	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:21994551_21994552insTAT	uc003ndj.2	+						FLJ22536_uc011djk.1_Intron|FLJ22536_uc003ndl.2_Intron	NR_015410				Homo sapiens cDNA FLJ12803 fis, clone NT2RP2002172.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	22601756	22601756	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:22601756delT								HDGFL1 (31007 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	23117053	23117054	+	IGR	INS	-	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:23117053_23117054insC								HDGFL1 (546304 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	23323291	23323291	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:23323291delT								HDGFL1 (752542 upstream) : NRSN1 (803123 downstream)																																			---	---	---	---
FAM65B	9750	broad.mit.edu	37	6	24832979	24832979	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24832979delT	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																		---	---	---	---
FAM65B	9750	broad.mit.edu	37	6	24833734	24833735	+	Intron	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24833734_24833735delAC	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																		---	---	---	---
FAM65B	9750	broad.mit.edu	37	6	24895764	24895764	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24895764delA	uc003neo.1	-						FAM65B_uc011djs.1_Intron|FAM65B_uc011dju.1_Intron	NM_014722	NP_055537			hypothetical protein LOC9750 isoform 1						cell differentiation|muscle organ development	cytoskeleton|filopodium|mitochondrion	binding			ovary(1)	1																		---	---	---	---
HIST1H1E	3008	broad.mit.edu	37	6	26156422	26156423	+	5'Flank	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26156422_26156423insT	uc003ngq.2	+						HIST1H2BD_uc003ngr.2_5'Flank|HIST1H2BD_uc003ngs.2_5'Flank	NM_005321	NP_005312			histone cluster 1, H1e						nucleosome assembly	nucleosome|nucleus	DNA binding|protein binding			large_intestine(1)|ovary(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	26558327	26558328	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26558327_26558328delTT								HMGN4 (11165 upstream) : ABT1 (38852 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	26995948	26995948	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26995948delA								C6orf41 (4196 upstream) : HIST1H2BJ (96814 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	27618589	27618589	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27618589delA								ZNF184 (177692 upstream) : HIST1H2BL (156669 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	28004456	28004456	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28004456delA								OR2B6 (78498 upstream) : ZNF165 (42116 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	29019484	29019484	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29019484delT								OR2W1 (6532 upstream) : OR2B3 (34502 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	29115929	29115929	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29115929delA								OR2J3 (35327 upstream) : OR2J2 (25382 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	29675203	29675204	+	IGR	DEL	CC	-	-	rs3116787		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29675203_29675204delCC								ZFP57 (26316 upstream) : HLA-F (15913 downstream)																																			---	---	---	---
HLA-G	3135	broad.mit.edu	37	6	29860530	29860530	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29860530delC	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	30117409	30117410	+	IGR	DEL	TT	-	-	rs68169392		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30117409_30117410delTT								TRIM40 (897 upstream) : TRIM10 (2313 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	30352987	30352987	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30352987delA								TRIM39 (38355 upstream) : HLA-E (104284 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	30665317	30665317	+	IGR	DEL	T	-	-	rs137943555		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30665317delT								NRM (6259 upstream) : MDC1 (2268 downstream)																																			---	---	---	---
DDR1	780	broad.mit.edu	37	6	30862041	30862041	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30862041delA	uc003nrr.2	+						DDR1_uc010jse.2_Intron|DDR1_uc003nrq.2_Intron|DDR1_uc003nrs.2_Intron|DDR1_uc003nrt.2_Intron|DDR1_uc011dms.1_Intron|DDR1_uc003nru.2_Intron|DDR1_uc003nrv.2_Intron|DDR1_uc003nrw.1_Intron|DDR1_uc003nry.1_Intron|DDR1_uc003nrx.1_Intron|DDR1_uc003nrz.1_5'Flank	NM_013993	NP_054699			discoidin domain receptor family, member 1						cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway	extracellular region|integral to plasma membrane	ATP binding|protein binding|protein binding|transmembrane receptor protein tyrosine kinase activity			lung(4)|central_nervous_system(3)|large_intestine(1)|ovary(1)	9					Imatinib(DB00619)													---	---	---	---
Unknown	0	broad.mit.edu	37	6	30981652	30981652	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30981652delG								MUC21 (23977 upstream) : HCG22 (40332 downstream)																																			---	---	---	---
HLA-B	3106	broad.mit.edu	37	6	31325236	31325236	+	5'Flank	DEL	A	-	-	rs150714763		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31325236delA	uc003nth.2	-						HLA-C_uc003ntb.2_5'Flank|HLA-C_uc003ntc.1_5'Flank|HLA-B_uc010jsm.1_5'Flank|HLA-B_uc011dnk.1_5'Flank|HLA-B_uc003ntf.2_5'Flank|HLA-B_uc003ntg.1_5'Flank|HLA-B_uc003nti.1_5'Flank|HLA-B_uc010jsn.1_5'Flank|HLA-B_uc010jso.2_5'Flank	NM_005514	NP_005505			major histocompatibility complex, class I, B						antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|regulation of immune response|type I interferon-mediated signaling pathway	integral to plasma membrane|MHC class I protein complex	MHC class I receptor activity				0														Melanoma_Familial_Clustering_of|Lichen_Sclerosis_et_Atrophicus_Familial_Clustering_of				---	---	---	---
MICA	4276	broad.mit.edu	37	6	31364967	31364968	+	5'Flank	DEL	GA	-	-	rs3997964		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31364967_31364968delGA	uc003rxz.1	+											SubName: Full=MHC class I polypeptide-related sequence A;												0		Ovarian(999;0.0253)																---	---	---	---
BAT1	7919	broad.mit.edu	37	6	31505940	31505941	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31505940_31505941insT	uc003ntt.2	-						BAT1_uc003nts.2_Intron|BAT1_uc011dnn.1_Intron|BAT1_uc003ntu.2_Intron|BAT1_uc003ntv.2_Intron|BAT1_uc003ntw.2_Intron|BAT1_uc003ntx.2_Intron|BAT1_uc011dno.1_Intron|BAT1_uc011dnp.1_Intron|SNORD117_uc003nty.1_5'Flank|BAT1_uc011dnq.1_Intron	NM_004640	NP_004631			HLA-B associated transcript 1						intronless viral mRNA export from host nucleus|RNA secondary structure unwinding|spliceosome assembly	nuclear speck|spliceosomal complex|transcription export complex	ATP binding|ATP-dependent protein binding|ATP-dependent RNA helicase activity|identical protein binding|U4 snRNA binding|U6 snRNA binding				0																		---	---	---	---
MSH5	4439	broad.mit.edu	37	6	31717319	31717319	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31717319delA	uc003nwv.1	+						MSH5_uc003nwt.1_Intron|MSH5_uc003nwu.1_Intron|MSH5_uc003nww.1_Intron|MSH5_uc003nwx.1_Intron|MSH5_uc011dof.1_Intron	NM_172166	NP_751898			mutS homolog 5 isoform c						chiasma assembly|homologous chromosome segregation|meiotic prophase II|mismatch repair|reciprocal meiotic recombination	synaptonemal complex	ATP binding|DNA-dependent ATPase activity|mismatched DNA binding			ovary(2)|breast(1)	3													Direct_reversal_of_damage|MMR					---	---	---	---
Unknown	0	broad.mit.edu	37	6	31798774	31798776	+	IGR	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31798774_31798776delTTT								HSPA1B (743 upstream) : C6orf48 (3917 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	32210220	32210227	+	IGR	DEL	TTCTTTCC	-	-	rs41286494		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32210220_32210227delTTCTTTCC								NOTCH4 (18376 upstream) : C6orf10 (46076 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	33825503	33825503	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33825503delC								MLN (53710 upstream) : MIR1275 (142246 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	33918368	33918371	+	IGR	DEL	GTGT	-	-	rs147700351		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33918368_33918371delGTGT								MLN (146575 upstream) : MIR1275 (49378 downstream)																																			---	---	---	---
GRM4	2914	broad.mit.edu	37	6	34035935	34035935	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34035935delG	uc003oir.3	-						GRM4_uc011dsn.1_Intron|GRM4_uc010jvh.2_Intron|GRM4_uc010jvi.2_Intron|GRM4_uc011dsl.1_Intron|GRM4_uc003oiq.2_Intron|GRM4_uc011dsm.1_Intron	NM_000841	NP_000832			glutamate receptor, metabotropic 4 precursor						activation of MAPK activity|inhibition of adenylate cyclase activity by metabotropic glutamate receptor signaling pathway|neuroprotection|neurotransmitter secretion|positive regulation of MAPKKK cascade	cytoplasmic vesicle|integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			lung(3)|upper_aerodigestive_tract(1)|ovary(1)|skin(1)	6					L-Glutamic Acid(DB00142)													---	---	---	---
GRM4	2914	broad.mit.edu	37	6	34039260	34039261	+	Intron	INS	-	A	A	rs145416490		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34039260_34039261insA	uc003oir.3	-						GRM4_uc011dsn.1_Intron|GRM4_uc010jvh.2_Intron|GRM4_uc010jvi.2_Intron|GRM4_uc011dsl.1_Intron|GRM4_uc003oiq.2_Intron|GRM4_uc011dsm.1_Intron	NM_000841	NP_000832			glutamate receptor, metabotropic 4 precursor						activation of MAPK activity|inhibition of adenylate cyclase activity by metabotropic glutamate receptor signaling pathway|neuroprotection|neurotransmitter secretion|positive regulation of MAPKKK cascade	cytoplasmic vesicle|integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			lung(3)|upper_aerodigestive_tract(1)|ovary(1)|skin(1)	6					L-Glutamic Acid(DB00142)													---	---	---	---
Unknown	0	broad.mit.edu	37	6	34158925	34158925	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34158925delA								GRM4 (45056 upstream) : HMGA1 (45652 downstream)																																			---	---	---	---
C6orf106	64771	broad.mit.edu	37	6	34639887	34639889	+	Intron	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34639887_34639889delTTT	uc003ojr.2	-						C6orf106_uc003ojs.2_Intron	NM_024294	NP_077270			chromosome 6 open reading frame 106 isoform a											skin(2)|ovary(1)	3																		---	---	---	---
C6orf106	64771	broad.mit.edu	37	6	34666248	34666248	+	5'Flank	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34666248delT	uc003ojr.2	-						C6orf106_uc003ojs.2_5'Flank	NM_024294	NP_077270			chromosome 6 open reading frame 106 isoform a											skin(2)|ovary(1)	3																		---	---	---	---
ANKS1A	23294	broad.mit.edu	37	6	35081369	35081369	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35081369delA	uc010jvp.1	+											SubName: Full=ANKS1A protein;							cytoplasm	protein binding			ovary(3)|upper_aerodigestive_tract(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	36118613	36118613	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36118613delT								MAPK13 (10772 upstream) : BRPF3 (45937 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	37031290	37031290	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37031290delA								FGD2 (34445 upstream) : PIM1 (106632 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	37304367	37304367	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37304367delT								TBC1D22B (3622 upstream) : RNF8 (17381 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	37579508	37579509	+	IGR	INS	-	AGAGACA	AGAGACA	rs145540436	by1000genomes;byFrequency	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37579508_37579509insAGAGACA								C6orf129 (111808 upstream) : MDGA1 (20775 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	37702042	37702045	+	IGR	DEL	AACA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37702042_37702045delAACA								MDGA1 (36276 upstream) : ZFAND3 (85262 downstream)																																			---	---	---	---
ZFAND3	60685	broad.mit.edu	37	6	37851325	37851325	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37851325delT	uc003onx.2	+							NM_021943	NP_068762			zinc finger, AN1-type domain 3								DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
BTBD9	114781	broad.mit.edu	37	6	38209644	38209644	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38209644delT	uc003ooa.3	-						BTBD9_uc003ony.3_Intron|BTBD9_uc010jwv.2_Intron|BTBD9_uc010jww.2_Intron|BTBD9_uc010jwx.2_Intron	NM_052893	NP_443125			BTB (POZ) domain containing 9 isoform a						cell adhesion						0																		---	---	---	---
DNAH8	1769	broad.mit.edu	37	6	38893643	38893643	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38893643delT	uc003ooe.1	+						uc003oof.1_Intron	NM_001371	NP_001362			dynein, axonemal, heavy polypeptide 8											skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	21																		---	---	---	---
DNAH8	1769	broad.mit.edu	37	6	38992929	38992930	+	Intron	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38992929_38992930delTG	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																		---	---	---	---
DAAM2	23500	broad.mit.edu	37	6	39780923	39780924	+	Intron	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39780923_39780924delTG	uc003oow.2	+						DAAM2_uc010jxc.2_Intron|DAAM2_uc003oox.2_Intron|DAAM2_uc003oov.3_Intron	NM_015345	NP_056160			dishevelled associated activator of						actin cytoskeleton organization		actin binding|Rho GTPase binding			ovary(2)|skin(1)	3	Ovarian(28;0.0355)|Colorectal(47;0.196)																	---	---	---	---
DAAM2	23500	broad.mit.edu	37	6	39866805	39866806	+	Intron	INS	-	ACAATGGGC	ACAATGGGC	rs147053229	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39866805_39866806insACAATGGGC	uc003oow.2	+						DAAM2_uc003oox.2_Intron	NM_015345	NP_056160			dishevelled associated activator of						actin cytoskeleton organization		actin binding|Rho GTPase binding			ovary(2)|skin(1)	3	Ovarian(28;0.0355)|Colorectal(47;0.196)																	---	---	---	---
Unknown	0	broad.mit.edu	37	6	40918616	40918616	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:40918616delT								LRFN2 (363490 upstream) : UNC5CL (76156 downstream)																																			---	---	---	---
UNC5CL	222643	broad.mit.edu	37	6	41004489	41004492	+	Intron	DEL	AAAA	-	-	rs112162551		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41004489_41004492delAAAA	uc003opi.2	-						UNC5CL_uc010jxe.1_Intron	NM_173561	NP_775832			unc-5 homolog C-like						signal transduction	cytoplasm|integral to membrane				ovary(2)	2	Ovarian(28;0.0418)|Colorectal(47;0.196)																	---	---	---	---
NFYA	4800	broad.mit.edu	37	6	41058162	41058162	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41058162delA	uc003opo.2	+						NFYA_uc003opp.2_Intron|NFYA_uc003opq.2_Intron	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	41599422	41599422	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41599422delA								FOXP4 (29301 upstream) : MDFI (5508 downstream)																																			---	---	---	---
TRERF1	55809	broad.mit.edu	37	6	42200318	42200319	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42200318_42200319insT	uc003osd.2	-						TRERF1_uc011duq.1_Intron|TRERF1_uc003osb.2_Intron|TRERF1_uc003osc.2_Intron|TRERF1_uc003ose.2_Intron	NM_033502	NP_277037			transcriptional regulating factor 1						cholesterol catabolic process|homeostatic process|multicellular organismal development|positive regulation of transcription, DNA-dependent|regulation of hormone biosynthetic process|steroid biosynthetic process	nucleus	DNA bending activity|ligand-dependent nuclear receptor transcription coactivator activity|RNA polymerase II transcription cofactor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding|zinc ion binding			ovary(3)|pancreas(1)|skin(1)	5	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	42440475	42440477	+	IGR	DEL	AAA	-	-	rs144712962		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42440475_42440477delAAA								TRERF1 (20610 upstream) : UBR2 (91581 downstream)																																			---	---	---	---
UBR2	23304	broad.mit.edu	37	6	42642498	42642501	+	Intron	DEL	AAAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42642498_42642501delAAAA	uc011dur.1	+						UBR2_uc011dus.1_Intron|UBR2_uc003osh.2_Intron|UBR2_uc011dut.1_Intron	NM_015255	NP_056070			ubiquitin protein ligase E3 component n-recognin						cellular response to leucine|chromatin silencing|histone H2A ubiquitination|negative regulation of TOR signaling cascade	nucleus|plasma membrane	leucine binding|zinc ion binding			ovary(3)|pancreas(1)	4	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	42700435	42700435	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42700435delT								PRPH2 (10077 upstream) : TBCC (11800 downstream)																																			---	---	---	---
KLHDC3	116138	broad.mit.edu	37	6	42983679	42983679	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42983679delT	uc003otl.2	+						MEA1_uc010jyc.1_5'Flank|MEA1_uc003otk.2_5'Flank|KLHDC3_uc003otm.2_Intron|KLHDC3_uc010jyf.2_Intron|KLHDC3_uc003otn.2_Intron|KLHDC3_uc003oto.2_5'Flank	NM_057161	NP_476502			kelch domain containing 3						reciprocal meiotic recombination	cytoplasm|nuclear chromatin	chromatin binding|protein binding			upper_aerodigestive_tract(1)	1			Colorectal(64;0.00237)|all cancers(41;0.0034)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0539)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)															---	---	---	---
CUL9	23113	broad.mit.edu	37	6	43165230	43165230	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43165230delT	uc003ouk.2	+						CUL9_uc003oul.2_Intron|CUL9_uc010jyk.2_Intron	NM_015089	NP_055904			p53-associated parkin-like cytoplasmic protein						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																		---	---	---	---
CUL9	23113	broad.mit.edu	37	6	43179306	43179306	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43179306delA	uc003ouk.2	+						CUL9_uc003oul.2_Intron|CUL9_uc010jyk.2_Intron|CUL9_uc003oun.2_5'Flank	NM_015089	NP_055904			p53-associated parkin-like cytoplasmic protein						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																		---	---	---	---
RSPH9	221421	broad.mit.edu	37	6	43613212	43613212	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43613212delG	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	43627124	43627126	+	Intron	DEL	TTT	-	-	rs13203731		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43627124_43627126delTTT	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				---	---	---	---
Unknown	0	broad.mit.edu	37	6	43813354	43813354	+	RNA	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43813354delA	uc003owl.1	-	4		c.628delT								Homo sapiens cDNA FLJ40534 fis, clone TESTI2047824.																														---	---	---	---
NFKBIE	4794	broad.mit.edu	37	6	44226069	44226069	+	3'UTR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44226069delA	uc003oxe.1	-	6					SLC35B2_uc003oxd.2_5'Flank|SLC35B2_uc011dvt.1_5'Flank|SLC35B2_uc011dvu.1_5'Flank	NM_004556	NP_004547			nuclear factor of kappa light polypeptide gene						cytoplasmic sequestering of transcription factor		protein binding			breast(2)	2	all_cancers(18;2e-05)|all_lung(25;0.00747)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)															---	---	---	---
TCTE1	202500	broad.mit.edu	37	6	44249130	44249130	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44249130delT	uc003oxi.2	-						SPATS1_uc003oxg.2_Intron|TMEM151B_uc003oxf.2_Intron	NM_182539	NP_872345			t-complex-associated testis expressed 1											ovary(2)|skin(2)	4	Hepatocellular(11;0.00908)|all_lung(25;0.0101)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	45774742	45774742	+	IGR	DEL	A	-	-	rs73452776	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:45774742delA								RUNX2 (255924 upstream) : CLIC5 (91448 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	45833837	45833840	+	IGR	DEL	TTTC	-	-	rs66706303		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:45833837_45833840delTTTC								RUNX2 (315019 upstream) : CLIC5 (32350 downstream)																																			---	---	---	---
RCAN2	10231	broad.mit.edu	37	6	46448369	46448369	+	Intron	DEL	T	-	-	rs71675654		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46448369delT	uc003oyc.1	-						RCAN2_uc003oyd.1_Intron					SubName: Full=cDNA, FLJ92723, highly similar to Homo sapiens Down syndrome critical region gene 1-like 1 (DSCR1L1), mRNA;						calcium-mediated signaling|central nervous system development		nucleotide binding|protein phosphatase 2B binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	46486000	46486000	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46486000delA	uc003oye.2	+											Homo sapiens cDNA clone IMAGE:4821026.																														---	---	---	---
CYP39A1	51302	broad.mit.edu	37	6	46521083	46521083	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46521083delT	uc003oyf.1	-						CYP39A1_uc011dwa.1_Intron|CYP39A1_uc010jzd.1_Intron	NM_016593	NP_057677			cytochrome P450, family 39, subfamily A,						bile acid biosynthetic process|bile acid catabolic process|digestion|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	24-hydroxycholesterol 7alpha-hydroxylase activity|electron carrier activity|heme binding|oxysterol 7-alpha-hydroxylase activity			ovary(1)	1																		---	---	---	---
SLC25A27	9481	broad.mit.edu	37	6	46638091	46638091	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46638091delT	uc003oyh.2	+						SLC25A27_uc011dwb.1_Intron|SLC25A27_uc003oyg.2_Intron|SLC25A27_uc011dwc.1_Intron|SLC25A27_uc003oyi.2_Intron	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	47399378	47399378	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:47399378delT								TNFRSF21 (121698 upstream) : CD2AP (46147 downstream)																																			---	---	---	---
CD2AP	23607	broad.mit.edu	37	6	47559945	47559945	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:47559945delT	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	48005714	48005714	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:48005714delA	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	48445671	48445673	+	IGR	DEL	AAA	-	-	rs34680989		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:48445671_48445673delAAA								C6orf138 (366728 upstream) : MUT (953321 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	49013983	49013983	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49013983delT								C6orf138 (935040 upstream) : MUT (385011 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	49088610	49088611	+	IGR	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49088610_49088611delAC								None (None upstream) : MUT (310383 downstream)																																			---	---	---	---
MUT	4594	broad.mit.edu	37	6	49408202	49408202	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49408202delT	uc003ozg.3	-							NM_000255	NP_000246			methylmalonyl Coenzyme A mutase precursor						fatty acid beta-oxidation	mitochondrial matrix	cobalamin binding|metal ion binding|methylmalonyl-CoA mutase activity				0	Lung NSC(77;0.0376)				Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)													---	---	---	---
Unknown	0	broad.mit.edu	37	6	49621963	49621965	+	IGR	DEL	TTC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49621963_49621965delTTC								RHAG (17376 upstream) : CRISP2 (38107 downstream)																																			---	---	---	---
CRISP3	10321	broad.mit.edu	37	6	49708427	49708428	+	Intron	INS	-	ATT	ATT	rs144753961	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49708427_49708428insATT	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)															---	---	---	---
PKHD1	5314	broad.mit.edu	37	6	51603719	51603720	+	Intron	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51603719_51603720delAC	uc003pah.1	-						PKHD1_uc010jzn.1_Intron|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)																	---	---	---	---
PKHD1	5314	broad.mit.edu	37	6	51771356	51771356	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51771356delA	uc003pah.1	-						PKHD1_uc010jzn.1_Intron|PKHD1_uc003pai.2_Intron	NM_138694	NP_619639			fibrocystin isoform 1						cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity			lung(15)|ovary(15)|large_intestine(5)|central_nervous_system(3)|skin(3)|breast(2)|upper_aerodigestive_tract(1)	44	Lung NSC(77;0.0605)																	---	---	---	---
Unknown	0	broad.mit.edu	37	6	52120126	52120126	+	IGR	DEL	A	-	-	rs35404882		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52120126delA								IL17F (10828 upstream) : MCM3 (8686 downstream)																																			---	---	---	---
ELOVL5	60481	broad.mit.edu	37	6	53133582	53133582	+	3'UTR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53133582delA	uc003pbq.1	-	8					ELOVL5_uc003pbr.1_3'UTR|ELOVL5_uc011dwx.1_3'UTR|ELOVL5_uc003pbs.1_3'UTR	NM_021814	NP_068586			elongation of very long chain fatty acids-like						fatty acid elongation, monounsaturated fatty acid|fatty acid elongation, polyunsaturated fatty acid|long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process|very long-chain fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	fatty acid elongase activity|protein binding				0	Lung NSC(77;0.116)																	---	---	---	---
ELOVL5	60481	broad.mit.edu	37	6	53172915	53172915	+	Intron	DEL	A	-	-	rs67118116		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53172915delA	uc003pbq.1	-						ELOVL5_uc003pbr.1_Intron|ELOVL5_uc011dwx.1_Intron|ELOVL5_uc003pbs.1_Intron|ELOVL5_uc003pbu.2_Intron|ELOVL5_uc011dwy.1_Intron	NM_021814	NP_068586			elongation of very long chain fatty acids-like						fatty acid elongation, monounsaturated fatty acid|fatty acid elongation, polyunsaturated fatty acid|long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process|very long-chain fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	fatty acid elongase activity|protein binding				0	Lung NSC(77;0.116)																	---	---	---	---
Unknown	0	broad.mit.edu	37	6	53219905	53219905	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53219905delA								ELOVL5 (5963 upstream) : GCLC (142235 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	53416807	53416808	+	IGR	INS	-	T	T	rs146219379	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53416807_53416808insT								GCLC (6976 upstream) : KLHL31 (95892 downstream)																																			---	---	---	---
LRRC1	55227	broad.mit.edu	37	6	53669821	53669821	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53669821delT	uc003pcd.1	+							NM_018214	NP_060684			leucine rich repeat containing 1							cytoplasm|membrane				ovary(1)	1	Lung NSC(77;0.0147)			BRCA - Breast invasive adenocarcinoma(397;0.0745)														---	---	---	---
C6orf142	90523	broad.mit.edu	37	6	53993725	53993725	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53993725delT	uc003pcg.3	+						C6orf142_uc003pcf.2_Intron|C6orf142_uc003pch.3_Intron|C6orf142_uc011dwz.1_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	54513052	54513052	+	IGR	DEL	T	-	-	rs149629015		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:54513052delT								TINAG (258102 upstream) : FAM83B (198517 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	54520935	54520935	+	IGR	DEL	T	-	-	rs77419250		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:54520935delT								TINAG (265985 upstream) : FAM83B (190634 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	54898191	54898191	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:54898191delA								FAM83B (91374 upstream) : HCRTR2 (111311 downstream)																																			---	---	---	---
HCRTR2	3062	broad.mit.edu	37	6	55147362	55147362	+	3'UTR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:55147362delT	uc003pcl.2	+	7					HCRTR2_uc010jzv.2_RNA	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)															---	---	---	---
BEND6	221336	broad.mit.edu	37	6	56829307	56829308	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56829307_56829308delTT	uc010kab.2	+						BEND6_uc003pdg.2_Intron	NM_152731	NP_689944			BEN domain containing 6												0																		---	---	---	---
PRIM2	5558	broad.mit.edu	37	6	57210261	57210262	+	Intron	INS	-	AT	AT	rs144911799		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57210261_57210262insAT	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	57245913	57245914	+	Intron	INS	-	C	C	rs146133879	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57245913_57245914insC	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	57246144	57246145	+	Intron	INS	-	T	T	rs148613760	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57246144_57246145insT	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	57257631	57257631	+	Intron	DEL	T	-	-	rs66510838		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57257631delT	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	57260058	57260059	+	Intron	INS	-	G	G	rs143626187	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57260058_57260059insG	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	57265090	57265091	+	Intron	INS	-	T	T	rs145763494	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57265090_57265091insT	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	57369651	57369651	+	Intron	DEL	T	-	-	rs67817875		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57369651delT	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	57394592	57394595	+	Intron	DEL	AATA	-	-	rs66604840		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57394592_57394595delAATA	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	57437778	57437779	+	Intron	INS	-	C	C	rs149492685	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57437778_57437779insC	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	57465439	57465448	+	Intron	DEL	AATCAGAAGT	-	-	rs33935554		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57465439_57465448delAATCAGAAGT	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	57495582	57495583	+	Intron	DEL	AA	-	-	rs66476328		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57495582_57495583delAA	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	57500198	57500198	+	Intron	DEL	A	-	-	rs11329134		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57500198delA	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	57767886	57767886	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57767886delT								PRIM2 (254511 upstream) : GUSBL2 (478273 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	57979942	57979942	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57979942delA								PRIM2 (466567 upstream) : GUSBL2 (266217 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	58159479	58159480	+	IGR	INS	-	GAAGGAAG	GAAGGAAG			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:58159479_58159480insGAAGGAAG								PRIM2 (646104 upstream) : GUSBL2 (86679 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	63310587	63310589	+	IGR	DEL	AAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:63310587_63310589delAAA								KHDRBS2 (314487 upstream) : LGSN (675268 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	64151114	64151114	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:64151114delA								LGSN (121232 upstream) : PTP4A1 (80537 downstream)																																			---	---	---	---
EYS	346007	broad.mit.edu	37	6	64437338	64437339	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:64437338_64437339insT	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	64493770	64493771	+	Intron	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:64493770_64493771delTG	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	64576124	64576125	+	Intron	DEL	GT	-	-	rs146490668		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:64576124_64576125delGT	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	64896142	64896145	+	Intron	DEL	ACAC	-	-	rs34727951		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:64896142_64896145delACAC	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	66423847	66423847	+	IGR	DEL	A	-	-	rs11367828		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:66423847delA								EYS (6729 upstream) : MCART3P (73925 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	67537367	67537367	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:67537367delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	68722524	68722524	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:68722524delA								None (None upstream) : BAI3 (623108 downstream)																																			---	---	---	---
BAI3	577	broad.mit.edu	37	6	69382917	69382918	+	Intron	DEL	TC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:69382917_69382918delTC	uc003pev.3	+						BAI3_uc010kak.2_Intron	NM_001704	NP_001695			brain-specific angiogenesis inhibitor 3						negative regulation of angiogenesis|neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			lung(27)|ovary(8)|skin(6)|pancreas(4)|central_nervous_system(3)|urinary_tract(1)|breast(1)	50		all_lung(197;0.212)																---	---	---	---
BAI3	577	broad.mit.edu	37	6	69748222	69748223	+	Intron	DEL	AC	-	-	rs71740195		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:69748222_69748223delAC	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)																---	---	---	---
SMAP1	60682	broad.mit.edu	37	6	71518527	71518527	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:71518527delT	uc003pfr.2	+						SMAP1_uc003pfs.2_Intron|SMAP1_uc010kao.2_Intron|SMAP1_uc010kap.2_Intron	NM_001044305	NP_001037770			stromal membrane-associated GTPase-activating						regulation of ARF GTPase activity	plasma membrane	ARF GTPase activator activity|zinc ion binding				0																		---	---	---	---
B3GAT2	135152	broad.mit.edu	37	6	71599965	71599965	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:71599965delC	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	71785261	71785261	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:71785261delT								B3GAT2 (118473 upstream) : OGFRL1 (213216 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	72120113	72120113	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:72120113delT								MIR30A (6789 upstream) : C6orf155 (4036 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	72260518	72260518	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:72260518delT								C6orf155 (130070 upstream) : RIMS1 (336132 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	72302123	72302123	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:72302123delG								C6orf155 (171675 upstream) : RIMS1 (294527 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	72549042	72549043	+	IGR	DEL	AT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:72549042_72549043delAT								C6orf155 (418594 upstream) : RIMS1 (47607 downstream)																																			---	---	---	---
RIMS1	22999	broad.mit.edu	37	6	72669311	72669312	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:72669311_72669312delTT	uc003pga.2	+							NM_014989	NP_055804			regulating synaptic membrane exocytosis 1						calcium ion-dependent exocytosis|cellular membrane fusion|glutamate secretion|intracellular protein transport|protein complex assembly|regulated secretory pathway|response to stimulus|synaptic vesicle exocytosis|visual perception	cell junction|presynaptic membrane	metal ion binding|Rab GTPase binding			ovary(7)|pancreas(2)|breast(1)	10		all_epithelial(107;0.179)|all_hematologic(105;0.212)																---	---	---	---
RIMS1	22999	broad.mit.edu	37	6	72800214	72800214	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:72800214delA	uc003pga.2	+							NM_014989	NP_055804			regulating synaptic membrane exocytosis 1						calcium ion-dependent exocytosis|cellular membrane fusion|glutamate secretion|intracellular protein transport|protein complex assembly|regulated secretory pathway|response to stimulus|synaptic vesicle exocytosis|visual perception	cell junction|presynaptic membrane	metal ion binding|Rab GTPase binding			ovary(7)|pancreas(2)|breast(1)	10		all_epithelial(107;0.179)|all_hematologic(105;0.212)																---	---	---	---
RIMS1	22999	broad.mit.edu	37	6	72952000	72952000	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:72952000delT	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_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)																---	---	---	---
KCNQ5	56479	broad.mit.edu	37	6	73575976	73575976	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:73575976delT	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	73894724	73894724	+	Intron	DEL	C	-	-	rs117082967	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:73894724delC	uc003pgk.2	+						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)														---	---	---	---
KHDC1	80759	broad.mit.edu	37	6	73977041	73977041	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:73977041delA	uc003pgo.2	-						uc003pgp.1_Intron|uc003pgq.2_5'Flank	NM_030568	NP_085045			KH homology domain containing 1							integral to membrane	RNA binding			skin(1)	1																		---	---	---	---
KHDC1	80759	broad.mit.edu	37	6	74004091	74004092	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74004091_74004092delAA	uc003pgo.2	-						C6orf147_uc011dym.1_Intron	NM_030568	NP_085045			KH homology domain containing 1							integral to membrane	RNA binding			skin(1)	1																		---	---	---	---
KHDC1	80759	broad.mit.edu	37	6	74007883	74007883	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74007883delA	uc003pgo.2	-						C6orf147_uc011dym.1_Intron	NM_030568	NP_085045			KH homology domain containing 1							integral to membrane	RNA binding			skin(1)	1																		---	---	---	---
SLC17A5	26503	broad.mit.edu	37	6	74360414	74360414	+	Intron	DEL	A	-	-	rs111807303		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74360414delA	uc003phn.3	-						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	74642886	74642886	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74642886delA								CD109 (104846 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	74666452	74666452	+	IGR	DEL	C	-	-	rs11335544		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74666452delC								CD109 (128412 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	74750239	74750239	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74750239delT								CD109 (212199 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	75192066	75192069	+	Intron	DEL	GTGT	-	-	rs112234299		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:75192066_75192069delGTGT	uc003phr.2	+											Homo sapiens full length insert cDNA clone ZD50H02.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	75533638	75533638	+	IGR	DEL	A	-	-	rs112991862		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:75533638delA								CD109 (995598 upstream) : COL12A1 (260405 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	75533731	75533731	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:75533731delT								CD109 (995691 upstream) : COL12A1 (260312 downstream)																																			---	---	---	---
COL12A1	1303	broad.mit.edu	37	6	75798175	75798175	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:75798175delA	uc003phs.2	-						COL12A1_uc003pht.2_Intron	NM_004370	NP_004361			collagen, type XII, alpha 1 long isoform						cell adhesion|collagen fibril organization|skeletal system development	collagen type XII|extracellular space	extracellular matrix structural constituent conferring tensile strength			ovary(6)|large_intestine(1)|breast(1)|skin(1)	9																		---	---	---	---
COL12A1	1303	broad.mit.edu	37	6	75874987	75874988	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:75874987_75874988delAA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	77111305	77111306	+	IGR	INS	-	AGTA	AGTA	rs148232760	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:77111305_77111306insAGTA								IMPG1 (328970 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	77737026	77737026	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:77737026delT								IMPG1 (954691 upstream) : HTR1B (434922 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	78280967	78280967	+	IGR	DEL	A	-	-	rs79010918		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:78280967delA								HTR1B (107847 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	78624551	78624551	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:78624551delT								HTR1B (451431 upstream) : IRAK1BP1 (952638 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	78815516	78815517	+	IGR	DEL	AG	-	-	rs71546096		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:78815516_78815517delAG								HTR1B (642396 upstream) : IRAK1BP1 (761672 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	79549128	79549128	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:79549128delA								None (None upstream) : IRAK1BP1 (28061 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	79879542	79879542	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:79879542delA								PHIP (91531 upstream) : HMGN3 (31422 downstream)																																			---	---	---	---
HMGN3	9324	broad.mit.edu	37	6	79947223	79947224	+	5'Flank	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:80409424delT	uc003piz.1	+	4						NM_031469	NP_113657			SH3 domain binding glutamic acid-rich protein							nucleus	SH3 domain binding				0		all_cancers(76;0.00188)|Acute lymphoblastic leukemia(125;1.24e-05)|all_hematologic(105;0.00223)|all_epithelial(107;0.174)		BRCA - Breast invasive adenocarcinoma(397;0.0278)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	80422636	80422637	+	IGR	DEL	AG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:80422636_80422637delAG								SH3BGRL2 (9267 upstream) : RNY4 (28999 downstream)																																			---	---	---	---
TTK	7272	broad.mit.edu	37	6	80751897	80751897	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	80797152	80797153	+	IGR	INS	-	CC	CC	rs66964485		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:80797152_80797153insCC								TTK (44915 upstream) : BCKDHB (19191 downstream)																																			---	---	---	---
BCKDHB	594	broad.mit.edu	37	6	81032857	81032857	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:81032857delC	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	81678238	81678239	+	IGR	INS	-	TGTC	TGTC	rs142757117	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:81678238_81678239insTGTC								BCKDHB (622251 upstream) : FAM46A (777209 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	83121496	83121496	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83121496delG								TPBG (44882 upstream) : UBE2CBP (480690 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	83216920	83216920	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83216920delA								TPBG (140306 upstream) : UBE2CBP (385266 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	83597431	83597431	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83597431delA								TPBG (520817 upstream) : UBE2CBP (4755 downstream)																																			---	---	---	---
DOPEY1	23033	broad.mit.edu	37	6	83850589	83850589	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83850589delT	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)														---	---	---	---
ME1	4199	broad.mit.edu	37	6	83924663	83924664	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83924663_83924664insT	uc003pjy.2	-						ME1_uc011dzb.1_Intron|ME1_uc011dzc.1_Intron	NM_002395	NP_002386			cytosolic malic enzyme 1						carbohydrate metabolic process|cellular lipid metabolic process|malate metabolic process|NADP biosynthetic process|response to carbohydrate stimulus|response to hormone stimulus	cytosol	ADP binding|electron carrier activity|malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) activity|manganese ion binding|NAD binding|NADP binding			upper_aerodigestive_tract(1)|ovary(1)	2		all_cancers(76;1.28e-06)|Acute lymphoblastic leukemia(125;5.03e-07)|all_hematologic(105;0.000238)|all_epithelial(107;0.00218)		BRCA - Breast invasive adenocarcinoma(397;0.0641)	NADH(DB00157)													---	---	---	---
ME1	4199	broad.mit.edu	37	6	83947034	83947034	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83947034delA	uc003pjy.2	-						ME1_uc011dzb.1_Intron|ME1_uc011dzc.1_Intron	NM_002395	NP_002386			cytosolic malic enzyme 1						carbohydrate metabolic process|cellular lipid metabolic process|malate metabolic process|NADP biosynthetic process|response to carbohydrate stimulus|response to hormone stimulus	cytosol	ADP binding|electron carrier activity|malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) activity|manganese ion binding|NAD binding|NADP binding			upper_aerodigestive_tract(1)|ovary(1)	2		all_cancers(76;1.28e-06)|Acute lymphoblastic leukemia(125;5.03e-07)|all_hematologic(105;0.000238)|all_epithelial(107;0.00218)		BRCA - Breast invasive adenocarcinoma(397;0.0641)	NADH(DB00157)													---	---	---	---
ME1	4199	broad.mit.edu	37	6	84010918	84010918	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84010918delA	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	84557028	84557029	+	IGR	INS	-	AC	AC	rs140088740	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84557028_84557029insAC								SNAP91 (137901 upstream) : RIPPLY2 (5956 downstream)																																			---	---	---	---
CYB5R4	51167	broad.mit.edu	37	6	84634468	84634468	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84634468delT	uc003pkf.2	+							NM_016230	NP_057314			cytochrome b5 reductase 4						cell development|detection of oxygen|generation of precursor metabolites and energy|glucose homeostasis|insulin secretion|response to antibiotic|superoxide metabolic process	endoplasmic reticulum|perinuclear region of cytoplasm	cytochrome-b5 reductase activity|heme binding|NAD(P)H oxidase activity			breast(2)	2		all_cancers(76;7e-07)|Acute lymphoblastic leukemia(125;2.69e-07)|all_hematologic(105;0.000151)|all_epithelial(107;0.00128)		BRCA - Breast invasive adenocarcinoma(397;0.0871)														---	---	---	---
KIAA1009	22832	broad.mit.edu	37	6	84926895	84926896	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84926895_84926896delAA	uc010kbp.2	-						KIAA1009_uc003pkj.3_Intron|KIAA1009_uc003pkk.2_Intron	NM_014895	NP_055710			KIAA1009 protein						cell division|mitosis	centrosome|nucleus|plasma membrane|spindle	protein binding			ovary(1)	1		all_cancers(76;1.5e-06)|Acute lymphoblastic leukemia(125;2.69e-07)|all_hematologic(105;0.000151)|all_epithelial(107;0.00258)		BRCA - Breast invasive adenocarcinoma(397;0.089)														---	---	---	---
TBX18	9096	broad.mit.edu	37	6	85402393	85402393	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:85402393delA	uc010kbq.1	-							NM_001080508	NP_001073977			T-box 18						multicellular organismal development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)|pancreas(2)|lung(1)	5		all_cancers(76;0.000283)|Acute lymphoblastic leukemia(125;3.66e-08)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0858)		BRCA - Breast invasive adenocarcinoma(108;0.0267)														---	---	---	---
TBX18	9096	broad.mit.edu	37	6	85455785	85455785	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:85455785delT	uc003pkl.1	-						TBX18_uc010kbq.1_Intron	NM_001080508	NP_001073977			T-box 18						multicellular organismal development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)|pancreas(2)|lung(1)	5		all_cancers(76;0.000283)|Acute lymphoblastic leukemia(125;3.66e-08)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0858)		BRCA - Breast invasive adenocarcinoma(108;0.0267)														---	---	---	---
TBX18	9096	broad.mit.edu	37	6	85465126	85465126	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:85465126delA	uc003pkl.1	-						TBX18_uc010kbq.1_Intron	NM_001080508	NP_001073977			T-box 18						multicellular organismal development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)|pancreas(2)|lung(1)	5		all_cancers(76;0.000283)|Acute lymphoblastic leukemia(125;3.66e-08)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0858)		BRCA - Breast invasive adenocarcinoma(108;0.0267)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	85501318	85501318	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:85501318delT								TBX18 (27419 upstream) : NT5E (657984 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	85532842	85532842	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:85532842delA								TBX18 (58943 upstream) : NT5E (626460 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	85668776	85668776	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:85668776delT								TBX18 (194877 upstream) : NT5E (490526 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	86067566	86067568	+	IGR	DEL	CAA	-	-	rs34151985		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:86067566_86067568delCAA								TBX18 (593667 upstream) : NT5E (91734 downstream)																																			---	---	---	---
NT5E	4907	broad.mit.edu	37	6	86191520	86191520	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:86191520delA	uc003pko.3	+						NT5E_uc010kbr.2_Intron	NM_002526	NP_002517			5' nucleotidase, ecto precursor						DNA metabolic process|purine base metabolic process|pyrimidine base metabolic process|pyrimidine nucleoside catabolic process	anchored to membrane|cytoplasm|membrane fraction|plasma membrane	5'-nucleotidase activity|nucleotide binding			ovary(3)|central_nervous_system(1)	4		all_cancers(76;0.000215)|Acute lymphoblastic leukemia(125;3.66e-08)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0427)		BRCA - Breast invasive adenocarcinoma(108;0.0417)	Pentoxifylline(DB00806)													---	---	---	---
SNX14	57231	broad.mit.edu	37	6	86271544	86271545	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:86271544_86271545delTT	uc003pkr.2	-						SNX14_uc003pkp.2_Intron|SNX14_uc003pkq.2_Intron|SNX14_uc011dzg.1_Intron|SNX14_uc003pks.2_Intron|SNX14_uc003pkt.2_Intron	NM_153816	NP_722523			sorting nexin 14 isoform a						cell communication|protein transport	integral to membrane	phosphatidylinositol binding|signal transducer activity				0		all_cancers(76;4.83e-07)|Acute lymphoblastic leukemia(125;3.3e-08)|Prostate(29;2.55e-07)|all_hematologic(105;3.66e-05)|all_epithelial(107;0.000695)|Lung NSC(302;0.197)|all_lung(197;0.24)		BRCA - Breast invasive adenocarcinoma(108;0.0423)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	86402039	86402039	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:86402039delG								SNHG5 (13588 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	86403329	86403329	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:86403329delA								SNHG5 (14878 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	86772142	86772143	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:86772142_86772143insT								SNHG5 (383691 upstream) : HTR1E (874881 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	86844917	86844918	+	IGR	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:86844917_86844918delAC								SNHG5 (456466 upstream) : HTR1E (802106 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	87022667	87022667	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87022667delG								SNHG5 (634216 upstream) : HTR1E (624357 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	87836703	87836704	+	IGR	INS	-	AGAG	AGAG	rs150388233	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87836703_87836704insAGAG								CGA (31879 upstream) : ZNF292 (25847 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	87836777	87836782	+	IGR	DEL	CACACC	-	-	rs35509377		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87836777_87836782delCACACC								CGA (31953 upstream) : ZNF292 (25769 downstream)																																			---	---	---	---
ZNF292	23036	broad.mit.edu	37	6	87872004	87872004	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87872004delT	uc003plm.3	+						ZNF292_uc003plk.2_Intron|ZNF292_uc003pll.1_Intron	NM_015021	NP_055836			zinc finger protein 292						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)	4		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)														---	---	---	---
ZNF292	23036	broad.mit.edu	37	6	87971653	87971653	+	3'UTR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87971653delA	uc003plm.3	+	8						NM_015021	NP_055836			zinc finger protein 292						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)	4		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)														---	---	---	---
C6orf162	57150	broad.mit.edu	37	6	88049044	88049051	+	Intron	DEL	GTGTGTGT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88049044_88049051delGTGTGTGT	uc003plp.1	+						C6orf164_uc003plr.2_Intron|C6orf162_uc003plq.1_Intron	NM_001042493	NP_001035958			hypothetical protein LOC57150							integral to membrane					0		all_cancers(76;3.81e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.15e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.3e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0164)														---	---	---	---
RARS2	57038	broad.mit.edu	37	6	88228194	88228195	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88228194_88228195delTT	uc003pme.2	-						RARS2_uc003pmb.2_Intron|RARS2_uc003pmc.2_Intron|RARS2_uc003pmd.2_Intron|RARS2_uc003pmf.2_Intron	NM_020320	NP_064716			arginyl-tRNA synthetase 2, mitochondrial						arginyl-tRNA aminoacylation	mitochondrial matrix	arginine-tRNA ligase activity|ATP binding|protein binding			ovary(2)|central_nervous_system(1)	3		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0456)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	88782846	88782846	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88782846delC								SPACA1 (6297 upstream) : CNR1 (66741 downstream)																																			---	---	---	---
RNGTT	8732	broad.mit.edu	37	6	89609321	89609321	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:89609321delA	uc003pmr.2	-						RNGTT_uc003pms.2_Intron|RNGTT_uc011dzu.1_Intron|RNGTT_uc003pmt.2_Intron	NM_003800	NP_003791			RNA guanylyltransferase and 5'-phosphatase						interspecies interaction between organisms|mRNA capping|transcription from RNA polymerase II promoter|viral reproduction	nucleoplasm	GTP binding|mRNA guanylyltransferase activity|polynucleotide 5'-phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			upper_aerodigestive_tract(1)	1		all_cancers(76;4.07e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.79e-07)|all_epithelial(107;6.86e-05)		BRCA - Breast invasive adenocarcinoma(108;0.151)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	89692039	89692039	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:89692039delA								RNGTT (18691 upstream) : PNRC1 (98390 downstream)																																			---	---	---	---
RRAGD	58528	broad.mit.edu	37	6	90105689	90105690	+	Intron	DEL	AA	-	-	rs76173954		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90105689_90105690delAA	uc003pnd.3	-						RRAGD_uc010kcc.2_Intron	NM_021244	NP_067067			Ras-related GTP binding D						cellular protein localization|cellular response to amino acid stimulus|positive regulation of TOR signaling cascade	lysosome|nucleus	GTP binding|protein heterodimerization activity			ovary(2)|central_nervous_system(1)	3		all_cancers(76;7.01e-07)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00139)		BRCA - Breast invasive adenocarcinoma(108;0.0144)														---	---	---	---
ANKRD6	22881	broad.mit.edu	37	6	90319022	90319022	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90319022delT	uc003pni.3	+						ANKRD6_uc003pne.3_Intron|ANKRD6_uc003pnf.3_Intron|ANKRD6_uc011dzy.1_Intron|ANKRD6_uc010kcd.2_Intron|LYRM2_uc010kce.1_Intron|LYRM2_uc003png.2_Intron|ANKRD6_uc003pnh.3_Intron	NM_014942	NP_055757			ankyrin repeat domain 6								protein binding			ovary(2)|pancreas(1)	3		all_cancers(76;1.22e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.79e-07)|all_epithelial(107;1.83e-05)|Lung NSC(302;0.239)		BRCA - Breast invasive adenocarcinoma(108;0.0209)														---	---	---	---
MDN1	23195	broad.mit.edu	37	6	90370071	90370071	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90370071delT	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	90374456	90374456	+	Intron	DEL	A	-	-	rs3818133	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90374456delA	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	90398012	90398012	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90398012delA	uc003pnn.1	-							NM_014611	NP_055426			MDN1, midasin homolog						protein complex assembly|regulation of protein complex assembly	nucleus	ATP binding|ATPase activity|unfolded protein binding			ovary(8)|skin(2)	10		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)														---	---	---	---
CASP8AP2	9994	broad.mit.edu	37	6	90539466	90539467	+	5'Flank	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90539466_90539467delTT	uc003pnr.2	+						CASP8AP2_uc003pns.2_5'Flank|CASP8AP2_uc003pnt.2_5'Flank|CASP8AP2_uc011dzz.1_5'Flank	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	90703522	90703523	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90703522_90703523delTT	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	90809108	90809109	+	Intron	INS	-	T	T	rs146137916	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90809108_90809109insT	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	90936417	90936417	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90936417delT	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	91186176	91186177	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:91186176_91186177delAA								BACH2 (179614 upstream) : MAP3K7 (39176 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	91194053	91194056	+	IGR	DEL	ACAG	-	-	rs71735859		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:91194053_91194056delACAG								BACH2 (187491 upstream) : MAP3K7 (31297 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	91214444	91214444	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:91214444delA								BACH2 (207882 upstream) : MAP3K7 (10909 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	92045130	92045131	+	IGR	DEL	GT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:92045130_92045131delGT								MAP3K7 (748223 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	92881403	92881403	+	IGR	DEL	A	-	-	rs78692365		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:92881403delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	93469929	93469929	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:93469929delA								None (None upstream) : EPHA7 (479813 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	93900536	93900537	+	IGR	INS	-	TC	TC	rs149503875	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:93900536_93900537insTC								None (None upstream) : EPHA7 (49205 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	95158811	95158811	+	IGR	DEL	A	-	-	rs71542078		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:95158811delA								TSG1 (672612 upstream) : MANEA (866602 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	95430734	95430734	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:95430734delA								TSG1 (944535 upstream) : MANEA (594679 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	95949218	95949218	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:95949218delT								None (None upstream) : MANEA (76195 downstream)																																			---	---	---	---
FHL5	9457	broad.mit.edu	37	6	97053626	97053626	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97053626delT	uc003pos.1	+						FHL5_uc003pot.1_Intron	NM_020482	NP_065228			activator of cAMP-responsive element modulator							nucleus	zinc ion binding			ovary(2)	2		all_cancers(76;1.57e-07)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00266)|Colorectal(196;0.0341)|Lung NSC(302;0.204)		BRCA - Breast invasive adenocarcinoma(108;0.0948)														---	---	---	---
FHL5	9457	broad.mit.edu	37	6	97054121	97054122	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97054121_97054122delTT	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)														---	---	---	---
C6orf167	253714	broad.mit.edu	37	6	97621376	97621376	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97621376delA	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	97629570	97629570	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97629570delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	98164083	98164084	+	IGR	INS	-	C	C	rs141152695	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:98164083_98164084insC								C6orf167 (433022 upstream) : MIR2113 (308323 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	98318814	98318814	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:98318814delA								C6orf167 (587753 upstream) : MIR2113 (153593 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	98659813	98659813	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:98659813delA								MIR2113 (187316 upstream) : POU3F2 (622767 downstream)																																			---	---	---	---
SFRS18	25957	broad.mit.edu	37	6	99874138	99874138	+	5'Flank	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:99874138delC	uc003ppo.3	-						SFRS18_uc003ppp.3_5'Flank|SFRS18_uc011eag.1_5'Flank|SFRS18_uc003ppr.2_5'Flank|SFRS18_uc003ppt.2_5'Flank|SFRS18_uc003pps.2_5'Flank|uc003ppu.3_RNA	NM_032870	NP_116259			splicing factor, arginine/serine-rich 130							nuclear speck					0		all_cancers(76;1.24e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.00716)|Colorectal(196;0.0691)|Lung NSC(302;0.186)		BRCA - Breast invasive adenocarcinoma(108;0.0631)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	100192803	100192803	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:100192803delT								PRDM13 (129349 upstream) : MCHR2 (174983 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	100321033	100321040	+	IGR	DEL	CTCTCTCT	-	-	rs34887237		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:100321033_100321040delCTCTCTCT								PRDM13 (257579 upstream) : MCHR2 (46746 downstream)																																			---	---	---	---
MCHR2	84539	broad.mit.edu	37	6	100431605	100431605	+	Intron	DEL	A	-	-	rs67301959		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:100431605delA	uc003pqh.1	-						MCHR2_uc003pqi.1_Intron	NM_001040179	NP_001035269			melanin-concentrating hormone receptor 2							integral to membrane|plasma membrane	G-protein coupled receptor activity			lung(3)|ovary(2)|breast(1)|central_nervous_system(1)|skin(1)	8		all_cancers(76;4.87e-05)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0309)|Colorectal(196;0.069)		BRCA - Breast invasive adenocarcinoma(108;0.0429)														---	---	---	---
ASCC3	10973	broad.mit.edu	37	6	100979446	100979446	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:100979446delT	uc003pqk.2	-							NM_006828	NP_006819			activating signal cointegrator 1 complex subunit						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|microtubule cytoskeleton	ATP binding|ATP-dependent helicase activity|nucleic acid binding			ovary(5)|skin(1)	6		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	101340153	101340153	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:101340153delG								ASCC3 (10929 upstream) : GRIK2 (506752 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	101657753	101657753	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:101657753delC								ASCC3 (328529 upstream) : GRIK2 (189152 downstream)																																			---	---	---	---
GRIK2	2898	broad.mit.edu	37	6	102104552	102104553	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:102104552_102104553insA	uc003pqp.3	+						GRIK2_uc003pqn.2_Intron|GRIK2_uc003pqo.3_Intron|GRIK2_uc010kcw.2_Intron	NM_021956	NP_068775			glutamate receptor, ionotropic, kainate 2						glutamate signaling pathway|induction of programmed cell death in response to chemical stimulus|neuron apoptosis|positive regulation of synaptic transmission|regulation of short-term neuronal synaptic plasticity	cell junction|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			ovary(2)|pancreas(1)|breast(1)|skin(1)	5		all_cancers(76;1.19e-07)|Acute lymphoblastic leukemia(125;6.17e-11)|all_hematologic(75;6.01e-08)|all_epithelial(87;0.0121)|Colorectal(196;0.14)		all cancers(137;0.112)|BRCA - Breast invasive adenocarcinoma(108;0.124)|GBM - Glioblastoma multiforme(226;0.206)	L-Glutamic Acid(DB00142)													---	---	---	---
GRIK2	2898	broad.mit.edu	37	6	102133965	102133966	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:102133965_102133966delAA	uc003pqp.3	+						GRIK2_uc003pqn.2_Intron|GRIK2_uc003pqo.3_Intron|GRIK2_uc010kcw.2_Intron	NM_021956	NP_068775			glutamate receptor, ionotropic, kainate 2						glutamate signaling pathway|induction of programmed cell death in response to chemical stimulus|neuron apoptosis|positive regulation of synaptic transmission|regulation of short-term neuronal synaptic plasticity	cell junction|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			ovary(2)|pancreas(1)|breast(1)|skin(1)	5		all_cancers(76;1.19e-07)|Acute lymphoblastic leukemia(125;6.17e-11)|all_hematologic(75;6.01e-08)|all_epithelial(87;0.0121)|Colorectal(196;0.14)		all cancers(137;0.112)|BRCA - Breast invasive adenocarcinoma(108;0.124)|GBM - Glioblastoma multiforme(226;0.206)	L-Glutamic Acid(DB00142)													---	---	---	---
GRIK2	2898	broad.mit.edu	37	6	102396190	102396190	+	Intron	DEL	T	-	-	rs76762565		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:102396190delT	uc003pqp.3	+						GRIK2_uc003pqo.3_Intron|GRIK2_uc010kcw.2_Intron	NM_021956	NP_068775			glutamate receptor, ionotropic, kainate 2						glutamate signaling pathway|induction of programmed cell death in response to chemical stimulus|neuron apoptosis|positive regulation of synaptic transmission|regulation of short-term neuronal synaptic plasticity	cell junction|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			ovary(2)|pancreas(1)|breast(1)|skin(1)	5		all_cancers(76;1.19e-07)|Acute lymphoblastic leukemia(125;6.17e-11)|all_hematologic(75;6.01e-08)|all_epithelial(87;0.0121)|Colorectal(196;0.14)		all cancers(137;0.112)|BRCA - Breast invasive adenocarcinoma(108;0.124)|GBM - Glioblastoma multiforme(226;0.206)	L-Glutamic Acid(DB00142)													---	---	---	---
GRIK2	2898	broad.mit.edu	37	6	102441060	102441060	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:102441060delA	uc003pqp.3	+						GRIK2_uc003pqo.3_Intron|GRIK2_uc010kcw.2_Intron	NM_021956	NP_068775			glutamate receptor, ionotropic, kainate 2						glutamate signaling pathway|induction of programmed cell death in response to chemical stimulus|neuron apoptosis|positive regulation of synaptic transmission|regulation of short-term neuronal synaptic plasticity	cell junction|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			ovary(2)|pancreas(1)|breast(1)|skin(1)	5		all_cancers(76;1.19e-07)|Acute lymphoblastic leukemia(125;6.17e-11)|all_hematologic(75;6.01e-08)|all_epithelial(87;0.0121)|Colorectal(196;0.14)		all cancers(137;0.112)|BRCA - Breast invasive adenocarcinoma(108;0.124)|GBM - Glioblastoma multiforme(226;0.206)	L-Glutamic Acid(DB00142)													---	---	---	---
Unknown	0	broad.mit.edu	37	6	104269398	104269398	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:104269398delA								None (None upstream) : HACE1 (906570 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	104389654	104389654	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:104389654delT								None (None upstream) : HACE1 (786314 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	104628321	104628321	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:104628321delA								None (None upstream) : HACE1 (547647 downstream)																																			---	---	---	---
HACE1	57531	broad.mit.edu	37	6	105300084	105300085	+	Intron	INS	-	TT	TT	rs45443697		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:105300084_105300085insTT	uc003pqu.1	-						HACE1_uc010kcy.1_Intron|HACE1_uc010kcz.1_Intron	NM_020771	NP_065822			HECT domain and ankyrin repeat containing, E3						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	endoplasmic reticulum	ubiquitin-protein ligase activity			ovary(5)|lung(2)	7		all_cancers(87;6.89e-05)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0216)|Colorectal(196;0.202)		BRCA - Breast invasive adenocarcinoma(108;0.122)|Epithelial(106;0.204)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	105902524	105902524	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:105902524delC								PREP (51555 upstream) : PRDM1 (631671 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	106230995	106230995	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:106230995delT								PREP (380026 upstream) : PRDM1 (303200 downstream)																																			---	---	---	---
ATG5	9474	broad.mit.edu	37	6	106646653	106646653	+	Intron	DEL	A	-	-	rs67324379		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:106646653delA	uc003prf.2	-						ATG5_uc010kdb.2_Intron|ATG5_uc003prg.2_Intron|ATG5_uc010kdc.2_Intron	NM_004849	NP_004840			APG5 autophagy 5-like						apoptosis|autophagic vacuole assembly|negative regulation of type I interferon production|post-translational protein modification	autophagic vacuole|pre-autophagosomal structure membrane	protein binding			large_intestine(1)	1	Breast(9;0.0296)	all_cancers(87;0.000301)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.0612)|Lung NSC(302;0.216)	BRCA - Breast invasive adenocarcinoma(8;0.00802)	OV - Ovarian serous cystadenocarcinoma(136;0.128)|Epithelial(106;0.159)|all cancers(137;0.18)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	107116510	107116510	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107116510delA								QRSL1 (220 upstream) : MIR587 (115490 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	107281042	107281043	+	IGR	INS	-	G	G	rs148470739	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107281042_107281043insG								MIR587 (48947 upstream) : C6orf203 (68364 downstream)																																			---	---	---	---
SOBP	55084	broad.mit.edu	37	6	107847155	107847155	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107847155delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	108595186	108595186	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108595186delA								SNX3 (12722 upstream) : LACE1 (20912 downstream)																																			---	---	---	---
ARMC2	84071	broad.mit.edu	37	6	109285993	109285994	+	Intron	DEL	AA	-	-	rs77214837		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109285993_109285994delAA	uc003pss.3	+						ARMC2_uc011eao.1_Intron	NM_032131	NP_115507			armadillo repeat containing 2								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	109312432	109312433	+	Intron	DEL	GT	-	-	rs112709389		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109312432_109312433delGT	uc003pst.3	-						SESN1_uc003psu.2_Intron	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)														---	---	---	---
SESN1	27244	broad.mit.edu	37	6	109343253	109343254	+	Intron	DEL	TT	-	-	rs72434251		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109343253_109343254delTT	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	109818530	109818531	+	Intron	DEL	CA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109818530_109818531delCA	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																		---	---	---	---
AKD1	221264	broad.mit.edu	37	6	109868402	109868402	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109868402delA	uc003ptn.2	-						AKD1_uc011eat.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																		---	---	---	---
CDC40	51362	broad.mit.edu	37	6	110514616	110514616	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:110514616delT	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)														---	---	---	---
SLC22A16	85413	broad.mit.edu	37	6	110779350	110779351	+	Intron	DEL	CT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:110779350_110779351delCT	uc003puf.2	-						SLC22A16_uc003pue.2_Intron|SLC22A16_uc003pug.2_Intron	NM_033125	NP_149116			solute carrier family 22, member 16						acid secretion|cell differentiation|multicellular organismal development|single fertilization|sperm motility|spermatogenesis	integral to membrane	carnitine transporter activity			ovary(1)	1		all_cancers(87;0.00221)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|all_epithelial(87;0.0485)|Colorectal(196;0.101)		OV - Ovarian serous cystadenocarcinoma(136;0.0513)|Epithelial(106;0.0921)|all cancers(137;0.115)														---	---	---	---
SLC22A16	85413	broad.mit.edu	37	6	110780207	110780208	+	Intron	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:110780207_110780208delTG	uc003puf.2	-						SLC22A16_uc003pue.2_Intron|SLC22A16_uc003pug.2_Intron	NM_033125	NP_149116			solute carrier family 22, member 16						acid secretion|cell differentiation|multicellular organismal development|single fertilization|sperm motility|spermatogenesis	integral to membrane	carnitine transporter activity			ovary(1)	1		all_cancers(87;0.00221)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|all_epithelial(87;0.0485)|Colorectal(196;0.101)		OV - Ovarian serous cystadenocarcinoma(136;0.0513)|Epithelial(106;0.0921)|all cancers(137;0.115)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	111296806	111296806	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111296806delT								GTF3C6 (7717 upstream) : RPF2 (6485 downstream)																																			---	---	---	---
FYN	2534	broad.mit.edu	37	6	112156834	112156834	+	Intron	DEL	T	-	-	rs67298731		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112156834delT	uc003pvk.2	-							NM_002037	NP_002028			protein-tyrosine kinase fyn isoform a						axon guidance|calcium ion transport|feeding behavior|interspecies interaction between organisms|intracellular protein kinase cascade|learning|leukocyte migration|platelet activation|regulation of defense response to virus by virus|T cell costimulation|T cell receptor signaling pathway|viral reproduction	cytosol|endosome|plasma membrane	ATP binding|glycoprotein binding|identical protein binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity			lung(5)|central_nervous_system(1)|skin(1)	7		all_cancers(87;1.37e-05)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.00125)|Colorectal(196;0.0211)		all cancers(137;0.0451)|OV - Ovarian serous cystadenocarcinoma(136;0.0476)|Epithelial(106;0.102)	Dasatinib(DB01254)													---	---	---	---
WISP3	8838	broad.mit.edu	37	6	112389434	112389434	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112389434delA	uc003pvm.2	+	5	726	c.616delA	c.(616-618)AAAfs	p.K206fs	WISP3_uc003pvn.2_RNA|WISP3_uc003pvo.2_Frame_Shift_Del_p.K224fs	NM_003880	NP_003871	O95389	WISP3_HUMAN	WNT1 inducible signaling pathway protein 3	206					cell-cell signaling|regulation of cell growth|signal transduction	extracellular region|soluble fraction	growth factor activity|insulin-like growth factor binding				0		all_cancers(87;0.000196)|Acute lymphoblastic leukemia(125;1.18e-05)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0283)|OV - Ovarian serous cystadenocarcinoma(136;0.0613)|Epithelial(106;0.0827)|GBM - Glioblastoma multiforme(226;0.0972)|BRCA - Breast invasive adenocarcinoma(108;0.246)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	113095046	113095047	+	IGR	DEL	GG	-	-	rs68192935		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:113095046_113095047delGG								RFPL4B (422548 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	114026117	114026117	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:114026117delA								None (None upstream) : MARCKS (152410 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	115656068	115656068	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:115656068delA								HS3ST5 (992528 upstream) : FRK (606625 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	116171478	116171479	+	IGR	INS	-	TG	TG			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116171478_116171479insTG								None (None upstream) : FRK (91214 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	116227181	116227182	+	IGR	DEL	AA	-	-	rs138281020		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116227181_116227182delAA								None (None upstream) : FRK (35511 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	116760104	116760104	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116760104delT								DSE (664 upstream) : FAM26F (22452 downstream)																																			---	---	---	---
RWDD1	51389	broad.mit.edu	37	6	116910213	116910213	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116910213delT	uc003pxd.2	+						RWDD1_uc003pxb.2_Intron|RWDD1_uc003pxc.2_Intron	NM_015952	NP_057036			RWD domain containing 1 isoform a								protein binding			ovary(2)|central_nervous_system(1)	3		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.026)|all cancers(137;0.0312)|OV - Ovarian serous cystadenocarcinoma(136;0.0689)|Epithelial(106;0.161)														---	---	---	---
KPNA5	3841	broad.mit.edu	37	6	117026119	117026119	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117026119delT	uc003pxh.2	+							NM_002269	NP_002260			karyopherin alpha 5						NLS-bearing substrate import into nucleus	cytoplasm|nuclear pore	protein binding|protein transporter activity			breast(3)|skin(1)	4		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0298)|all cancers(137;0.0461)|OV - Ovarian serous cystadenocarcinoma(136;0.0513)|Epithelial(106;0.212)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	117465436	117465436	+	IGR	DEL	A	-	-	rs67104805		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117465436delA								RFX6 (212128 upstream) : VGLL2 (121285 downstream)																																			---	---	---	---
ROS1	6098	broad.mit.edu	37	6	117687160	117687160	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117687160delA	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								---	---	---	---
SLC35F1	222553	broad.mit.edu	37	6	118265754	118265755	+	Intron	DEL	AT	-	-	rs59570452		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:118265754_118265755delAT	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)														---	---	---	---
C6orf204	387119	broad.mit.edu	37	6	118883526	118883526	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:118883526delT	uc003pxz.1	-						C6orf204_uc003pya.1_Intron|C6orf204_uc003pyb.2_Intron|C6orf204_uc011ebj.1_Intron|C6orf204_uc003pyc.2_Intron	NM_001042475	NP_001035940			chromosome 6 open reading frame 204 isoform a							centrosome				breast(1)	1		all_cancers(87;0.0814)|all_epithelial(87;0.115)		GBM - Glioblastoma multiforme(226;0.0114)|all cancers(137;0.035)|OV - Ovarian serous cystadenocarcinoma(136;0.0618)														---	---	---	---
C6orf204	387119	broad.mit.edu	37	6	119017841	119017843	+	Intron	DEL	TTT	-	-	rs1771757		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:119017841_119017843delTTT	uc003pya.1	-						C6orf204_uc003pyc.2_Intron	NM_206921	NP_996804			chromosome 6 open reading frame 204 isoform b							centrosome				breast(1)	1		all_cancers(87;0.0814)|all_epithelial(87;0.115)		GBM - Glioblastoma multiforme(226;0.0114)|all cancers(137;0.035)|OV - Ovarian serous cystadenocarcinoma(136;0.0618)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	119116802	119116803	+	IGR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:119116802_119116803insA								C6orf204 (85564 upstream) : ASF1A (98438 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	119786562	119786562	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:119786562delT	uc003pyn.1	-											Homo sapiens cDNA FLJ39782 fis, clone SPLEN2002175.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	120119243	120119244	+	IGR	INS	-	TTCC	TTCC	rs142572854	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:120119243_120119244insTTCC								MAN1A1 (448317 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	122367200	122367200	+	IGR	DEL	A	-	-	rs71857273		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:122367200delA								GJA1 (596328 upstream) : HSF2 (353496 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	122437790	122437790	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:122437790delG								GJA1 (666918 upstream) : HSF2 (282906 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	123190677	123190678	+	IGR	INS	-	TG	TG	rs139664990	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:123190677_123190678insTG								SMPDL3A (59815 upstream) : CLVS2 (126904 downstream)																																			---	---	---	---
TRDN	10345	broad.mit.edu	37	6	123786033	123786033	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:123786033delA	uc003pzj.1	-						TRDN_uc003pzk.1_Intron|TRDN_uc003pzl.1_Intron|TRDN_uc010ken.2_Frame_Shift_Del_p.S297fs|uc003pzm.1_Intron	NM_006073	NP_006064			triadin						muscle contraction	integral to membrane|plasma membrane|sarcoplasmic reticulum membrane	receptor binding			ovary(1)	1				GBM - Glioblastoma multiforme(226;0.184)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	123967457	123967457	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:123967457delA								TRDN (9515 upstream) : NKAIN2 (157612 downstream)																																			---	---	---	---
NKAIN2	154215	broad.mit.edu	37	6	124260950	124260950	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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	124313112	124313112	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:124313112delA	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	124905945	124905945	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:124905945delA	uc003pzo.2	+						NKAIN2_uc003pzn.1_Intron|NKAIN2_uc003pzp.2_Intron|NKAIN2_uc010keq.2_Intron|NKAIN2_uc010ker.2_Intron	NM_001040214	NP_001035304			T-cell lymphoma breakpoint-associated target 1							integral to membrane|plasma membrane					0				GBM - Glioblastoma multiforme(226;0.104)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	125187344	125187345	+	IGR	INS	-	TC	TC	rs140753166	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:125187344_125187345insTC								NKAIN2 (40560 upstream) : STL (42049 downstream)																																			---	---	---	---
NCOA7	135112	broad.mit.edu	37	6	126156533	126156534	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:126156533_126156534delAA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	126400882	126400882	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:126400882delA								TRMT11 (40464 upstream) : CENPW (260371 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	126866912	126866912	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:126866912delA	uc003qaq.1	-											Homo sapiens cDNA FLJ45564 fis, clone BRTHA3007469.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	127330243	127330243	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:127330243delA	uc003qaq.1	-											Homo sapiens cDNA FLJ45564 fis, clone BRTHA3007469.																														---	---	---	---
C6orf174	387104	broad.mit.edu	37	6	127778155	127778155	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:127778155delA	uc003qbd.2	-						C6orf174_uc003qbc.2_Intron|KIAA0408_uc011ebs.1_Intron	NM_001012279	NP_001012279			hypothetical protein LOC387104 precursor							integral to membrane				breast(3)|ovary(2)|skin(1)	6				GBM - Glioblastoma multiforme(226;0.026)|all cancers(137;0.161)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	127956542	127956542	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:127956542delT								C6orf58 (43584 upstream) : THEMIS (72804 downstream)																																			---	---	---	---
PTPRK	5796	broad.mit.edu	37	6	128469133	128469133	+	Intron	DEL	A	-	-	rs71717019		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:128469133delA	uc003qbk.2	-						PTPRK_uc003qbj.2_Intron|PTPRK_uc010kfc.2_Intron|PTPRK_uc011ebu.1_Intron|PTPRK_uc003qbl.1_Intron|PTPRK_uc011ebv.1_Intron	NM_002844	NP_002835			protein tyrosine phosphatase, receptor type, K						cell migration|cellular response to reactive oxygen species|cellular response to UV|focal adhesion assembly|negative regulation of cell cycle|negative regulation of cell migration|negative regulation of keratinocyte proliferation|negative regulation of transcription, DNA-dependent|protein localization at cell surface|transforming growth factor beta receptor signaling pathway	adherens junction|cell surface|cell-cell junction|integral to plasma membrane|leading edge membrane	beta-catenin binding|gamma-catenin binding|protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(3)|skin(2)|pancreas(1)|kidney(1)|central_nervous_system(1)	8				all cancers(137;0.0118)|GBM - Glioblastoma multiforme(226;0.0372)|OV - Ovarian serous cystadenocarcinoma(136;0.24)														---	---	---	---
PTPRK	5796	broad.mit.edu	37	6	128718505	128718505	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:128718505delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	128867532	128867532	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:128867532delT								PTPRK (25662 upstream) : LAMA2 (336754 downstream)																																			---	---	---	---
ARHGAP18	93663	broad.mit.edu	37	6	129930151	129930151	+	Intron	DEL	A	-	-	rs79905860		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:129930151delA	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	129976746	129976746	+	Intron	DEL	T	-	-	rs75431369		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:129976746delT	uc003qbr.2	-						ARHGAP18_uc011ebw.1_Intron	NM_033515	NP_277050			Rho GTPase activating protein 18						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding			ovary(2)|skin(1)	3				OV - Ovarian serous cystadenocarcinoma(136;0.0621)|GBM - Glioblastoma multiforme(226;0.0638)|all cancers(137;0.074)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	130138622	130138622	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:130138622delA								ARHGAP18 (107252 upstream) : C6orf191 (13769 downstream)																																			---	---	---	---
L3MBTL3	84456	broad.mit.edu	37	6	130387432	130387435	+	Intron	DEL	TATA	-	-	rs66543366		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:130387432_130387435delTATA	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	131102806	131102806	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131102806delA								TMEM200A (338598 upstream) : LOC285733 (45518 downstream)																																			---	---	---	---
AKAP7	9465	broad.mit.edu	37	6	131475351	131475351	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131475351delA	uc003qck.2	+						AKAP7_uc011ebz.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)														---	---	---	---
ENPP3	5169	broad.mit.edu	37	6	132061607	132061607	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132061607delT	uc003qcu.3	+						ENPP3_uc010kfq.2_Intron|ENPP3_uc003qcv.2_Intron	NM_005021	NP_005012			ectonucleotide pyrophosphatase/phosphodiesterase						immune response|nucleoside triphosphate catabolic process|phosphate metabolic process	extracellular region|integral to plasma membrane|perinuclear region of cytoplasm	metal ion binding|nucleic acid binding|nucleoside-triphosphate diphosphatase activity|nucleotide diphosphatase activity|phosphodiesterase I activity|polysaccharide binding|scavenger receptor activity			ovary(3)|skin(1)	4	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0252)|OV - Ovarian serous cystadenocarcinoma(155;0.0511)														---	---	---	---
ENPP1	5167	broad.mit.edu	37	6	132190481	132190481	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132190481delT	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)													---	---	---	---
TAAR8	83551	broad.mit.edu	37	6	132871987	132871987	+	5'Flank	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132871987delT	uc011ecj.1	+							NM_053278	NP_444508			trace amine associated receptor 8							plasma membrane	G-protein coupled receptor activity			ovary(1)	1	Breast(56;0.112)			OV - Ovarian serous cystadenocarcinoma(155;0.00412)|GBM - Glioblastoma multiforme(226;0.00792)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	133524175	133524175	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:133524175delG								LOC285735 (96465 upstream) : EYA4 (37561 downstream)																																			---	---	---	---
EYA4	2070	broad.mit.edu	37	6	133723860	133723861	+	Intron	DEL	AC	-	-	rs66487611		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:133723860_133723861delAC	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	134397336	134397339	+	IGR	DEL	GCGC	-	-	rs62425854		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:134397336_134397339delGCGC								SLC2A12 (23547 upstream) : SGK1 (93046 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	134712892	134712892	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:134712892delT								SGK1 (73696 upstream) : ALDH8A1 (525637 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	134911426	134911426	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:134911426delT	uc003qev.1	-											AJ606331																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	135209714	135209714	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:135209714delA								SGK1 (570518 upstream) : ALDH8A1 (28815 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	135463581	135463581	+	IGR	DEL	T	-	-	rs76422346		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:135463581delT								HBS1L (87545 upstream) : MYB (38872 downstream)																																			---	---	---	---
C6orf217	100131814	broad.mit.edu	37	6	135929531	135929532	+	Intron	INS	-	T	T	rs147691661	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:135929531_135929532insT	uc003qgn.2	+						C6orf217_uc003qgo.2_Intron|C6orf217_uc010kgo.2_Intron					Homo sapiens cDNA clone IMAGE:4795512.												0																		---	---	---	---
MAP7	9053	broad.mit.edu	37	6	136683397	136683398	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136683397_136683398insA	uc003qgz.2	-						MAP7_uc011edf.1_Intron|MAP7_uc011edg.1_Intron|MAP7_uc010kgu.2_Intron|MAP7_uc011edh.1_Intron|MAP7_uc010kgv.2_Intron|MAP7_uc010kgs.2_Intron|MAP7_uc011edi.1_Intron|MAP7_uc010kgq.1_Intron|MAP7_uc003qha.1_Intron	NM_003980	NP_003971			microtubule-associated protein 7						establishment or maintenance of cell polarity|microtubule cytoskeleton organization|protein localization in plasma membrane|response to osmotic stress	basolateral plasma membrane|microtubule|microtubule associated complex|nucleus|perinuclear region of cytoplasm	receptor binding|structural molecule activity				0	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00199)|OV - Ovarian serous cystadenocarcinoma(155;0.00643)														---	---	---	---
PEX7	5191	broad.mit.edu	37	6	137232554	137232554	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:137232554delT	uc003qhd.2	+						PEX7_uc010kgx.2_Intron	NM_000288	NP_000279			peroxisomal biogenesis factor 7						ether lipid biosynthetic process|protein import into peroxisome matrix	peroxisome	peroxisome matrix targeting signal-2 binding				0	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000257)|OV - Ovarian serous cystadenocarcinoma(155;0.00492)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	137424915	137424917	+	IGR	DEL	TTC	-	-	rs67341759		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:137424915_137424917delTTC								IL20RA (58617 upstream) : IL22RA2 (40041 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	138375116	138375116	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138375116delC								TNFAIP3 (170671 upstream) : PERP (34526 downstream)																																			---	---	---	---
NHSL1	57224	broad.mit.edu	37	6	138782293	138782293	+	Intron	DEL	T	-	-	rs73573247	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138782293delT	uc003qhx.2	-						NHSL1_uc011edp.1_Intron|NHSL1_uc003qhy.2_Intron	NM_020464	NP_065197			NHS-like 1 isoform 1												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	138943484	138943484	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138943484delA								NHSL1 (49816 upstream) : CCDC28A (151173 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	139091907	139091907	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139091907delT	uc003qid.1	-						CCDC28A_uc003qie.2_5'Flank					Homo sapiens cDNA FLJ35273 fis, clone PROST2006020.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	139425139	139425139	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139425139delT								C6orf115 (60700 upstream) : HECA (31110 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	139687149	139687149	+	IGR	DEL	A	-	-	rs66578087		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139687149delA								TXLNB (73941 upstream) : CITED2 (6248 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	139815085	139815086	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139815085_139815086delAA								CITED2 (119300 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	140144680	140144680	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:140144680delT	uc003qir.2	+											Homo sapiens, clone IMAGE:5557975, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	141418407	141418407	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:141418407delA								None (None upstream) : NMBR (978339 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	142561359	142561360	+	IGR	INS	-	TG	TG	rs76184559	byFrequency;by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:142561359_142561360insTG								VTA1 (19276 upstream) : GPR126 (61696 downstream)																																			---	---	---	---
GPR126	57211	broad.mit.edu	37	6	142636108	142636109	+	Intron	INS	-	GT	GT	rs142026286	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:142636108_142636109insGT	uc010khc.2	+						GPR126_uc010khd.2_Intron|GPR126_uc010khe.2_Intron|GPR126_uc010khf.2_Intron|GPR126_uc003qix.2_Intron	NM_020455	NP_065188			G protein-coupled receptor 126 alpha 1						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(1)	1	Breast(32;0.176)			OV - Ovarian serous cystadenocarcinoma(155;9.33e-06)|GBM - Glioblastoma multiforme(68;0.00121)														---	---	---	---
GPR126	57211	broad.mit.edu	37	6	142643542	142643542	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:142643542delA	uc010khc.2	+						GPR126_uc010khd.2_Intron|GPR126_uc010khe.2_Intron|GPR126_uc010khf.2_Intron|GPR126_uc003qix.2_Intron	NM_020455	NP_065188			G protein-coupled receptor 126 alpha 1						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(1)	1	Breast(32;0.176)			OV - Ovarian serous cystadenocarcinoma(155;9.33e-06)|GBM - Glioblastoma multiforme(68;0.00121)														---	---	---	---
GPR126	57211	broad.mit.edu	37	6	142728435	142728435	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:142728435delT	uc010khc.2	+						GPR126_uc010khd.2_Intron|GPR126_uc010khe.2_Intron|GPR126_uc010khf.2_Intron	NM_020455	NP_065188			G protein-coupled receptor 126 alpha 1						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(1)	1	Breast(32;0.176)			OV - Ovarian serous cystadenocarcinoma(155;9.33e-06)|GBM - Glioblastoma multiforme(68;0.00121)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	143307254	143307254	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:143307254delC	uc003qje.1	-											Homo sapiens cDNA FLJ32928 fis, clone TESTI2007405.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	143373038	143373039	+	IGR	DEL	AA	-	-	rs113421732		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:143373038_143373039delAA								HIVEP2 (106700 upstream) : AIG1 (7461 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	143676496	143676497	+	IGR	DEL	CT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:143676496_143676497delCT								AIG1 (15057 upstream) : ADAT2 (67473 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	143898909	143898910	+	IGR	INS	-	A	A	rs111979430		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:143898909_143898910insA								LOC285740 (8433 upstream) : PHACTR2 (30407 downstream)																																			---	---	---	---
UTRN	7402	broad.mit.edu	37	6	144843999	144843999	+	Intron	DEL	A	-	-	rs150930485		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144843999delA	uc003qkt.2	+							NM_007124	NP_009055			utrophin						muscle contraction|muscle organ development|positive regulation of cell-matrix adhesion	cell junction|cytoplasm|cytoskeleton|membrane fraction|nucleus|postsynaptic membrane	actin binding|calcium ion binding|zinc ion binding			ovary(4)|pancreas(1)	5		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)														---	---	---	---
UTRN	7402	broad.mit.edu	37	6	144905813	144905813	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144905813delT	uc003qkt.2	+							NM_007124	NP_009055			utrophin						muscle contraction|muscle organ development|positive regulation of cell-matrix adhesion	cell junction|cytoplasm|cytoskeleton|membrane fraction|nucleus|postsynaptic membrane	actin binding|calcium ion binding|zinc ion binding			ovary(4)|pancreas(1)	5		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)														---	---	---	---
UTRN	7402	broad.mit.edu	37	6	144950368	144950368	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144950368delA	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)														---	---	---	---
GRM1	2911	broad.mit.edu	37	6	146367031	146367031	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146367031delT	uc010khw.1	+						GRM1_uc010khu.1_Intron|GRM1_uc010khv.1_Intron|GRM1_uc003qll.2_Intron|GRM1_uc011edz.1_Intron|GRM1_uc011eea.1_Intron	NM_000838	NP_000829			glutamate receptor, metabotropic 1 isoform alpha						synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			lung(8)|ovary(4)|central_nervous_system(3)|large_intestine(2)|breast(2)	19		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)	Acamprosate(DB00659)|L-Glutamic Acid(DB00142)													---	---	---	---
GRM1	2911	broad.mit.edu	37	6	146579892	146579892	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146579892delT	uc010khw.1	+						GRM1_uc010khv.1_Intron|GRM1_uc003qll.2_Intron|GRM1_uc011edz.1_Intron|GRM1_uc011eea.1_Intron	NM_000838	NP_000829			glutamate receptor, metabotropic 1 isoform alpha						synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			lung(8)|ovary(4)|central_nervous_system(3)|large_intestine(2)|breast(2)	19		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)	Acamprosate(DB00659)|L-Glutamic Acid(DB00142)													---	---	---	---
GRM1	2911	broad.mit.edu	37	6	146754617	146754617	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146754617delT	uc010khw.1	+						GRM1_uc010khv.1_Intron|GRM1_uc003qll.2_Intron|GRM1_uc011edz.1_Intron|GRM1_uc011eea.1_Intron	NM_000838	NP_000829			glutamate receptor, metabotropic 1 isoform alpha						synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			lung(8)|ovary(4)|central_nervous_system(3)|large_intestine(2)|breast(2)	19		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)	Acamprosate(DB00659)|L-Glutamic Acid(DB00142)													---	---	---	---
Unknown	0	broad.mit.edu	37	6	147785347	147785347	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:147785347delT								STXBP5 (76640 upstream) : SAMD5 (44716 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	148039826	148039827	+	IGR	INS	-	T	T	rs142459792	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:148039826_148039827insT								SAMD5 (148669 upstream) : SASH1 (623902 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	148045876	148045877	+	IGR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:148045876_148045877insA								SAMD5 (154719 upstream) : SASH1 (617852 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	148189334	148189334	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:148189334delA								SAMD5 (298177 upstream) : SASH1 (474395 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	149008778	149008778	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:149008778delC								SASH1 (135594 upstream) : UST (59493 downstream)																																			---	---	---	---
TAB2	23118	broad.mit.edu	37	6	149631019	149631020	+	Intron	INS	-	GT	GT	rs141557575	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:149631019_149631020insGT	uc011eec.1	+							NM_015093	NP_055908			mitogen-activated protein kinase kinase kinase 7						activation of MAPK activity|heart development|I-kappaB kinase/NF-kappaB cascade|innate immune response|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|stress-activated MAPK cascade|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|endosome membrane|plasma membrane	K63-linked polyubiquitin binding|zinc ion binding				0																		---	---	---	---
PPIL4	85313	broad.mit.edu	37	6	149811631	149811634	+	Intron	DEL	TTTT	-	-	rs111814026		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:149811631_149811634delTTTT	uc010kic.2	-							NM_139126				peptidylprolyl isomerase-like 4						protein folding	nucleus	nucleotide binding|peptidyl-prolyl cis-trans isomerase activity|RNA binding				0		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;1.11e-11)|GBM - Glioblastoma multiforme(68;0.0885)														---	---	---	---
PCMT1	5110	broad.mit.edu	37	6	150113096	150113096	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150113096delT	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)														---	---	---	---
LRP11	84918	broad.mit.edu	37	6	150147740	150147741	+	Intron	INS	-	G	G	rs146291329	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150147740_150147741insG	uc003qng.2	-						LRP11_uc003qnh.1_Intron	NM_032832	NP_116221			low density lipoprotein receptor-related protein							integral to membrane	receptor activity				0		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;4.56e-12)|GBM - Glioblastoma multiforme(68;0.225)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	150361068	150361068	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150361068delT								RAET1L (14400 upstream) : ULBP3 (22273 downstream)																																			---	---	---	---
MTHFD1L	25902	broad.mit.edu	37	6	151314468	151314469	+	Intron	INS	-	T	T	rs113885544		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151314468_151314469insT	uc003qob.2	+						MTHFD1L_uc011een.1_Intron|MTHFD1L_uc011eeo.1_Intron|MTHFD1L_uc003qoc.2_Intron	NM_015440	NP_056255			methylenetetrahydrofolate dehydrogenase (NADP+						folic acid-containing compound biosynthetic process|formate metabolic process|one-carbon metabolic process|tetrahydrofolate metabolic process	mitochondrion	ATP binding|formate-tetrahydrofolate ligase activity|protein homodimerization activity			ovary(3)|large_intestine(1)	4		Ovarian(120;0.128)		OV - Ovarian serous cystadenocarcinoma(155;8.7e-12)														---	---	---	---
AKAP12	9590	broad.mit.edu	37	6	151560252	151560252	+	5'Flank	DEL	T	-	-	rs35796247		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151560252delT	uc011eep.1	+						AKAP12_uc003qoe.2_5'Flank	NM_005100	NP_005091			A kinase (PRKA) anchor protein 12 isoform 1						G-protein coupled receptor protein signaling pathway|positive regulation of cAMP biosynthetic process|positive regulation of protein kinase A signaling cascade|protein targeting	cell cortex|cytoskeleton|plasma membrane	adenylate cyclase binding|protein kinase A binding			large_intestine(2)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)|skin(1)|pancreas(1)	8		Ovarian(120;0.125)	BRCA - Breast invasive adenocarcinoma(37;0.175)	OV - Ovarian serous cystadenocarcinoma(155;2.98e-11)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	151800849	151800850	+	IGR	DEL	TC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151800849_151800850delTC								C6orf211 (9617 upstream) : C6orf97 (14325 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	151800862	151800862	+	IGR	DEL	T	-	-	rs77114387		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151800862delT								C6orf211 (9630 upstream) : C6orf97 (14313 downstream)																																			---	---	---	---
C6orf97	80129	broad.mit.edu	37	6	151892867	151892868	+	Intron	INS	-	A	A	rs147165422	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151892867_151892868insA	uc003qol.2	+							NM_025059	NP_079335			hypothetical protein LOC80129												0		Ovarian(120;0.126)	BRCA - Breast invasive adenocarcinoma(37;0.111)	OV - Ovarian serous cystadenocarcinoma(155;1.48e-10)														---	---	---	---
SYNE1	23345	broad.mit.edu	37	6	152688715	152688715	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152688715delA	uc010kiw.2	-						SYNE1_uc003qot.3_Intron|SYNE1_uc003qou.3_Intron|SYNE1_uc010kja.1_5'UTR|SYNE1_uc003qov.2_Intron	NM_182961	NP_892006			spectrin repeat containing, nuclear envelope 1						cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)											HNSCC(10;0.0054)			---	---	---	---
SYNE1	23345	broad.mit.edu	37	6	152854895	152854895	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152854895delT	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	153101925	153101933	+	IGR	DEL	GTGTTCCCC	-	-	rs58632883		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:153101925_153101933delGTGTTCCCC								VIP (21027 upstream) : FBXO5 (189727 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	154283259	154283260	+	IGR	INS	-	AT	AT	rs138793852	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:154283259_154283260insAT								RGS17 (830870 upstream) : OPRM1 (48376 downstream)																																			---	---	---	---
TIAM2	26230	broad.mit.edu	37	6	155300344	155300344	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155300344delT	uc003qqb.2	+							NM_012454	NP_036586			T-cell lymphoma invasion and metastasis 2						apoptosis|cellular lipid metabolic process|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|filopodium|growth cone|lamellipodium	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			ovary(3)|breast(1)	4		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)														---	---	---	---
TIAM2	26230	broad.mit.edu	37	6	155356361	155356362	+	Intron	DEL	TT	-	-	rs67126072		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155356361_155356362delTT	uc003qqb.2	+							NM_012454	NP_036586			T-cell lymphoma invasion and metastasis 2						apoptosis|cellular lipid metabolic process|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|filopodium|growth cone|lamellipodium	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			ovary(3)|breast(1)	4		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	156147267	156147267	+	IGR	DEL	A	-	-	rs36107935		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:156147267delA								NOX3 (370230 upstream) : MIR1202 (120664 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	156432681	156432681	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:156432681delT								MIR1202 (164668 upstream) : ARID1B (666405 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	157031810	157031811	+	IGR	INS	-	GT	GT	rs149124583	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:157031810_157031811insGT								MIR1202 (763797 upstream) : ARID1B (67275 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	157043771	157043771	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:157043771delT								MIR1202 (775758 upstream) : ARID1B (55315 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	157077930	157077931	+	IGR	INS	-	GAAG	GAAG			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:157077930_157077931insGAAG								MIR1202 (809917 upstream) : ARID1B (21155 downstream)																																			---	---	---	---
ARID1B	57492	broad.mit.edu	37	6	157467745	157467746	+	Intron	DEL	CA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:157467745_157467746delCA	uc003qqn.2	+						ARID1B_uc003qqo.2_Intron|ARID1B_uc003qqp.2_Intron|ARID1B_uc003qqq.1_Intron|ARID1B_uc010kjl.2_5'Flank	NM_017519	NP_059989			AT rich interactive domain 1B (SWI1-like)						chromatin-mediated maintenance of transcription|nervous system development|transcription, DNA-dependent	SWI/SNF complex	DNA binding|protein binding|transcription coactivator activity			ovary(1)|breast(1)	2		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)														---	---	---	---
SYNJ2	8871	broad.mit.edu	37	6	158502667	158502668	+	Intron	DEL	TC	-	-	rs149018292	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158502667_158502668delTC	uc003qqx.1	+						SYNJ2_uc003qqw.1_Intron|SYNJ2_uc003qqy.1_Intron|SYNJ2_uc003qqz.1_Intron|SYNJ2_uc003qra.1_Intron	NM_003898	NP_003889			synaptojanin 2								nucleotide binding|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity|RNA binding			skin(1)	1				OV - Ovarian serous cystadenocarcinoma(65;4.42e-18)|BRCA - Breast invasive adenocarcinoma(81;4.23e-05)														---	---	---	---
TMEM181	57583	broad.mit.edu	37	6	159048837	159048838	+	Intron	INS	-	AATG	AATG	rs148403177	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:159048837_159048838insAATG	uc003qrm.3	+						TMEM181_uc010kjr.1_Intron	NM_020823	NP_065874			G protein-coupled receptor 178						pathogenesis	integral to membrane	toxin binding			ovary(2)|central_nervous_system(1)	3		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;8.15e-18)|BRCA - Breast invasive adenocarcinoma(81;1.38e-05)														---	---	---	---
SYTL3	94120	broad.mit.edu	37	6	159100406	159100406	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:159100406delA	uc003qrp.2	+						SYTL3_uc011efp.1_Intron|SYTL3_uc003qro.2_Intron|SYTL3_uc003qrq.2_Intron|SYTL3_uc003qrr.2_Intron|SYTL3_uc003qrs.2_Intron|SYTL3_uc011efq.1_Intron	NM_001009991	NP_001009991			synaptotagmin-like 3						intracellular protein transport	endomembrane system|membrane	Rab GTPase binding				0		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.54e-17)|BRCA - Breast invasive adenocarcinoma(81;8.24e-06)														---	---	---	---
SYTL3	94120	broad.mit.edu	37	6	159101784	159101784	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:159101784delA	uc003qrp.2	+						SYTL3_uc011efp.1_Intron|SYTL3_uc003qro.2_Intron|SYTL3_uc003qrq.2_Intron|SYTL3_uc003qrr.2_Intron|SYTL3_uc003qrs.2_Intron|SYTL3_uc011efq.1_Intron	NM_001009991	NP_001009991			synaptotagmin-like 3						intracellular protein transport	endomembrane system|membrane	Rab GTPase binding				0		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.54e-17)|BRCA - Breast invasive adenocarcinoma(81;8.24e-06)														---	---	---	---
EZR	7430	broad.mit.edu	37	6	159186948	159186951	+	3'UTR	DEL	CAAA	-	-	rs79446163		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:159186948_159186951delCAAA	uc003qrt.3	-	13					EZR_uc011efr.1_3'UTR|EZR_uc011efs.1_3'UTR|EZR_uc003qru.3_3'UTR	NM_003379	NP_003370			ezrin						actin filament bundle assembly|axon guidance|cytoskeletal anchoring at plasma membrane|leukocyte cell-cell adhesion|membrane to membrane docking|regulation of cell shape	actin filament|apical plasma membrane|basolateral plasma membrane|cortical cytoskeleton|cytosol|extrinsic to membrane|filopodium|microvillus membrane|nucleolus|ruffle membrane	actin filament binding|cell adhesion molecule binding			ovary(1)	1		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.16e-17)|BRCA - Breast invasive adenocarcinoma(81;6.58e-06)														---	---	---	---
FNDC1	84624	broad.mit.edu	37	6	159668786	159668786	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:159668786delT	uc010kjv.2	+							NM_032532	NP_115921			fibronectin type III domain containing 1							extracellular region				large_intestine(4)|ovary(3)|central_nervous_system(1)	8		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	160381300	160381300	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160381300delT								MAS1 (52195 upstream) : IGF2R (8831 downstream)																																			---	---	---	---
SLC22A3	6581	broad.mit.edu	37	6	160820341	160820341	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160820341delT	uc003qti.2	+						SLC22A3_uc011efx.1_Intron	NM_021977	NP_068812			solute carrier family 22 member 3							integral to plasma membrane|membrane fraction	protein binding|quaternary ammonium group transmembrane transporter activity			skin(2)|ovary(1)|central_nervous_system(1)	4		Breast(66;0.00028)|Ovarian(120;0.0308)|Prostate(117;0.218)		OV - Ovarian serous cystadenocarcinoma(65;9.47e-17)|BRCA - Breast invasive adenocarcinoma(81;9.75e-06)														---	---	---	---
SLC22A3	6581	broad.mit.edu	37	6	160869014	160869014	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160869014delA	uc003qti.2	+						SLC22A3_uc011efx.1_Intron	NM_021977	NP_068812			solute carrier family 22 member 3							integral to plasma membrane|membrane fraction	protein binding|quaternary ammonium group transmembrane transporter activity			skin(2)|ovary(1)|central_nervous_system(1)	4		Breast(66;0.00028)|Ovarian(120;0.0308)|Prostate(117;0.218)		OV - Ovarian serous cystadenocarcinoma(65;9.47e-17)|BRCA - Breast invasive adenocarcinoma(81;9.75e-06)														---	---	---	---
LPA	4018	broad.mit.edu	37	6	161081800	161081801	+	Intron	INS	-	A	A	rs150415123	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161081800_161081801insA	uc003qtl.2	-							NM_005577	NP_005568			lipoprotein Lp(a) precursor						blood circulation|lipid metabolic process|lipid transport|lipoprotein metabolic process|proteolysis|receptor-mediated endocytosis	plasma lipoprotein particle	apolipoprotein binding|endopeptidase inhibitor activity|fibronectin binding|heparin binding|serine-type endopeptidase activity			ovary(3)|skin(2)|pancreas(1)	6		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	Aminocaproic Acid(DB00513)													---	---	---	---
PACRG	135138	broad.mit.edu	37	6	163254542	163254542	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:163254542delA	uc003qua.2	+						PACRG_uc003qub.2_Intron|PACRG_uc003quc.2_Intron	NM_152410	NP_689623			parkin co-regulated gene protein isoform 1												0		Breast(66;2.41e-05)|Ovarian(120;0.0245)|Prostate(117;0.0273)|all_neural(5;0.0416)|Glioma(2;0.203)		OV - Ovarian serous cystadenocarcinoma(33;4.31e-19)|GBM - Glioblastoma multiforme(2;7.42e-11)|BRCA - Breast invasive adenocarcinoma(81;3.19e-05)|KIRC - Kidney renal clear cell carcinoma(3;0.205)|Kidney(3;0.242)														---	---	---	---
PACRG	135138	broad.mit.edu	37	6	163360709	163360710	+	Intron	DEL	GT	-	-	rs142409395		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:163360709_163360710delGT	uc003qua.2	+						PACRG_uc003qub.2_Intron|PACRG_uc003quc.2_Intron	NM_152410	NP_689623			parkin co-regulated gene protein isoform 1												0		Breast(66;2.41e-05)|Ovarian(120;0.0245)|Prostate(117;0.0273)|all_neural(5;0.0416)|Glioma(2;0.203)		OV - Ovarian serous cystadenocarcinoma(33;4.31e-19)|GBM - Glioblastoma multiforme(2;7.42e-11)|BRCA - Breast invasive adenocarcinoma(81;3.19e-05)|KIRC - Kidney renal clear cell carcinoma(3;0.205)|Kidney(3;0.242)														---	---	---	---
PACRG	135138	broad.mit.edu	37	6	163393450	163393451	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:163393450_163393451insT	uc003qua.2	+						PACRG_uc003qub.2_Intron|PACRG_uc003quc.2_Intron	NM_152410	NP_689623			parkin co-regulated gene protein isoform 1												0		Breast(66;2.41e-05)|Ovarian(120;0.0245)|Prostate(117;0.0273)|all_neural(5;0.0416)|Glioma(2;0.203)		OV - Ovarian serous cystadenocarcinoma(33;4.31e-19)|GBM - Glioblastoma multiforme(2;7.42e-11)|BRCA - Breast invasive adenocarcinoma(81;3.19e-05)|KIRC - Kidney renal clear cell carcinoma(3;0.205)|Kidney(3;0.242)														---	---	---	---
PACRG	135138	broad.mit.edu	37	6	163697000	163697001	+	Intron	DEL	TT	-	-	rs79000543		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:163697000_163697001delTT	uc003qua.2	+						PACRG_uc003qub.2_Intron|PACRG_uc003quc.2_Intron	NM_152410	NP_689623			parkin co-regulated gene protein isoform 1												0		Breast(66;2.41e-05)|Ovarian(120;0.0245)|Prostate(117;0.0273)|all_neural(5;0.0416)|Glioma(2;0.203)		OV - Ovarian serous cystadenocarcinoma(33;4.31e-19)|GBM - Glioblastoma multiforme(2;7.42e-11)|BRCA - Breast invasive adenocarcinoma(81;3.19e-05)|KIRC - Kidney renal clear cell carcinoma(3;0.205)|Kidney(3;0.242)														---	---	---	---
QKI	9444	broad.mit.edu	37	6	163970240	163970240	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:163970240delG	uc003qui.2	+						QKI_uc003que.2_Intron|QKI_uc003quf.2_Intron|QKI_uc003qug.2_Intron|QKI_uc003quh.2_Intron|QKI_uc003quj.2_Intron	NM_006775	NP_006766			quaking homolog, KH domain RNA binding isoform						mRNA processing|mRNA transport|regulation of translation|RNA splicing	cytoplasm|nucleus|plasma membrane	RNA binding|SH3 domain binding			large_intestine(1)|ovary(1)	2		Breast(66;5e-05)|Prostate(117;0.0235)|all_neural(5;0.0416)|Ovarian(120;0.0448)|Glioma(2;0.203)		all cancers(1;4.4e-46)|OV - Ovarian serous cystadenocarcinoma(33;6.91e-23)|GBM - Glioblastoma multiforme(1;2.94e-19)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|Kidney(3;0.000199)|KIRC - Kidney renal clear cell carcinoma(3;0.000234)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	164266558	164266558	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:164266558delT								QKI (271666 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	164418054	164418054	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:164418054delT								QKI (423162 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	164435615	164435615	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:164435615delA								QKI (440723 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	164437104	164437105	+	IGR	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:164437104_164437105delTG								QKI (442212 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	165000683	165000683	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:165000683delT								None (None upstream) : C6orf118 (692472 downstream)																																			---	---	---	---
RPS6KA2	6196	broad.mit.edu	37	6	167073875	167073878	+	Intron	DEL	GGCA	-	-	rs9348165		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167073875_167073878delGGCA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	167606722	167606723	+	IGR	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167606722_167606723delAC								TCP10L2 (10327 upstream) : UNC93A (98080 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	167657621	167657700	+	IGR	DEL	GTGCTGGTCTGCCTTCTCTGTGAGCTGTGCCTTGGGTACTGCACCATCCTGCTTTGCGTGAGGCTGCTGACGGAGGAGGA	-	-	rs147084678	by1000genomes;by1000genomes;by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167657621_167657700delGTGCTGGTCTGCCTTCTCTGTGAGCTGTGCCTTGGGTACTGCACCATCCTGCTTTGCGTGAGGCTGCTGACGGAGGAGGA								TCP10L2 (61226 upstream) : UNC93A (47103 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	168133253	168133255	+	IGR	DEL	CAT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168133253_168133255delCAT								TCP10 (335255 upstream) : C6orf123 (51966 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	169219695	169219696	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169219695_169219696insT								SMOC2 (151024 upstream) : THBS2 (396180 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	169486793	169486793	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169486793delT								SMOC2 (418122 upstream) : THBS2 (129083 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	169793782	169793782	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169793782delA								THBS2 (139645 upstream) : WDR27 (63525 downstream)																																			---	---	---	---
WDR27	253769	broad.mit.edu	37	6	169975335	169975336	+	Intron	INS	-	ATCC	ATCC	rs146834488	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169975335_169975336insATCC	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	170484665	170484666	+	IGR	DEL	CT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170484665_170484666delCT								C6orf208 (281696 upstream) : LOC154449 (78756 downstream)																																			---	---	---	---
FAM120B	84498	broad.mit.edu	37	6	170642870	170642871	+	Intron	INS	-	GTATG	GTATG	rs148217775	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170642870_170642871insGTATG	uc003qxp.2	+						FAM120B_uc003qxo.1_Intron|FAM120B_uc011ehd.1_Intron	NM_032448	NP_115824			family with sequence similarity 120B						cell differentiation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			ovary(1)	1		Breast(66;0.000338)|Esophageal squamous(34;0.241)		OV - Ovarian serous cystadenocarcinoma(33;3.94e-22)|BRCA - Breast invasive adenocarcinoma(81;6.47e-06)|GBM - Glioblastoma multiforme(31;0.0899)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	170763830	170763831	+	IGR	INS	-	G	G	rs139128866	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170763830_170763831insG								FAM120B (49594 upstream) : PSMB1 (16276 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	170900161	170900161	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170900161delA								PDCD2 (6413 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	10186	10188	+	IGR	DEL	AAC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:10186_10188delAAC								None (None upstream) : FAM20C (182781 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	108476	108477	+	IGR	INS	-	TT	TT	rs10650061		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:108476_108477insTT								None (None upstream) : FAM20C (84492 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	436497	436498	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:436497_436498insT								FAM20C (135786 upstream) : PDGFA (100401 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	521935	521938	+	IGR	DEL	TGGT	-	-	rs73041892	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:521935_521938delTGGT								FAM20C (221224 upstream) : PDGFA (14961 downstream)																																			---	---	---	---
PRKAR1B	5575	broad.mit.edu	37	7	628158	628166	+	Intron	DEL	GGTGGTGAC	-	-	rs72254630		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:628158_628166delGGTGGTGAC	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)														---	---	---	---
MAFK	7975	broad.mit.edu	37	7	1569441	1569441	+	5'Flank	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1569441delG	uc003skr.2	+							NM_002360	NP_002351			v-maf musculoaponeurotic fibrosarcoma oncogene						blood coagulation	nucleoplasm	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;5.75e-15)														---	---	---	---
KIAA1908	114796	broad.mit.edu	37	7	1617353	1617356	+	Intron	DEL	CATC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1617353_1617356delCATC	uc003sla.2	+						KIAA1908_uc003sky.1_Intron|KIAA1908_uc003skz.1_Intron	NR_021487				Homo sapiens mRNA for KIAA1908 protein, partial cds.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	1634356	1634363	+	IGR	DEL	CATCCATC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1634356_1634363delCATCCATC								KIAA1908 (5097 upstream) : TFAMP1 (19743 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	1817189	1817190	+	IGR	INS	-	T	T	rs113945044		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1817189_1817190insT								ELFN1 (29599 upstream) : MAD1L1 (38238 downstream)																																			---	---	---	---
MAD1L1	8379	broad.mit.edu	37	7	1888684	1888685	+	Intron	DEL	AC	-	-	rs112226413		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1888684_1888685delAC	uc003slh.1	-						MAD1L1_uc003sle.1_Intron|MAD1L1_uc003slf.1_Intron|MAD1L1_uc003slg.1_Intron|MAD1L1_uc010ksh.1_Intron|MAD1L1_uc003sli.1_Intron|MAD1L1_uc003sld.1_Intron|uc003slj.1_RNA	NM_001013836	NP_001013858			MAD1-like 1 protein						cell division|mitotic anaphase|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase|mitotic prometaphase|mitotic telophase	actin cytoskeleton|centrosome|condensed chromosome kinetochore|cytosol|mitochondrion|nucleus|spindle	protein binding			lung(1)|central_nervous_system(1)	2		Ovarian(82;0.0272)		UCEC - Uterine corpus endometrioid carcinoma (27;0.134)|OV - Ovarian serous cystadenocarcinoma(56;3.63e-14)														---	---	---	---
SNX8	29886	broad.mit.edu	37	7	2330933	2330934	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2330933_2330934delAA	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)														---	---	---	---
SNX8	29886	broad.mit.edu	37	7	2332483	2332483	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2332483delT	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)														---	---	---	---
SNX8	29886	broad.mit.edu	37	7	2341714	2341714	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2341714delA	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)														---	---	---	---
EIF3B	8662	broad.mit.edu	37	7	2401899	2401899	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2401899delT	uc003slx.2	+						EIF3B_uc003sly.2_Intron|EIF3B_uc003slz.1_Intron|EIF3B_uc003sma.2_Intron	NM_003751	NP_003742			eukaryotic translation initiation factor 3,						regulation of translational initiation	cytosol|eukaryotic translation initiation factor 3 complex	nucleotide binding|protein complex scaffold|translation initiation factor activity				0		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0833)|OV - Ovarian serous cystadenocarcinoma(56;7.76e-14)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	3282112	3282112	+	IGR	DEL	T	-	-	rs72181072		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:3282112delT								CARD11 (198533 upstream) : SDK1 (58968 downstream)																																			---	---	---	---
FOXK1	221937	broad.mit.edu	37	7	4807399	4807399	+	3'UTR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4807399delT	uc003snc.1	+	9					FOXK1_uc003sna.1_3'UTR|FOXK1_uc003snd.1_5'Flank	NM_001037165	NP_001032242			forkhead box K1						cell differentiation|embryo development|muscle organ development|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|magnesium ion binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			upper_aerodigestive_tract(1)|skin(1)	2		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;7.43e-15)														---	---	---	---
KIAA0415	9907	broad.mit.edu	37	7	4827515	4827515	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4827515delC	uc003sne.2	+						KIAA0415_uc010ksp.2_Intron|KIAA0415_uc003snf.2_5'Flank	NM_014855	NP_055670			hypothetical protein LOC9907						cell death|double-strand break repair via homologous recombination	cytoplasm|nucleus	protein binding			central_nervous_system(1)	1		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.091)|OV - Ovarian serous cystadenocarcinoma(56;8.35e-15)														---	---	---	---
SLC29A4	222962	broad.mit.edu	37	7	5332651	5332651	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5332651delT	uc003sod.2	+						SLC29A4_uc011jwg.1_Intron|SLC29A4_uc003soc.2_Intron|SLC29A4_uc003soe.2_Intron	NM_153247	NP_694979			solute carrier family 29 (nucleoside						nucleobase, nucleoside and nucleotide metabolic process	apical plasma membrane|integral to membrane	nucleoside transmembrane transporter activity			liver(1)	1		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0903)|OV - Ovarian serous cystadenocarcinoma(56;2.65e-15)														---	---	---	---
RNF216	54476	broad.mit.edu	37	7	5755043	5755043	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5755043delT	uc003soy.1	-						RNF216_uc010ksz.1_Intron|RNF216_uc010kta.1_Intron|RNF216_uc011jwj.1_Intron|RNF216_uc003sox.1_Intron	NM_207116	NP_996999			ring finger protein 216 isoform b						apoptosis|interspecies interaction between organisms|proteasomal ubiquitin-dependent protein catabolic process|protein K48-linked ubiquitination|regulation of defense response to virus by host|regulation of interferon-beta production	cytoplasm|nucleus|nucleus	ligase activity|protein binding|protein binding|zinc ion binding			ovary(3)|breast(2)	5		Ovarian(82;0.07)		UCEC - Uterine corpus endometrioid carcinoma (126;0.135)|OV - Ovarian serous cystadenocarcinoma(56;2.69e-13)														---	---	---	---
RNF216	54476	broad.mit.edu	37	7	5794664	5794665	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5794664_5794665delAA	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)														---	---	---	---
ZNF815	401303	broad.mit.edu	37	7	5890795	5890795	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5890795delT	uc003spc.2	+						ZNF815_uc003spd.2_Intron	NR_023382				Homo sapiens cDNA FLJ38969 fis, clone NT2RI2002359.												0																		---	---	---	---
C7orf26	79034	broad.mit.edu	37	7	6643471	6643471	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6643471delA	uc003sqo.1	+						C7orf26_uc003sqp.1_Intron|C7orf26_uc003sqq.1_Intron	NM_024067	NP_076972			hypothetical protein LOC79034											ovary(1)	1		Ovarian(82;0.232)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)														---	---	---	---
PMS2CL	441194	broad.mit.edu	37	7	6757355	6757356	+	Intron	DEL	GA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6757355_6757356delGA	uc003squ.2	+											Homo sapiens PMS2CL mRNA for PMS2-C terminal -like, complete cds.												0																		---	---	---	---
COL28A1	340267	broad.mit.edu	37	7	7452175	7452175	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:7452175delA	uc003src.1	-						COL28A1_uc011jxe.1_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)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	7580945	7580945	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:7580945delT								COL28A1 (5485 upstream) : MIOS (25671 downstream)																																			---	---	---	---
NXPH1	30010	broad.mit.edu	37	7	8682480	8682480	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:8682480delT	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	9027956	9027957	+	IGR	DEL	AA	-	-	rs111924485		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:9027956_9027957delAA								NXPH1 (235364 upstream) : PER4 (645943 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	10153897	10153898	+	IGR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:10153897_10153898insA								PER4 (478450 upstream) : NDUFA4 (818917 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	10558171	10558173	+	IGR	DEL	GAG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:10558171_10558173delGAG								PER4 (882724 upstream) : NDUFA4 (414642 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	10584078	10584079	+	IGR	INS	-	A	A	rs150300096	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:10584078_10584079insA								PER4 (908631 upstream) : NDUFA4 (388736 downstream)																																			---	---	---	---
THSD7A	221981	broad.mit.edu	37	7	11548061	11548061	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11548061delA	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	12530396	12530396	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:12530396delT								VWDE (86544 upstream) : SCIN (65791 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	13042703	13042703	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:13042703delC								ARL4A (312147 upstream) : ETV1 (888155 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	13289079	13289079	+	IGR	DEL	G	-	-	rs10950445	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:13289079delG								ARL4A (558523 upstream) : ETV1 (641779 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	13586327	13586329	+	IGR	DEL	AAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:13586327_13586329delAAA								ARL4A (855771 upstream) : ETV1 (344529 downstream)																																			---	---	---	---
ETV1	2115	broad.mit.edu	37	7	14002050	14002050	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:14002050delT	uc011jxq.1	-						ETV1_uc011jxn.1_Intron|ETV1_uc011jxo.1_Intron|ETV1_uc011jxp.1_Intron|ETV1_uc003ssw.3_Intron|ETV1_uc003ssx.2_Intron|ETV1_uc011jxr.1_Intron|ETV1_uc011jxs.1_Intron|ETV1_uc010ktv.2_Intron	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								---	---	---	---
ETV1	2115	broad.mit.edu	37	7	14032496	14032496	+	5'Flank	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:14032496delC	uc011jxq.1	-						ETV1_uc003ssw.3_5'Flank|ETV1_uc003ssx.2_5'Flank|ETV1_uc011jxr.1_5'Flank|ETV1_uc011jxs.1_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	14977396	14977401	+	IGR	DEL	TACTTC	-	-	rs113832668		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:14977396_14977401delTACTTC								DGKB (34846 upstream) : TMEM195 (262542 downstream)																																			---	---	---	---
TMEM195	392636	broad.mit.edu	37	7	15273176	15273177	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:15273176_15273177delTT	uc003stb.1	-							NM_001004320	NP_001004320			transmembrane protein 195						ether lipid metabolic process|fatty acid biosynthetic process|membrane lipid metabolic process	endoplasmic reticulum membrane|integral to membrane	glyceryl-ether monooxygenase activity|iron ion binding				0																		---	---	---	---
TMEM195	392636	broad.mit.edu	37	7	15486023	15486024	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:15486023_15486024delAA	uc003stb.1	-							NM_001004320	NP_001004320			transmembrane protein 195						ether lipid metabolic process|fatty acid biosynthetic process|membrane lipid metabolic process	endoplasmic reticulum membrane|integral to membrane	glyceryl-ether monooxygenase activity|iron ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	15942221	15942222	+	IGR	INS	-	T	T	rs71835259		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:15942221_15942222insT								MEOX2 (215913 upstream) : ISPD (184930 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	16066559	16066561	+	IGR	DEL	AAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:16066559_16066561delAAA								MEOX2 (340251 upstream) : ISPD (60591 downstream)																																			---	---	---	---
ISPD	729920	broad.mit.edu	37	7	16309152	16309152	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:16309152delT	uc010ktx.2	-						ISPD_uc010kty.2_Intron|uc003stf.2_RNA	NM_001101426	NP_001094896			notch1-induced protein isoform a						isoprenoid biosynthetic process		nucleotidyltransferase activity			ovary(1)	1															Multiple Myeloma(15;0.18)			---	---	---	---
Unknown	0	broad.mit.edu	37	7	16482215	16482215	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:16482215delA								ISPD (21268 upstream) : SOSTDC1 (18893 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	16620935	16620936	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:16772117_16772120delCCTC								BZW2 (25969 upstream) : TSPAN13 (21231 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	17214602	17214602	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:17214602delT								AGR3 (292989 upstream) : AHR (123674 downstream)																																			---	---	---	---
MACC1	346389	broad.mit.edu	37	7	20194103	20194103	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20194103delT	uc003sus.3	-						MACC1_uc010kug.2_Intron	NM_182762	NP_877439			putative binding protein 7a5						positive regulation of cell division|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	growth factor activity			ovary(2)|skin(1)	3																		---	---	---	---
MACC1	346389	broad.mit.edu	37	7	20245129	20245129	+	Intron	DEL	T	-	-	rs112484661		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20245129delT	uc003sus.3	-						MACC1_uc010kug.2_Intron	NM_182762	NP_877439			putative binding protein 7a5						positive regulation of cell division|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	growth factor activity			ovary(2)|skin(1)	3																		---	---	---	---
ABCB5	340273	broad.mit.edu	37	7	20719095	20719097	+	Intron	DEL	AAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20719095_20719097delAAA	uc003suw.3	+						ABCB5_uc010kuh.2_Intron	NM_178559	NP_848654			ATP-binding cassette, sub-family B, member 5						regulation of membrane potential	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus	ATP binding|ATPase activity, coupled to transmembrane movement of substances|efflux transmembrane transporter activity			skin(2)|large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)|pancreas(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	20937496	20937499	+	IGR	DEL	CTCC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20937496_20937499delCTCC								RPL23P8 (70057 upstream) : SP4 (530190 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	20984145	20984146	+	IGR	INS	-	G	G	rs139960010	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20984145_20984146insG								RPL23P8 (116706 upstream) : SP4 (483543 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	21036435	21036437	+	IGR	DEL	TTT	-	-	rs35846964		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21036435_21036437delTTT								RPL23P8 (168996 upstream) : SP4 (431252 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	21163136	21163136	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21163136delA								RPL23P8 (295697 upstream) : SP4 (304553 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	21415569	21415570	+	IGR	DEL	GT	-	-	rs142303810		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21415569_21415570delGT								RPL23P8 (548130 upstream) : SP4 (52119 downstream)																																			---	---	---	---
DNAH11	8701	broad.mit.edu	37	7	21755479	21755480	+	Intron	DEL	CT	-	-	rs75764225	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21755479_21755480delCT	uc003svc.2	+							NM_003777	NP_003768			dynein, axonemal, heavy chain 11						microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(8)|large_intestine(3)|pancreas(3)|central_nervous_system(1)	15														Kartagener_syndrome				---	---	---	---
DNAH11	8701	broad.mit.edu	37	7	21755480	21755480	+	Intron	DEL	T	-	-	rs10714624		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21755480delT	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				---	---	---	---
Unknown	0	broad.mit.edu	37	7	21999284	21999284	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21999284delT								CDCA7L (13742 upstream) : RAPGEF5 (158625 downstream)																																			---	---	---	---
RAPGEF5	9771	broad.mit.edu	37	7	22295046	22295046	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:22295046delA	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																		---	---	---	---
TOMM7	54543	broad.mit.edu	37	7	22857031	22857032	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:22857031_22857032delTT	uc003svk.2	-							NM_019059	NP_061932			translocase of outer mitochondrial membrane 7						protein targeting to mitochondrion	integral to membrane|mitochondrial outer membrane translocase complex	P-P-bond-hydrolysis-driven protein transmembrane transporter activity				0																		---	---	---	---
IGF2BP3	10643	broad.mit.edu	37	7	23429996	23429996	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23429996delA	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	24057650	24057650	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:24057650delT								STK31 (113285 upstream) : NPY (266159 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	24067402	24067402	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:24067402delT								STK31 (123037 upstream) : NPY (256407 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	24315235	24315235	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:24315235delT								STK31 (370870 upstream) : NPY (8574 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	25068388	25068388	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:25068388delT								OSBPL3 (48628 upstream) : CYCS (89889 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	26316301	26316302	+	IGR	INS	-	AAAT	AAAT	rs142084046	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26316301_26316302insAAAT								CBX3 (63327 upstream) : SNX10 (15213 downstream)																																			---	---	---	---
SKAP2	8935	broad.mit.edu	37	7	26904884	26904884	+	5'Flank	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26904884delA	uc003syc.2	-						SKAP2_uc011jzj.1_Intron	NM_003930	NP_003921			src kinase associated phosphoprotein 2						B cell activation|cell junction assembly|protein complex assembly|signal transduction	cytosol|plasma membrane	SH3/SH2 adaptor activity			pancreas(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	27070371	27070372	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27070371_27070372delAA								SKAP2 (35513 upstream) : HOXA1 (62244 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	27436946	27436947	+	IGR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27436946_27436947insA								EVX1 (150754 upstream) : HIBADH (128116 downstream)																																			---	---	---	---
HIBADH	11112	broad.mit.edu	37	7	27609548	27609548	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27609548delA	uc003szf.2	-						HIBADH_uc003szg.2_Intron|HIBADH_uc003szh.2_Intron|HIBADH_uc003szi.2_Intron	NM_152740	NP_689953			3-hydroxyisobutyrate dehydrogenase precursor						branched chain family amino acid catabolic process|pentose-phosphate shunt|valine metabolic process	mitochondrial matrix	3-hydroxyisobutyrate dehydrogenase activity|NAD binding|phosphogluconate dehydrogenase (decarboxylating) activity			ovary(2)	2			GBM - Glioblastoma multiforme(3;0.0368)		NADH(DB00157)													---	---	---	---
TAX1BP1	8887	broad.mit.edu	37	7	27832587	27832587	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27832587delA	uc003szl.2	+						TAX1BP1_uc011jzo.1_Intron|TAX1BP1_uc003szk.2_Intron|TAX1BP1_uc011jzp.1_Intron	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	28148492	28148492	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:28148492delA	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	28397723	28397723	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:28397723delT	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	28649828	28649828	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:28649828delC	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	28744098	28744098	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:28744098delT	uc003szq.2	+						CREB5_uc003szo.2_Intron|CREB5_uc003szr.2_Intron|CREB5_uc003szs.2_Intron|CREB5_uc011jzr.1_Intron	NM_182898	NP_878901			cAMP responsive element binding protein 5						positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter		protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)	2																		---	---	---	---
CREB5	9586	broad.mit.edu	37	7	28775431	28775431	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:28775431delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	29033375	29033375	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:29033375delA								TRIL (35346 upstream) : CPVL (1874 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	29843624	29843626	+	IGR	DEL	AAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:29843624_29843626delAAA								LOC646762 (118870 upstream) : WIPF3 (30715 downstream)																																			---	---	---	---
PLEKHA8	84725	broad.mit.edu	37	7	30101797	30101797	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30101797delT	uc003tam.1	+						PLEKHA8_uc003tao.2_Intron|PLEKHA8_uc003tap.1_Intron|PLEKHA8_uc003tan.2_Intron	NM_032639	NP_116028			pleckstrin homology domain containing, family A						protein transport	cytoplasm	glycolipid binding|glycolipid transporter activity			breast(3)|ovary(1)	4																OREG0017934	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
NOD1	10392	broad.mit.edu	37	7	30494431	30494431	+	Intron	DEL	A	-	-	rs71557460		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30494431delA	uc003tav.2	-						NOD1_uc010kvs.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																		---	---	---	---
CRHR2	1395	broad.mit.edu	37	7	30716839	30716840	+	Intron	DEL	GA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30716839_30716840delGA	uc003tbn.2	-						CRHR2_uc010kvw.1_Intron|CRHR2_uc010kvx.1_Intron|CRHR2_uc010kvy.1_Intron|CRHR2_uc003tbo.2_Intron|CRHR2_uc003tbp.2_Intron	NM_001883	NP_001874			corticotropin releasing hormone receptor 2						G-protein signaling, coupled to cAMP nucleotide second messenger	integral to plasma membrane	corticotrophin-releasing factor receptor activity|protein binding			lung(2)|ovary(1)|skin(1)	4																		---	---	---	---
CRHR2	1395	broad.mit.edu	37	7	30735795	30735795	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30735795delA	uc003tbp.2	-						CRHR2_uc010kvz.1_Intron|CRHR2_uc003tbq.1_Intron|CRHR2_uc003tbr.1_Intron|CRHR2_uc010kwa.1_Intron|uc010kwb.1_Intron|INMT_uc010kwc.1_5'Flank	NM_001883	NP_001874			corticotropin releasing hormone receptor 2						G-protein signaling, coupled to cAMP nucleotide second messenger	integral to plasma membrane	corticotrophin-releasing factor receptor activity|protein binding			lung(2)|ovary(1)|skin(1)	4																		---	---	---	---
INMT	11185	broad.mit.edu	37	7	30784306	30784307	+	Intron	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30784306_30784307delTG	uc010kwc.1	+											Homo sapiens indolethylamine N-methyltransferase (INMT) mRNA, INMT-1 allele, complete cds.							cytoplasm	amine N-methyltransferase activity				0																		---	---	---	---
PDE1C	5137	broad.mit.edu	37	7	31876560	31876560	+	Intron	DEL	T	-	-	rs34163039		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31876560delT	uc003tcm.1	-						PDE1C_uc003tcn.1_Intron|PDE1C_uc003tco.1_Intron|PDE1C_uc003tcr.2_Intron|PDE1C_uc003tcs.2_Intron	NM_005020	NP_005011			phosphodiesterase 1C						activation of phospholipase C activity|nerve growth factor receptor signaling pathway	cytosol	calmodulin binding|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity|metal ion binding			skin(3)|central_nervous_system(1)	4			GBM - Glioblastoma multiforme(11;0.216)															---	---	---	---
AVL9	23080	broad.mit.edu	37	7	32721804	32721807	+	Intron	DEL	CTCT	-	-	rs145238109		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:32721804_32721807delCTCT	uc011kai.1	+						uc003tcw.2_Intron	NM_015060	NP_055875			AVL9 homolog (S. cerevisiase)							integral to membrane					0																		---	---	---	---
AVL9	23080	broad.mit.edu	37	7	32767041	32767041	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:32767041delA	uc011kai.1	+						LOC441208_uc010kwk.2_5'Flank	NM_015060	NP_055875			AVL9 homolog (S. cerevisiase)							integral to membrane					0																		---	---	---	---
AVL9	23080	broad.mit.edu	37	7	32837234	32837234	+	Intron	DEL	C	-	-	rs10706061		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:32837234delC	uc011kai.1	+							NM_015060	NP_055875			AVL9 homolog (S. cerevisiase)							integral to membrane					0																		---	---	---	---
BBS9	27241	broad.mit.edu	37	7	33342789	33342789	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33342789delT	uc003tdn.1	+						BBS9_uc003tdo.1_Intron|BBS9_uc003tdp.1_Intron|BBS9_uc003tdq.1_Intron|BBS9_uc010kwn.1_Intron|BBS9_uc011kan.1_Intron|BBS9_uc011kao.1_Intron	NM_198428	NP_940820			parathyroid hormone-responsive B1 isoform 2						fat cell differentiation|response to stimulus|visual perception	BBSome|cilium membrane|microtubule organizing center|nucleus	protein binding			ovary(3)|upper_aerodigestive_tract(1)|skin(1)	5			GBM - Glioblastoma multiforme(11;0.0894)											Bardet-Biedl_syndrome				---	---	---	---
BMPER	168667	broad.mit.edu	37	7	33977126	33977127	+	Intron	DEL	GT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33977126_33977127delGT	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																		---	---	---	---
NPSR1	387129	broad.mit.edu	37	7	34707525	34707525	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:34707525delA	uc003teg.1	+						AAA1_uc010kwo.1_Intron|AAA1_uc010kwp.1_Intron|AAA1_uc003tdz.2_Intron|AAA1_uc010kwq.1_Intron|AAA1_uc003teb.1_Intron|AAA1_uc011kaq.1_Intron|NPSR1_uc003teh.1_Intron|NPSR1_uc010kwt.1_Intron|NPSR1_uc010kwu.1_Intron|NPSR1_uc010kwv.1_Intron|NPSR1_uc003tei.1_Intron|NPSR1_uc010kww.1_Intron|NPSR1_uc011kar.1_Intron	NM_207172	NP_997055			G protein-coupled receptor for asthma							cytoplasm|integral to membrane|plasma membrane	vasopressin receptor activity			skin(3)|pancreas(1)	4					Halothane(DB01159)													---	---	---	---
DPY19L1	23333	broad.mit.edu	37	7	35013097	35013097	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35013097delA	uc003tem.3	-							NM_015283	NP_056098			dpy-19-like 1							integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	35381153	35381153	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35381153delT								TBX20 (87911 upstream) : HERPUD2 (291119 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	35542607	35542607	+	IGR	DEL	A	-	-	rs71553009		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35542607delA								TBX20 (249365 upstream) : HERPUD2 (129665 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	36170919	36170920	+	IGR	INS	-	A	A	rs148519185	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36170919_36170920insA								SEPT7 (226004 upstream) : EEPD1 (21916 downstream)																																			---	---	---	---
EEPD1	80820	broad.mit.edu	37	7	36258939	36258939	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36258939delA	uc003tfa.2	+							NM_030636	NP_085139			endonuclease/exonuclease/phosphatase family						DNA repair		DNA binding				0																		---	---	---	---
KIAA0895	23366	broad.mit.edu	37	7	36399192	36399192	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36399192delT	uc003tfd.2	-						KIAA0895_uc003tfc.2_Intron|KIAA0895_uc011kaw.1_Intron|KIAA0895_uc003tfb.2_Intron|KIAA0895_uc011kax.1_Intron|KIAA0895_uc003tfe.2_Intron|KIAA0895_uc011kay.1_Intron	NM_001100425	NP_001093895			hypothetical protein LOC23366 isoform 1												0																		---	---	---	---
ELMO1	9844	broad.mit.edu	37	7	36907953	36907954	+	Intron	INS	-	T	T	rs71553092		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36907953_36907954insT	uc003tfk.1	-						ELMO1_uc003tfi.1_Intron|ELMO1_uc003tfj.1_Intron|ELMO1_uc011kbb.1_Intron|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	37360022	37360022	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37360022delA	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	37618204	37618207	+	IGR	DEL	TGCT	-	-	rs140401006		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37618204_37618207delTGCT								ELMO1 (129674 upstream) : GPR141 (161789 downstream)																																			---	---	---	---
TXNDC3	51314	broad.mit.edu	37	7	37925937	37925937	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37925937delG	uc003tfn.2	+							NM_016616	NP_057700			thioredoxin domain containing 3						cell differentiation|cell redox homeostasis|CTP biosynthetic process|GTP biosynthetic process|multicellular organismal development|spermatogenesis|UTP biosynthetic process	cytoplasm|microtubule cytoskeleton	ATP binding|nucleoside diphosphate kinase activity			ovary(1)|breast(1)|central_nervous_system(1)	3														Kartagener_syndrome				---	---	---	---
EPDR1	54749	broad.mit.edu	37	7	37968002	37968002	+	Intron	DEL	A	-	-	rs34272919		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37968002delA	uc003tfp.2	+						EPDR1_uc003tfq.2_Intron|EPDR1_uc010kxh.2_Intron	NM_017549	NP_060019			ependymin related protein 1 precursor						cell-matrix adhesion	extracellular region	calcium ion binding			upper_aerodigestive_tract(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	38214734	38214734	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38214734delC								EPDR1 (223195 upstream) : STARD3NL (3199 downstream)																																			---	---	---	---
AMPH	273	broad.mit.edu	37	7	38469204	38469204	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38469204delA	uc003tgu.2	-						AMPH_uc003tgv.2_Intron|AMPH_uc003tgt.2_Intron|AMPH_uc003tgw.1_5'Flank|AMPH_uc010kxl.1_5'Flank	NM_001635	NP_001626			amphiphysin isoform 1						endocytosis|synaptic transmission	actin cytoskeleton|cell junction|synaptic vesicle membrane				ovary(3)|liver(1)|skin(1)	5																		---	---	---	---
POU6F2	11281	broad.mit.edu	37	7	39415224	39415224	+	Intron	DEL	T	-	-	rs72463292		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:39415224delT	uc003thb.1	+							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	41172935	41172935	+	IGR	DEL	A	-	-	rs4720398	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:41172935delA								C7orf10 (272578 upstream) : INHBA (555668 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	41222995	41222998	+	IGR	DEL	CTCC	-	-	rs39776		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:41222995_41222998delCTCC								C7orf10 (322638 upstream) : INHBA (505605 downstream)																																			---	---	---	---
INHBA	3624	broad.mit.edu	37	7	41740083	41740083	+	5'UTR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:41740083delT	uc003thq.2	-	1					LOC285954_uc003tht.3_Intron|INHBA_uc003thr.2_5'UTR|LOC285954_uc003ths.2_Intron	NM_002192	NP_002183			inhibin beta A precursor						cell cycle arrest|cell surface receptor linked signaling pathway|defense response|erythrocyte differentiation|eyelid development in camera-type eye|G1/S transition of mitotic cell cycle|growth|hair follicle development|hemoglobin biosynthetic process|hemopoietic progenitor cell differentiation|induction of apoptosis|male gonad development|negative regulation of B cell differentiation|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of follicle-stimulating hormone secretion|negative regulation of interferon-gamma biosynthetic process|negative regulation of macrophage differentiation|negative regulation of phosphorylation|nervous system development|odontogenesis|ovarian follicle development|palate development|positive regulation of erythrocyte differentiation|positive regulation of follicle-stimulating hormone secretion|positive regulation of ovulation|positive regulation of transcription from RNA polymerase II promoter|progesterone secretion|regulation of activin receptor signaling pathway	activin A complex|inhibin A complex	cytokine activity|follistatin binding|growth factor activity|hormone activity|identical protein binding|signal transducer activity			lung(5)|ovary(1)	6															TSP Lung(11;0.080)			---	---	---	---
Unknown	0	broad.mit.edu	37	7	41855011	41855012	+	IGR	DEL	GA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:41855011_41855012delGA								LOC285954 (36037 upstream) : GLI3 (145538 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	42479140	42479140	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:42479140delA								GLI3 (202522 upstream) : C7orf25 (469734 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	42574585	42574585	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:42574585delA								GLI3 (297967 upstream) : C7orf25 (374289 downstream)																																			---	---	---	---
HECW1	23072	broad.mit.edu	37	7	43274110	43274110	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43274110delT	uc003tid.1	+						HECW1_uc011kbi.1_Intron|HECW1_uc003tie.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-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	44140749	44140749	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44140749delC								POLM (18620 upstream) : AEBP1 (3211 downstream)																																			---	---	---	---
NUDCD3	23386	broad.mit.edu	37	7	44474692	44474694	+	Intron	DEL	TTT	-	-	rs10572254		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44474692_44474694delTTT	uc003tkz.2	-						NUDCD3_uc010kye.2_Intron	NM_015332	NP_056147			NudC domain containing 3												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	44549475	44549475	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44549475delT								NUDCD3 (19090 upstream) : NPC1L1 (2661 downstream)																																			---	---	---	---
NPC1L1	29881	broad.mit.edu	37	7	44572705	44572705	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44572705delA	uc003tlb.2	-						NPC1L1_uc003tlc.2_Intron|NPC1L1_uc011kbw.1_Intron	NM_013389	NP_037521			Niemann-Pick C1-like protein 1 isoform 1						cholesterol biosynthetic process|intestinal cholesterol absorption|lipoprotein metabolic process	apical plasma membrane|cytoplasmic vesicle membrane|integral to membrane	hedgehog receptor activity|protein binding			ovary(3)|central_nervous_system(1)|skin(1)	5					Ezetimibe(DB00973)													---	---	---	---
OGDH	4967	broad.mit.edu	37	7	44672212	44672212	+	Intron	DEL	G	-	-	rs73109424	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44672212delG	uc003tln.2	+						OGDH_uc003tlm.2_Intron|OGDH_uc011kbx.1_Intron|OGDH_uc011kby.1_Intron|OGDH_uc003tlp.2_Intron|OGDH_uc011kbz.1_Intron	NM_002541	NP_002532			oxoglutarate dehydrogenase isoform 1 precursor						glycolysis|lysine catabolic process|tricarboxylic acid cycle	mitochondrial matrix|mitochondrial membrane	oxoglutarate dehydrogenase (succinyl-transferring) activity|thiamine pyrophosphate binding			upper_aerodigestive_tract(1)|ovary(1)	2					NADH(DB00157)													---	---	---	---
RAMP3	10268	broad.mit.edu	37	7	45196723	45196724	+	5'Flank	DEL	CA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45196723_45196724delCA	uc003tnb.2	+							NM_005856	NP_005847			receptor activity modifying protein 3 precursor						intracellular protein transport|receptor-mediated endocytosis|regulation of G-protein coupled receptor protein signaling pathway	integral to plasma membrane|lysosome	protein transporter activity				0					Pramlintide(DB01278)													---	---	---	---
Unknown	0	broad.mit.edu	37	7	45449920	45449920	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45449920delG								RAMP3 (226073 upstream) : ADCY1 (163819 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	45497485	45497486	+	IGR	DEL	GA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45497485_45497486delGA								RAMP3 (273638 upstream) : ADCY1 (116253 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	45558669	45558669	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45558669delA								RAMP3 (334822 upstream) : ADCY1 (55070 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	46378254	46378254	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:46378254delT								IGFBP3 (417383 upstream) : TNS3 (936499 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	46791765	46791768	+	IGR	DEL	TTTT	-	-	rs111504442		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:46791765_46791768delTTTT								IGFBP3 (830894 upstream) : TNS3 (522985 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	46981460	46981460	+	IGR	DEL	G	-	-	rs6950797		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:46981460delG								None (None upstream) : TNS3 (333293 downstream)																																			---	---	---	---
PKD1L1	168507	broad.mit.edu	37	7	47932486	47932486	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:47932486delA	uc003tny.1	-							NM_138295	NP_612152			polycystin-1L1						cell-cell adhesion	integral to membrane				ovary(8)|upper_aerodigestive_tract(2)|breast(1)	11																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	48001374	48001374	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48001374delA								PKD1L1 (13337 upstream) : HUS1 (1609 downstream)																																			---	---	---	---
HUS1	3364	broad.mit.edu	37	7	48017489	48017489	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48017489delA	uc003tod.1	-						HUS1_uc003toe.1_Intron|HUS1_uc011kce.1_Intron	NM_004507	NP_004498			HUS1 checkpoint protein						DNA damage checkpoint|DNA replication	Golgi apparatus|nucleolus|nucleoplasm	protein binding			ovary(2)|lung(2)|kidney(1)	5		Breast(660;0.00139)											Direct_reversal_of_damage|Other_conserved_DNA_damage_response_genes					---	---	---	---
Unknown	0	broad.mit.edu	37	7	48151310	48151310	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48151310delA								UPP1 (2981 upstream) : ABCA13 (59747 downstream)																																			---	---	---	---
ABCA13	154664	broad.mit.edu	37	7	48266654	48266654	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48266654delA	uc003toq.2	+						ABCA13_uc003top.2_Intron|ABCA13_uc010kyr.2_Intron	NM_152701	NP_689914			ATP binding cassette, sub-family A (ABC1),						transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10																		---	---	---	---
ABCA13	154664	broad.mit.edu	37	7	48503374	48503378	+	Intron	DEL	GGAAT	-	-	rs71993401		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48503374_48503378delGGAAT	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	49110789	49110789	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:49110789delA								CDC14C (143740 upstream) : VWC2 (702468 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	49590543	49590543	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:49590543delG								CDC14C (623494 upstream) : VWC2 (222714 downstream)																																			---	---	---	---
VWC2	375567	broad.mit.edu	37	7	49899385	49899388	+	Intron	DEL	TGCA	-	-	rs10571154	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:49899385_49899388delTGCA	uc003tot.1	+							NM_198570	NP_940972			von Willebrand factor C domain containing 2						negative regulation of BMP signaling pathway|positive regulation of neuron differentiation	basement membrane|extracellular space					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	50911078	50911078	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:50911078delT								GRB10 (49919 upstream) : COBL (172832 downstream)																																			---	---	---	---
COBL	23242	broad.mit.edu	37	7	51290412	51290412	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:51290412delG	uc003tpr.3	-						COBL_uc003tps.2_Intron|COBL_uc011kcl.1_Intron|COBL_uc010kzc.2_Intron|COBL_uc003tpt.2_Intron	NM_015198	NP_056013			cordon-bleu homolog											skin(3)|ovary(2)	5	Glioma(55;0.08)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	51459541	51459541	+	5'Flank	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:51459541delA	uc011kcm.1	-						uc003tpu.2_5'Flank|uc003tpw.1_5'Flank|uc011kcn.1_5'Flank					DQ573852																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	51782364	51782364	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:51782364delT								COBL (397849 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	52223039	52223040	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:52223039_52223040insT								COBL (838524 upstream) : POM121L12 (880309 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	53828050	53828050	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:53828050delA								POM121L12 (723433 upstream) : HPVC1 (440867 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	53979513	53979513	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:53979513delT								POM121L12 (874896 upstream) : HPVC1 (289404 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	54008076	54008076	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:54008076delT								POM121L12 (903459 upstream) : HPVC1 (260841 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	54409811	54409811	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:54409811delA								HPVC1 (139697 upstream) : VSTM2A (200208 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	54556558	54556559	+	IGR	DEL	CT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:54556558_54556559delCT								HPVC1 (286444 upstream) : VSTM2A (53460 downstream)																																			---	---	---	---
EGFR	1956	broad.mit.edu	37	7	55165918	55165919	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55165918_55165919insT	uc003tqk.2	+						EGFR_uc003tqh.2_Intron|EGFR_uc003tqi.2_Intron|EGFR_uc003tqj.2_Intron|EGFR_uc010kzg.1_Intron	NM_005228	NP_005219			epidermal growth factor receptor isoform a						activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A	basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex	actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity			lung(9213)|central_nervous_system(103)|stomach(41)|upper_aerodigestive_tract(39)|prostate(32)|ovary(31)|thyroid(24)|breast(11)|peritoneum(9)|oesophagus(9)|salivary_gland(9)|large_intestine(8)|kidney(8)|urinary_tract(6)|skin(5)|adrenal_gland(5)|soft_tissue(4)|bone(3)|NS(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(2)|thymus(2)|liver(2)|eye(1)	9571	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)		8	A|O|Mis		glioma|NSCLC	NSCLC			Lung_Cancer_Familial_Clustering_of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)			---	---	---	---
Unknown	0	broad.mit.edu	37	7	55289939	55289940	+	IGR	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55289939_55289940delAC								EGFR (14909 upstream) : LANCL2 (143201 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	55398577	55398578	+	IGR	INS	-	CA	CA	rs147621980	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55398577_55398578insCA								EGFR (123547 upstream) : LANCL2 (34563 downstream)																																			---	---	---	---
MRPS17	51373	broad.mit.edu	37	7	56020724	56020725	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56020724_56020725delAA	uc003trd.2	+						MRPS17_uc003trb.2_Intron	NM_015969	NP_057053			mitochondrial ribosomal protein S17 precursor						translation	mitochondrial small ribosomal subunit	rRNA binding|structural constituent of ribosome				0	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	57212794	57212794	+	IGR	DEL	T	-	-	rs34002920		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57212794delT								ZNF479 (5223 upstream) : ZNF716 (297089 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	57607910	57607910	+	IGR	DEL	G	-	-	rs77252234		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57607910delG								ZNF716 (74645 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	57701099	57701099	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57701099delT								ZNF716 (167834 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	57732065	57732066	+	IGR	INS	-	CAT	CAT	rs145832029	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57732065_57732066insCAT								ZNF716 (198800 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	57768704	57768704	+	IGR	DEL	A	-	-	rs112374695		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57768704delA								ZNF716 (235439 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	57796360	57796361	+	IGR	DEL	AT	-	-	rs139262292		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57796360_57796361delAT								ZNF716 (263095 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	57844261	57844262	+	IGR	INS	-	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57844261_57844262insC								ZNF716 (310996 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	57863734	57863734	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57863734delC								ZNF716 (330469 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	57882274	57882289	+	IGR	DEL	TGTGTGTGTGTGTCCA	-	-	rs115418770	by1000genomes;by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57882274_57882289delTGTGTGTGTGTGTCCA								ZNF716 (349009 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	61077032	61077032	+	IGR	DEL	A	-	-	rs74858662		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61077032delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	61738104	61738104	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61738104delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	61769524	61769524	+	IGR	DEL	A	-	-	rs150670066		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61769524delA								None (None upstream) : LOC643955 (982148 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	61804622	61804622	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61804622delA								None (None upstream) : LOC643955 (947050 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	61857183	61857183	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61857183delT								None (None upstream) : LOC643955 (894489 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	61887248	61887248	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61887248delC								None (None upstream) : LOC643955 (864424 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	62981752	62981753	+	IGR	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:62981752_62981753delTG								LOC100287704 (169601 upstream) : ZNF727 (524068 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	62983561	62983562	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:62983561_62983562delTT								LOC100287704 (171410 upstream) : ZNF727 (522259 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	63032004	63032004	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:63032004delA								LOC100287704 (219853 upstream) : ZNF727 (473817 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	63552015	63552016	+	IGR	DEL	TA	-	-	rs72398672		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:63552015_63552016delTA								ZNF727 (13090 upstream) : ZNF735 (115565 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	63639424	63639427	+	IGR	DEL	GCGC	-	-	rs76376355	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:63639424_63639427delGCGC								ZNF727 (100499 upstream) : ZNF735 (28154 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	64173154	64173154	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64173154delT								ZNF107 (1755 upstream) : ZNF138 (81617 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	64194982	64194982	+	IGR	DEL	T	-	-	rs112273003		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64194982delT								ZNF107 (23583 upstream) : ZNF138 (59789 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	65047473	65047473	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65047473delA								ZNF92 (181476 upstream) : INTS4L2 (65304 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	65133884	65133885	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65133884_65133885delTT	uc003tud.1	-						INTS4L2_uc003tue.2_Intron					Homo sapiens hypothetical LOC441242, mRNA (cDNA clone MGC:87648 IMAGE:5267764), complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	65230088	65230091	+	Intron	DEL	AAAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65230088_65230091delAAAA	uc003tud.1	-											Homo sapiens hypothetical LOC441242, mRNA (cDNA clone MGC:87648 IMAGE:5267764), complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	65236466	65236467	+	5'Flank	INS	-	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65236466_65236467insG	uc003tud.1	-											Homo sapiens hypothetical LOC441242, mRNA (cDNA clone MGC:87648 IMAGE:5267764), complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	65280578	65280578	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65280578delT								CCT6P1 (51917 upstream) : VKORC1L1 (57679 downstream)																																			---	---	---	---
GUSB	2990	broad.mit.edu	37	7	65440370	65440370	+	Intron	DEL	A	-	-	rs781145	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65440370delA	uc003tun.2	-						GUSB_uc011kdt.1_Intron	NM_000181	NP_000172			glucuronidase, beta precursor						glycosaminoglycan catabolic process	lysosome	beta-glucuronidase activity|cation binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	65899617	65899617	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65899617delA								NCRNA00174 (34222 upstream) : LOC493754 (93829 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	66086266	66086267	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66086266_66086267delAA								LOC493754 (28903 upstream) : RABGEF1 (7623 downstream)																																			---	---	---	---
RABGEF1	27342	broad.mit.edu	37	7	66117373	66117373	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66117373delA	uc003tvf.2	+							NM_014504	NP_055319			RAB guanine nucleotide exchange factor (GEF) 1						endocytosis|protein transport	early endosome|recycling endosome	DNA binding|protein binding|zinc ion binding			ovary(1)	1																		---	---	---	---
RABGEF1	27342	broad.mit.edu	37	7	66209009	66209013	+	Intron	DEL	TTTTC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66209009_66209013delTTTTC	uc010lag.2	+						RABGEF1_uc003tvf.2_Intron|RABGEF1_uc003tvg.2_Intron|RABGEF1_uc003tvh.2_Intron	NM_014504	NP_055319			RAB guanine nucleotide exchange factor (GEF) 1						endocytosis|protein transport	early endosome|recycling endosome	DNA binding|protein binding|zinc ion binding			ovary(1)	1																		---	---	---	---
SBDS	51119	broad.mit.edu	37	7	66452977	66452978	+	3'UTR	INS	-	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66452977_66452978insC	uc003tvm.1	-	5						NM_016038	NP_057122			Shwachman-Bodian-Diamond syndrome protein						bone marrow development|bone mineralization|leukocyte chemotaxis|mature ribosome assembly|mitotic spindle stabilization|positive regulation of translation|ribosomal large subunit biogenesis|rRNA processing	cytoplasm|nucleolus|nucleoplasm|spindle pole	microtubule binding|ribosome binding|rRNA binding			ovary(1)	1								Gene Conversion			AML|MDS			Shwachman-Diamond_syndrome				---	---	---	---
TYW1	55253	broad.mit.edu	37	7	66472629	66472629	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66472629delT	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	66581016	66581016	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66581016delA	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	66924780	66924781	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66924780_66924781delTT								STAG3L4 (138268 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	67025276	67025276	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:67025276delT								STAG3L4 (238764 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	67244238	67244239	+	IGR	DEL	TG	-	-	rs75372006		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:67244238_67244239delTG								STAG3L4 (457726 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	67765290	67765291	+	IGR	DEL	AA	-	-	rs77138714		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:67765290_67765291delAA								STAG3L4 (978778 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	68289464	68289464	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68289464delA								None (None upstream) : AUTS2 (774441 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	68413563	68413575	+	IGR	DEL	TTCTCTTCTTTCT	-	-	rs55692855		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68413563_68413575delTTCTCTTCTTTCT								None (None upstream) : AUTS2 (650330 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	68424741	68424746	+	IGR	DEL	AGAAAG	-	-	rs72085762	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68424741_68424746delAGAAAG								None (None upstream) : AUTS2 (639159 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	68669565	68669565	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68669565delA								None (None upstream) : AUTS2 (394340 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	70258342	70258342	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70258342delT								AUTS2 (458 upstream) : WBSCR17 (339447 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	70281957	70281957	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70281957delA								AUTS2 (24073 upstream) : WBSCR17 (315832 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	70540616	70540617	+	IGR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70540616_70540617insA								AUTS2 (282732 upstream) : WBSCR17 (57172 downstream)																																			---	---	---	---
WBSCR17	64409	broad.mit.edu	37	7	70813935	70813936	+	Intron	DEL	CA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70813935_70813936delCA	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	71198080	71198081	+	IGR	INS	-	GGAG	GGAG	rs137894080	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71198080_71198081insGGAG								WBSCR17 (19497 upstream) : CALN1 (46396 downstream)																																			---	---	---	---
CALN1	83698	broad.mit.edu	37	7	71551557	71551558	+	Intron	INS	-	A	A	rs146281663	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71551557_71551558insA	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	71702720	71702721	+	Intron	DEL	AG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71702720_71702721delAG	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	73067481	73067481	+	IGR	DEL	T	-	-	rs11342839		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73067481delT								MLXIPL (28611 upstream) : VPS37D (14693 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	73140020	73140027	+	IGR	DEL	AAACAAAC	-	-	rs72018891		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73140020_73140027delAAACAAAC								STX1A (6032 upstream) : WBSCR26 (9372 downstream)																																			---	---	---	---
ELN	2006	broad.mit.edu	37	7	73456758	73456759	+	Intron	DEL	AA	-	-	rs72489767		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73456758_73456759delAA	uc003tzw.2	+						RFC2_uc011kfa.1_Intron|ELN_uc003tzm.1_Intron|ELN_uc011kfe.1_Intron|ELN_uc003tzn.2_Intron|ELN_uc003tzz.2_Intron|ELN_uc003tzo.2_Intron|ELN_uc003tzp.2_Intron|ELN_uc003tzq.2_Intron|ELN_uc003tzr.2_Intron|ELN_uc003tzs.2_Intron|ELN_uc003tzt.2_Intron|ELN_uc003tzu.2_Intron|ELN_uc003tzv.2_Intron|ELN_uc003tzx.2_Intron|ELN_uc011kff.1_Intron|ELN_uc003tzy.2_Intron	NM_000501	NP_001075224			elastin isoform a precursor						blood circulation|cell proliferation|organ morphogenesis|respiratory gaseous exchange	proteinaceous extracellular matrix	extracellular matrix constituent conferring elasticity|protein binding			ovary(3)|pancreas(2)	5		Lung NSC(55;0.159)			Rofecoxib(DB00533)			T	PAX5	B-ALL		Supravalvular Aortic Stenosis|Cutis laxa |Williams-Beuren Syndrome						---	---	---	---
RFC2	5982	broad.mit.edu	37	7	73547615	73547615	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73547615delT	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	73659360	73659363	+	Intron	DEL	TTTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73659360_73659363delTTTT	uc003uaj.2	-						RFC2_uc011kfa.1_Intron|RFC2_uc003uak.2_Intron|RFC2_uc010lbp.2_Intron|RFC2_uc003ual.2_Intron	NM_181471	NP_852136			replication factor C 2 isoform 1						cell cycle checkpoint|DNA strand elongation involved in DNA replication|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	DNA replication factor C complex|nucleoplasm	ATP binding|DNA clamp loader activity|protein binding			liver(1)|central_nervous_system(1)	2																		---	---	---	---
GTF2IRD1	9569	broad.mit.edu	37	7	73900257	73900257	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73900257delA	uc003uaq.2	+						GTF2IRD1_uc010lbq.2_Intron|GTF2IRD1_uc003uap.2_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	73910816	73910817	+	Intron	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73910816_73910817delTG	uc003uaq.2	+						GTF2IRD1_uc010lbq.2_Intron|GTF2IRD1_uc003uap.2_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	73977910	73977910	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73977910delA	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	74012551	74012552	+	Intron	DEL	AA	-	-	rs113012530		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74012551_74012552delAA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	74050407	74050407	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74050407delT								GTF2IRD1 (33489 upstream) : GTF2I (21623 downstream)																																			---	---	---	---
GTF2I	2969	broad.mit.edu	37	7	74085799	74085800	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74085799_74085800insT	uc003uau.2	+						GTF2I_uc003uat.2_Intron|GTF2I_uc003uav.2_Intron|GTF2I_uc003uaw.2_Intron|GTF2I_uc003uay.2_Intron|GTF2I_uc003uax.2_Intron	NM_032999	NP_127492			general transcription factor IIi isoform 1						negative regulation of angiogenesis|signal transduction|transcription initiation from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
GTF2I	2969	broad.mit.edu	37	7	74146723	74146723	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74146723delA	uc003uau.2	+						GTF2I_uc003uav.2_Intron|GTF2I_uc003uaw.2_Intron|GTF2I_uc003uay.2_Intron|GTF2I_uc003uax.2_Intron	NM_032999	NP_127492			general transcription factor IIi isoform 1						negative regulation of angiogenesis|signal transduction|transcription initiation from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	75501490	75501492	+	IGR	DEL	AAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75501490_75501492delAAA								CCL24 (58457 upstream) : RHBDD2 (6825 downstream)																																			---	---	---	---
POR	5447	broad.mit.edu	37	7	75614021	75614021	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75614021delC	uc003udy.2	+						POR_uc011kgc.1_Intron|POR_uc011kgd.1_Intron|POR_uc011kge.1_Intron|POR_uc003uea.2_5'Flank	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)													---	---	---	---
SRRM3	222183	broad.mit.edu	37	7	75844099	75844099	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75844099delA	uc010ldi.2	+							NM_001110199	NP_001103669			serine/arginine repetitive matrix 3												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	75949259	75949259	+	IGR	DEL	A	-	-	rs75698288		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75949259delA								HSPB1 (15649 upstream) : YWHAG (6849 downstream)																																			---	---	---	---
PMS2L11	441263	broad.mit.edu	37	7	76626342	76626344	+	Intron	DEL	GTG	-	-	rs36027405		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76626342_76626344delGTG	uc003ufw.3	+						PMS2L11_uc011kgn.1_Intron	NR_023383				Homo sapiens cDNA FLJ59034 complete cds, moderately similar to Protein deltex-2.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	77063157	77063157	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77063157delA								PION (17440 upstream) : PTPN12 (103616 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	77305108	77305108	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77305108delG	uc003ugj.1	-											Homo sapiens clone 124-1V1, mRNA sequence.																														---	---	---	---
TMEM60	85025	broad.mit.edu	37	7	77424832	77424833	+	Intron	DEL	AA	-	-	rs68144197		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77424832_77424833delAA	uc003ugn.2	-							NM_032936	NP_116325			transmembrane protein 60							integral to membrane					0																		---	---	---	---
PHTF2	57157	broad.mit.edu	37	7	77509774	77509776	+	Intron	DEL	CTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77509774_77509776delCTT	uc003ugs.3	+						PHTF2_uc003ugo.3_Intron|PHTF2_uc003ugp.2_Intron|PHTF2_uc003ugq.3_Intron|PHTF2_uc010ldv.2_Intron|PHTF2_uc003ugr.3_Intron|PHTF2_uc003ugt.3_Intron|PHTF2_uc003ugu.3_Intron	NM_001127357	NP_001120829			putative homeodomain transcription factor 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	endoplasmic reticulum|nucleus	DNA binding			ovary(1)	1																		---	---	---	---
PHTF2	57157	broad.mit.edu	37	7	77572754	77572754	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77572754delT	uc003ugs.3	+						PHTF2_uc003ugq.3_Intron|PHTF2_uc010ldv.2_Intron|PHTF2_uc003ugt.3_Intron|PHTF2_uc003ugu.3_Intron	NM_001127357	NP_001120829			putative homeodomain transcription factor 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	endoplasmic reticulum|nucleus	DNA binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	77624016	77624029	+	IGR	DEL	CACACACACACACG	-	-	rs140020505		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77624016_77624029delCACACACACACACG								PHTF2 (37198 upstream) : MAGI2 (22346 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	79399480	79399481	+	IGR	DEL	GT	-	-	rs71824695		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:79399480_79399481delGT								MAGI2 (316590 upstream) : GNAI1 (364659 downstream)																																			---	---	---	---
CD36	948	broad.mit.edu	37	7	80225901	80225901	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:80225901delA	uc003uhc.2	+							NM_001127444	NP_001120916			CD36 antigen						cell adhesion|cGMP-mediated signaling|cholesterol transport|lipid metabolic process|lipid storage|lipoprotein transport|low-density lipoprotein particle clearance|nitric oxide mediated signal transduction|plasma membrane long-chain fatty acid transport|platelet activation|platelet degranulation|positive regulation of cell-matrix adhesion|positive regulation of macrophage derived foam cell differentiation	integral to plasma membrane|membrane fraction|platelet alpha granule membrane	lipid binding|low-density lipoprotein receptor activity|thrombospondin receptor activity|transforming growth factor beta binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	81562339	81562339	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:81562339delA								HGF (162887 upstream) : CACNA2D1 (17079 downstream)																																			---	---	---	---
CACNA2D1	781	broad.mit.edu	37	7	81659042	81659045	+	Intron	DEL	TATG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:81659042_81659045delTATG	uc003uhr.1	-						uc003uhs.1_RNA	NM_000722	NP_000713			calcium channel, voltage-dependent, alpha							voltage-gated calcium channel complex	metal ion binding			ovary(5)|pancreas(1)	6					Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)													---	---	---	---
PCLO	27445	broad.mit.edu	37	7	82716538	82716539	+	Intron	DEL	AA	-	-	rs34272716		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82716538_82716539delAA	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	82881524	82881524	+	IGR	DEL	G	-	-	rs57316849		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82881524delG								PCLO (89327 upstream) : SEMA3E (111698 downstream)																																			---	---	---	---
SEMA3A	10371	broad.mit.edu	37	7	83671923	83671923	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:83671923delT	uc003uhz.2	-							NM_006080	NP_006071			semaphorin 3A precursor						axon guidance	extracellular region|membrane	receptor activity			ovary(2)|breast(1)|kidney(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	85176537	85176538	+	IGR	INS	-	A	A	rs139708338	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:85176537_85176538insA								SEMA3D (360366 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	85512787	85512787	+	IGR	DEL	A	-	-	rs5885499		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:85512787delA								SEMA3D (696616 upstream) : GRM3 (760443 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	85657641	85657642	+	IGR	DEL	AC	-	-	rs141865009	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:85657641_85657642delAC								SEMA3D (841470 upstream) : GRM3 (615588 downstream)																																			---	---	---	---
GRM3	2913	broad.mit.edu	37	7	86445605	86445605	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:86445605delT	uc003uid.2	+						GRM3_uc010lef.2_Intron|GRM3_uc010leg.2_Intron|GRM3_uc010leh.2_Intron	NM_000840	NP_000831			glutamate receptor, metabotropic 3 precursor						synaptic transmission	integral to plasma membrane				lung(4)|ovary(3)|central_nervous_system(2)|skin(2)|haematopoietic_and_lymphoid_tissue(1)|prostate(1)	13	Esophageal squamous(14;0.0058)|all_lung(186;0.132)|Lung NSC(181;0.142)				Acamprosate(DB00659)|Nicotine(DB00184)													---	---	---	---
CROT	54677	broad.mit.edu	37	7	86994394	86994394	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:86994394delT	uc003uit.2	+						CROT_uc003uiu.2_Intron	NM_021151	NP_066974			peroxisomal carnitine O-octanoyltransferase						fatty acid beta-oxidation using acyl-CoA oxidase|generation of precursor metabolites and energy|transport	peroxisomal matrix	carnitine O-octanoyltransferase activity			ovary(2)|lung(1)	3	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)				L-Carnitine(DB00583)													---	---	---	---
ZNF804B	219578	broad.mit.edu	37	7	88740175	88740175	+	Intron	DEL	T	-	-	rs71809438		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:88740175delT	uc011khi.1	+							NM_181646	NP_857597			zinc finger protein 804B							intracellular	zinc ion binding			ovary(5)|skin(3)|pancreas(2)|upper_aerodigestive_tract(1)	11	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)												HNSCC(36;0.09)			---	---	---	---
Unknown	0	broad.mit.edu	37	7	89347778	89347778	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:89347778delA								ZNF804B (381434 upstream) : DPY19L2P4 (400936 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	89568925	89568925	+	IGR	DEL	T	-	-	rs72376257		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:89568925delT								ZNF804B (602581 upstream) : DPY19L2P4 (179789 downstream)																																			---	---	---	---
STEAP1	26872	broad.mit.edu	37	7	89782843	89782843	+	5'Flank	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:89782843delT	uc003ujx.2	+						STEAP1_uc010lem.2_5'Flank	NM_012449	NP_036581			six transmembrane epithelial antigen of the						electron transport chain|ion transport|iron ion homeostasis	cell-cell junction|endosome membrane|integral to plasma membrane	channel activity|electron carrier activity|flavin adenine dinucleotide binding|iron ion binding|oxidoreductase activity				0	all_hematologic(106;0.112)																	---	---	---	---
CDK14	5218	broad.mit.edu	37	7	90613962	90613962	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90613962delG	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	91280297	91280297	+	IGR	DEL	C	-	-	rs34584302		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91280297delC								FZD1 (382166 upstream) : MTERF (151163 downstream)																																			---	---	---	---
AKAP9	10142	broad.mit.edu	37	7	91722747	91722747	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91722747delT	uc003ulg.2	+						AKAP9_uc003ulf.2_Intron|AKAP9_uc003uli.2_Intron|AKAP9_uc003ulj.2_Intron|AKAP9_uc003ull.2_Intron	NM_005751	NP_005742			A-kinase anchor protein 9 isoform 2						G2/M transition of mitotic cell cycle|signal transduction|synaptic transmission|transport	centrosome|cytosol|Golgi apparatus	receptor binding			breast(7)|ovary(6)|lung(5)|skin(3)|large_intestine(2)|prostate(2)|central_nervous_system(1)	26	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)					T	BRAF	papillary thyroid								---	---	---	---
ANKIB1	54467	broad.mit.edu	37	7	92000724	92000724	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92000724delT	uc003ulw.2	+						ANKIB1_uc010lew.1_5'Flank	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	92053143	92053144	+	IGR	DEL	GT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92053143_92053144delGT								ANKIB1 (22445 upstream) : GATAD1 (23621 downstream)																																			---	---	---	---
CDK6	1021	broad.mit.edu	37	7	92321584	92321584	+	Intron	DEL	G	-	-	rs1972508	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92321584delG	uc011khw.1	-						CDK6_uc010lez.2_Intron	NM_001259	NP_001250			cyclin-dependent kinase 6						cell dedifferentiation|cell division|G1 phase of mitotic cell cycle|gliogenesis|negative regulation of cell cycle|negative regulation of epithelial cell proliferation|negative regulation of osteoblast differentiation|positive regulation of cell-matrix adhesion|positive regulation of fibroblast proliferation|regulation of erythrocyte differentiation|regulation of gene expression|response to virus	cyclin-dependent protein kinase holoenzyme complex|cytosol|nucleus|ruffle	ATP binding|cyclin binding|cyclin-dependent protein kinase activity			central_nervous_system(1)|skin(1)	2	all_cancers(62;8.72e-12)|all_epithelial(64;3.65e-10)|Breast(17;0.000675)|all_lung(186;0.0392)|Lung NSC(181;0.053)|all_neural(327;0.219)|all_hematologic(106;0.237)		STAD - Stomach adenocarcinoma(4;6.16e-07)|GBM - Glioblastoma multiforme(5;1.2e-06)|all cancers(6;3.1e-05)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23)					T	MLLT10	ALL								---	---	---	---
CCDC132	55610	broad.mit.edu	37	7	92978195	92978195	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92978195delT	uc003umo.2	+						CCDC132_uc003umq.2_Intron|CCDC132_uc003ump.2_Intron|CCDC132_uc003umr.2_Intron|CCDC132_uc011khz.1_Intron	NM_017667	NP_060137			coiled-coil domain containing 132 isoform a												0	all_cancers(62;2.64e-11)|all_epithelial(64;1.4e-10)|Breast(17;0.000675)|Lung NSC(181;0.0618)|all_lung(186;0.0837)		STAD - Stomach adenocarcinoma(171;0.000302)															---	---	---	---
TFPI2	7980	broad.mit.edu	37	7	93517857	93517860	+	Intron	DEL	GAAG	-	-	rs72257308		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:93517857_93517860delGAAG	uc003umy.1	-						GNGT1_uc003umx.1_Intron|TFPI2_uc003umz.1_Intron|TFPI2_uc003una.1_Intron|TFPI2_uc003unb.1_Intron|TFPI2_uc010lfg.1_Intron	NM_006528	NP_006519			tissue factor pathway inhibitor 2 precursor						blood coagulation	proteinaceous extracellular matrix	extracellular matrix structural constituent|serine-type endopeptidase inhibitor activity			pancreas(1)	1	all_cancers(62;4.45e-10)|all_epithelial(64;2.92e-09)|Lung NSC(181;0.218)		STAD - Stomach adenocarcinoma(171;0.000967)															---	---	---	---
CASD1	64921	broad.mit.edu	37	7	94138118	94138119	+	5'Flank	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94138118_94138119insT	uc003uni.3	+						CASD1_uc003unh.2_5'Flank|CASD1_uc003unj.3_5'Flank	NM_022900	NP_075051			CAS1 domain containing 1 precursor							integral to membrane				ovary(2)	2	all_cancers(62;6.71e-10)|all_epithelial(64;5e-09)|Lung NSC(181;0.188)|all_lung(186;0.215)		STAD - Stomach adenocarcinoma(171;0.0031)															---	---	---	---
DYNC1I1	1780	broad.mit.edu	37	7	95420053	95420054	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:95420053_95420054insA	uc003uoc.3	+						DYNC1I1_uc003uod.3_Intron|DYNC1I1_uc003uob.2_Intron|DYNC1I1_uc003uoe.3_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	95516034	95516034	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:95516034delA	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	95690122	95690122	+	Intron	DEL	A	-	-	rs146518871	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:95690122delA	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	95926652	95926652	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:95926652delT	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	96014318	96014321	+	IGR	DEL	AGAG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96014318_96014321delAGAG								SLC25A13 (62859 upstream) : SHFM1 (287916 downstream)																																			---	---	---	---
DLX5	1749	broad.mit.edu	37	7	96652807	96652807	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96652807delA	uc003uon.2	-						DLX5_uc011kim.1_Intron	NM_005221	NP_005212			distal-less homeobox 5						cell proliferation|endochondral ossification|osteoblast differentiation|positive regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			ovary(1)	1	all_cancers(62;9.56e-09)|all_epithelial(64;7.38e-09)|Esophageal squamous(72;0.0125)|all_lung(186;0.0855)|Lung NSC(181;0.0858)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	96920980	96920981	+	IGR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96920980_96920981insA								ACN9 (109907 upstream) : TAC1 (440290 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	97613969	97613970	+	IGR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97613969_97613970insA								MGC72080 (12331 upstream) : OCM2 (45 downstream)																																			---	---	---	---
TECPR1	25851	broad.mit.edu	37	7	97846693	97846693	+	3'UTR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97846693delG	uc003upg.2	-	26						NM_015395	NP_056210			tectonin beta-propeller repeat containing 1							integral to membrane	protein binding			pancreas(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	98142463	98142463	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98142463delT								BAIAP2L1 (112036 upstream) : NPTX2 (104134 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	98371010	98371010	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98371010delT								NPTX2 (111829 upstream) : TMEM130 (73102 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	99085397	99085399	+	IGR	DEL	AAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99085397_99085399delAAA								ZNF789 (180 upstream) : ZNF394 (5456 downstream)																																			---	---	---	---
ZKSCAN5	23660	broad.mit.edu	37	7	99113617	99113617	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99113617delT	uc003uqv.2	+						ZKSCAN5_uc010lfx.2_Intron|ZKSCAN5_uc003uqw.2_Intron|ZKSCAN5_uc003uqx.2_Intron|ZKSCAN5_uc003uqy.2_Intron	NM_145102	NP_659570			zinc finger with KRAB and SCAN domains 5						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			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)																	---	---	---	---
ZSCAN21	7589	broad.mit.edu	37	7	99648323	99648323	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99648323delA	uc003uso.2	+						ZSCAN21_uc011kje.1_Intron|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)															---	---	---	---
TAF6	6878	broad.mit.edu	37	7	99710344	99710344	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99710344delA	uc003uti.2	-						TAF6_uc003utg.2_Intron|TAF6_uc003uth.2_Intron|TAF6_uc003utk.2_Intron|TAF6_uc011kji.1_Intron|TAF6_uc003utj.2_Intron|TAF6_uc003utl.2_Intron|TAF6_uc003utm.2_Intron|TAF6_uc003utn.1_Intron	NM_139315	NP_647476			TBP-associated factor 6 isoform alpha						negative regulation of cell cycle|negative regulation of cell proliferation|regulation of sequence-specific DNA binding transcription factor activity|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	cytoplasm|MLL1 complex|transcription factor TFIID complex|transcription factor TFIID complex|transcription factor TFTC complex	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)	2	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)																	---	---	---	---
STAG3	10734	broad.mit.edu	37	7	99778452	99778452	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99778452delT	uc003utx.1	+						STAG3_uc010lgs.1_Intron|STAG3_uc011kjk.1_Intron	NM_012447	NP_036579			stromal antigen 3						chromosome segregation|synaptonemal complex assembly	chromosome, centromeric region|meiotic cohesin complex|synaptonemal complex	binding			ovary(4)|skin(2)|lung(1)|kidney(1)	8	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)																	---	---	---	---
GATS	352954	broad.mit.edu	37	7	99845449	99845450	+	Intron	DEL	TA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99845449_99845450delTA	uc003uua.3	-						GATS_uc003uty.3_Intron|GATS_uc003utz.3_Intron|GATS_uc010lgt.2_Intron|GATS_uc010lgu.2_Intron	NM_178831	NP_849153			GATS, stromal antigen 3 opposite strand												0	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)																	---	---	---	---
TSC22D4	81628	broad.mit.edu	37	7	100070538	100070538	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100070538delC	uc003uva.2	-						TSC22D4_uc003uvb.2_Intron|TSC22D4_uc011kjv.1_Intron|TSC22D4_uc010lgx.2_Intron	NM_030935	NP_112197			TSC22 domain family, member 4						negative regulation of transcription, DNA-dependent	nucleus	protein binding|sequence-specific DNA binding transcription factor activity			breast(2)	2	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	100092611	100092611	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100092611delT								C7orf51 (189 upstream) : AGFG2 (44223 downstream)																																			---	---	---	---
ZAN	7455	broad.mit.edu	37	7	100342493	100342493	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100342493delT	uc003uwj.2	+						ZAN_uc003uwk.2_Intron|ZAN_uc003uwl.2_Intron|ZAN_uc010lhh.2_Intron|ZAN_uc010lhi.2_Intron	NM_003386	NP_003377			zonadhesin isoform 3						binding of sperm to zona pellucida|cell-cell adhesion	integral to membrane|plasma membrane				ovary(4)|large_intestine(3)|central_nervous_system(2)|pancreas(2)	11	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)															---	---	---	---
SLC12A9	56996	broad.mit.edu	37	7	100447501	100447501	+	5'Flank	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100447501delT	uc003uwp.2	+						SLC12A9_uc003uwo.1_5'Flank|SLC12A9_uc003uwq.2_5'Flank	NM_020246	NP_064631			solute carrier family 12 (potassium/chloride							integral to membrane|plasma membrane	cation:chloride symporter activity				0	Lung NSC(181;0.041)|all_lung(186;0.0581)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	100611279	100611279	+	5'Flank	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100611279delT	uc003uxm.1	-						uc003uxn.1_Intron					Homo sapiens cDNA FLJ32697 fis, clone TESTI2000372.																														---	---	---	---
MUC17	140453	broad.mit.edu	37	7	100697651	100697651	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100697651delA	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)																	---	---	---	---
FIS1	51024	broad.mit.edu	37	7	100891440	100891440	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100891440delA	uc010lht.2	-						FIS1_uc010lhu.2_Intron					Homo sapiens CGI-135 protein mRNA, complete cds.						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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	100907037	100907037	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100907037delG								FIS1 (11444 upstream) : RABL5 (49612 downstream)																																			---	---	---	---
CUX1	1523	broad.mit.edu	37	7	101633479	101633480	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101633479_101633480delAA	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	101903381	101903383	+	Intron	DEL	GGA	-	-	rs148765196		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101903381_101903383delGGA	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																		---	---	---	---
SPDYE6	729597	broad.mit.edu	37	7	101994098	101994098	+	Intron	DEL	C	-	-	rs79613475		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101994098delC	uc011kkp.1	-						SPDYE6_uc003uzb.2_5'Flank	NM_001146210	NP_001139682			speedy homolog E6												0																		---	---	---	---
FBXL13	222235	broad.mit.edu	37	7	102603768	102603769	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102603768_102603769delAA	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																		---	---	---	---
DPY19L2P2	349152	broad.mit.edu	37	7	102902926	102902926	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102902926delA	uc003vbh.3	-						DPY19L2P2_uc003vbg.3_Intron|DPY19L2P2_uc010lit.2_Intron	NR_003561				RecName: Full=Protein dpy-19 homolog 2-like 2; AltName: Full=Dpy-19-like protein 2 pseudogene 2;												0																		---	---	---	---
PMPCB	9512	broad.mit.edu	37	7	102938681	102938682	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102938681_102938682delTT	uc003vbl.2	+						PMPCB_uc010liu.1_Intron|PMPCB_uc003vbk.1_Intron|PMPCB_uc003vbm.2_Intron|PMPCB_uc010liv.2_Intron|PMPCB_uc010liw.2_Intron|PMPCB_uc011kll.1_Intron|PMPCB_uc011klm.1_5'Flank	NM_004279	NP_004270			mitochondrial processing peptidase beta subunit						proteolysis	mitochondrial matrix	metalloendopeptidase activity|zinc ion binding			ovary(4)	4																		---	---	---	---
SLC26A5	375611	broad.mit.edu	37	7	103000809	103000809	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103000809delT	uc003vbt.1	-						SLC26A5_uc003vbu.1_Intron|SLC26A5_uc003vbv.1_Intron|PSMC2_uc011kln.1_Intron|PSMC2_uc003vbs.2_Intron|PSMC2_uc011klo.1_Intron	NM_206883	NP_996766			prestin isoform b						regulation of cell shape|sensory perception of sound	integral to membrane	secondary active sulfate transmembrane transporter activity			ovary(1)	1																		---	---	---	---
RELN	5649	broad.mit.edu	37	7	103593002	103593003	+	Intron	DEL	TC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103593002_103593003delTC	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	103906342	103906342	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103906342delT								ORC5L (57879 upstream) : LHFPL3 (62762 downstream)																																			---	---	---	---
LHFPL3	375612	broad.mit.edu	37	7	103986785	103986785	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103986785delT	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	104005892	104005892	+	Intron	DEL	T	-	-	rs72201674		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:104005892delT	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	104146467	104146470	+	Intron	DEL	TTTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:104146467_104146470delTTTT	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	104214765	104214765	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:104214765delG	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	104418201	104418203	+	Intron	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:104418201_104418203delTTT	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	104443062	104443062	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:104443062delT	uc003vce.2	+						LHFPL3_uc003vcf.2_Intron|uc003vcg.2_Intron	NM_199000	NP_945351			lipoma HMGIC fusion partner-like 3							integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	105168877	105168878	+	IGR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105168877_105168878insA								PUS7 (6192 upstream) : RINT1 (3654 downstream)																																			---	---	---	---
ATXN7L1	222255	broad.mit.edu	37	7	105359826	105359826	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105359826delA	uc003vde.2	-							NM_020725	NP_065776			ataxin 7-like 1 isoform 1												0																		---	---	---	---
ATXN7L1	222255	broad.mit.edu	37	7	105516074	105516074	+	Intron	DEL	C	-	-	rs140602368		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105516074delC	uc003vde.2	-						ATXN7L1_uc003vdi.2_Intron|CDHR3_uc003vdk.2_5'Flank|uc003vdj.1_5'Flank	NM_020725	NP_065776			ataxin 7-like 1 isoform 1												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	106394527	106394527	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:106394527delT	uc003vds.2	-											Homo sapiens full length insert cDNA clone ZC44D09.																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	106575287	106575287	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:106575287delT								PIK3CG (27702 upstream) : PRKAR2B (109891 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	106620620	106620620	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:106620620delT								PIK3CG (73035 upstream) : PRKAR2B (64558 downstream)																																			---	---	---	---
COG5	10466	broad.mit.edu	37	7	107198154	107198154	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107198154delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	108109517	108109517	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:108109517delA								NRCAM (12691 upstream) : PNPLA8 (2554 downstream)																																			---	---	---	---
PNPLA8	50640	broad.mit.edu	37	7	108157361	108157361	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:108157361delA	uc003vff.1	-						PNPLA8_uc003vfg.1_Intron|PNPLA8_uc003vfh.1_Intron|PNPLA8_uc003vfi.1_Intron|PNPLA8_uc003vfj.1_Intron|PNPLA8_uc003vfk.1_Intron	NM_015723	NP_056538			patatin-like phospholipase domain containing 8						fatty acid metabolic process|lipid catabolic process	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|membrane fraction|perinuclear region of cytoplasm|peroxisomal membrane	ATP binding|calcium-independent phospholipase A2 activity|lysophospholipase activity			breast(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	108266175	108266175	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:108266175delA								DNAJB9 (50883 upstream) : C7orf66 (257865 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	108437044	108437044	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:108437044delT								DNAJB9 (221752 upstream) : C7orf66 (86996 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	108808463	108808464	+	IGR	DEL	TG	-	-	rs67530732		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:108808463_108808464delTG								C7orf66 (283826 upstream) : EIF3IP1 (790820 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	109525291	109525292	+	IGR	INS	-	GATA	GATA	rs138298596	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:109525291_109525292insGATA								None (None upstream) : EIF3IP1 (73992 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	109963622	109963622	+	IGR	DEL	T	-	-	rs142763084		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:109963622delT								EIF3IP1 (363352 upstream) : IMMP2L (339488 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	110044193	110044193	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:110044193delT								EIF3IP1 (443923 upstream) : IMMP2L (258917 downstream)																																			---	---	---	---
IMMP2L	83943	broad.mit.edu	37	7	110633173	110633173	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:110633173delT	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	111789568	111789568	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:111789568delA	uc003vfx.2	-						DOCK4_uc003vfy.2_Intron|DOCK4_uc003vga.1_Intron|DOCK4_uc010ljt.1_Intron	NM_014705	NP_055520			dedicator of cytokinesis 4						cell chemotaxis	cytosol|endomembrane system|membrane|stereocilium	GTP binding|guanyl-nucleotide exchange factor activity|PDZ domain binding|Rac GTPase activator activity|Rac GTPase binding|receptor tyrosine kinase binding|SH3 domain binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)	4		Acute lymphoblastic leukemia(1;0.0441)																---	---	---	---
ZNF277	11179	broad.mit.edu	37	7	111860344	111860344	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:111860344delT	uc003vge.2	+						ZNF277_uc003vgd.2_Intron|ZNF277_uc003vgf.2_Intron|ZNF277_uc003vgc.2_Intron	NM_021994	NP_068834			zinc finger protein (C2H2 type) 277							nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|breast(2)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	112307312	112307313	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:112307312_112307313delAA								C7orf53 (176377 upstream) : TMEM168 (98476 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	115325483	115325483	+	5'Flank	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:115325483delT	uc003vhi.3	-											Homo sapiens, clone IMAGE:5163213, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	115471816	115471817	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:115471816_115471817insT								MDFIC (812553 upstream) : TFEC (103385 downstream)																																			---	---	---	---
TFEC	22797	broad.mit.edu	37	7	115763578	115763578	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:115763578delA	uc011kmw.1	-											SubName: Full=cDNA FLJ55256, highly similar to Homo sapiens transcription factor EC (TFEC), transcript variant 1, mRNA;							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity			large_intestine(1)	1			STAD - Stomach adenocarcinoma(10;0.00878)															---	---	---	---
ST7	7982	broad.mit.edu	37	7	116677673	116677673	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:116677673delT	uc003vin.2	+						ST7_uc011knl.1_Intron|ST7_uc003vio.2_Intron|ST7_uc003viq.2_Intron|ST7_uc011knm.1_Intron|ST7_uc003vir.2_Intron	NM_021908	NP_068708			suppression of tumorigenicity 7 isoform b							integral to membrane	binding			central_nervous_system(1)|skin(1)	2	all_cancers(3;3.88e-07)|all_epithelial(6;3.42e-07)|Lung NSC(10;0.00072)|all_lung(10;0.000847)		STAD - Stomach adenocarcinoma(10;0.000512)	LUSC - Lung squamous cell carcinoma(290;0.133)														---	---	---	---
ST7	7982	broad.mit.edu	37	7	116772445	116772445	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:116772445delA	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)														---	---	---	---
ST7	7982	broad.mit.edu	37	7	116811711	116811711	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:116811711delC	uc003vin.2	+						ST7_uc011knl.1_Intron|ST7_uc003vio.2_Intron|ST7_uc003viq.2_Intron|ST7_uc011knm.1_Intron|ST7_uc003vir.2_Intron|ST7_uc011knn.1_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)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	117640876	117640877	+	IGR	DEL	GA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117640876_117640877delGA								CTTNBP2 (127315 upstream) : NAA38 (183209 downstream)																																			---	---	---	---
ANKRD7	56311	broad.mit.edu	37	7	117867205	117867205	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117867205delT	uc003vji.2	+							NM_019644	NP_062618			ankyrin repeat domain 7						male gonad development						0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	119623420	119623421	+	IGR	INS	-	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:119623420_119623421insC								None (None upstream) : KCND2 (290301 downstream)																																			---	---	---	---
KCND2	3751	broad.mit.edu	37	7	120071894	120071895	+	Intron	DEL	CA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:120071894_120071895delCA	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	120190230	120190230	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:120190230delT	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	120222405	120222405	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:120222405delT	uc003vjj.1	+							NM_012281	NP_036413			potassium voltage-gated channel, Shal-related						regulation of action potential|synaptic transmission	cell surface|dendritic spine	metal ion binding			ovary(2)|central_nervous_system(2)|skin(1)	5	all_neural(327;0.117)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	120396495	120396496	+	IGR	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:120396495_120396496delAC								KCND2 (6108 upstream) : TSPAN12 (30880 downstream)																																			---	---	---	---
TSPAN12	23554	broad.mit.edu	37	7	120441174	120441174	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:120441174delT	uc003vjk.2	-						TSPAN12_uc010lkj.2_Intron	NM_012338	NP_036470			transmembrane 4 superfamily member 12						angiogenesis|cell surface receptor linked signaling pathway|regulation of angiogenesis|retina layer formation	integral to plasma membrane|membrane fraction					0	all_neural(327;0.117)																	---	---	---	---
C7orf58	79974	broad.mit.edu	37	7	120675155	120675155	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:120675155delA	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)																	---	---	---	---
C7orf58	79974	broad.mit.edu	37	7	120712240	120712245	+	Intron	DEL	AAAAAA	-	-	rs11318194		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:120712240_120712245delAAAAAA	uc003vjq.3	+						C7orf58_uc003vjr.1_Intron|C7orf58_uc003vjs.3_Intron|C7orf58_uc003vjt.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	121022812	121022812	+	Intron	DEL	A	-	-	rs77488516		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121022812delA	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)																	---	---	---	---
FAM3C	10447	broad.mit.edu	37	7	121023197	121023198	+	Intron	DEL	AA	-	-	rs35702337		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121023197_121023198delAA	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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	121337749	121337749	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121337749delT								FAM3C (301327 upstream) : PTPRZ1 (175410 downstream)																																			---	---	---	---
CADPS2	93664	broad.mit.edu	37	7	122140466	122140467	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122140466_122140467insA	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	122598995	122598995	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122598995delA								CADPS2 (72441 upstream) : TAS2R16 (35764 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	122986993	122986993	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122986993delA								SLC13A1 (146968 upstream) : IQUB (105245 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	124159814	124159814	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:124159814delA								TMEM229A (486291 upstream) : GPR37 (226302 downstream)																																			---	---	---	---
POT1	25913	broad.mit.edu	37	7	124537069	124537069	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:124537069delA	uc003vlm.2	-						POT1_uc011koe.1_Intron|POT1_uc003vlk.2_Intron|POT1_uc003vll.2_Intron|POT1_uc003vlo.2_Intron|POT1_uc003vln.2_Intron	NM_015450	NP_056265			protection of telomeres 1 isoform 1						DNA duplex unwinding|negative regulation of telomere maintenance via telomerase|positive regulation of DNA strand elongation|positive regulation of helicase activity|positive regulation of telomerase activity|positive regulation of telomere maintenance via telomerase|telomere capping|telomere formation via telomerase|telomere maintenance via telomerase	nuclear telomere cap complex|nucleoplasm	DEAD/H-box RNA helicase binding|single-stranded telomeric DNA binding|telomerase inhibitor activity			central_nervous_system(1)	1																		---	---	---	---
POT1	25913	broad.mit.edu	37	7	124560320	124560321	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:124560320_124560321insA	uc003vlm.2	-						POT1_uc011koe.1_Intron|POT1_uc003vlk.2_Intron|POT1_uc003vll.2_Intron|POT1_uc003vlo.2_Intron|POT1_uc003vln.2_Intron	NM_015450	NP_056265			protection of telomeres 1 isoform 1						DNA duplex unwinding|negative regulation of telomere maintenance via telomerase|positive regulation of DNA strand elongation|positive regulation of helicase activity|positive regulation of telomerase activity|positive regulation of telomere maintenance via telomerase|telomere capping|telomere formation via telomerase|telomere maintenance via telomerase	nuclear telomere cap complex|nucleoplasm	DEAD/H-box RNA helicase binding|single-stranded telomeric DNA binding|telomerase inhibitor activity			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	125063822	125063823	+	IGR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:125063822_125063823insA								POT1 (493785 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	125560488	125560488	+	IGR	DEL	C	-	-	rs113404656		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:125560488delC								POT1 (990451 upstream) : GRM8 (518164 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	125763143	125763144	+	IGR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:125763143_125763144insA								None (None upstream) : GRM8 (315508 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	126035333	126035334	+	IGR	DEL	AC	-	-	rs35832366		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:126035333_126035334delAC								None (None upstream) : GRM8 (43318 downstream)																																			---	---	---	---
GRM8	2918	broad.mit.edu	37	7	126164749	126164749	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:126164749delT	uc003vlr.2	-						GRM8_uc003vls.2_Intron|GRM8_uc011kof.1_Intron|GRM8_uc003vlt.2_Intron|GRM8_uc010lkz.1_Intron	NM_000845	NP_000836			glutamate receptor, metabotropic 8 isoform a						negative regulation of cAMP biosynthetic process|sensory perception of smell|visual perception	integral to plasma membrane				lung(15)|ovary(5)|pancreas(1)|breast(1)|skin(1)	23		Prostate(267;0.186)			L-Glutamic Acid(DB00142)										HNSCC(24;0.065)			---	---	---	---
GRM8	2918	broad.mit.edu	37	7	126551945	126551946	+	Intron	DEL	TC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:126551945_126551946delTC	uc003vlr.2	-						GRM8_uc003vls.2_Intron|GRM8_uc011kof.1_Intron|GRM8_uc003vlt.2_Intron|GRM8_uc010lkz.1_Intron|GRM8_uc003vlu.1_Intron	NM_000845	NP_000836			glutamate receptor, metabotropic 8 isoform a						negative regulation of cAMP biosynthetic process|sensory perception of smell|visual perception	integral to plasma membrane				lung(15)|ovary(5)|pancreas(1)|breast(1)|skin(1)	23		Prostate(267;0.186)			L-Glutamic Acid(DB00142)										HNSCC(24;0.065)			---	---	---	---
Unknown	0	broad.mit.edu	37	7	126924882	126924882	+	IGR	DEL	T	-	-	rs72281463		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:126924882delT								GRM8 (31735 upstream) : ZNF800 (85472 downstream)																																			---	---	---	---
SND1	27044	broad.mit.edu	37	7	127666070	127666070	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127666070delA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	128154009	128154009	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128154009delT								METTL2B (11032 upstream) : FLJ45340 (127286 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	128225657	128225657	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128225657delT								METTL2B (82680 upstream) : FLJ45340 (55638 downstream)																																			---	---	---	---
KCP	375616	broad.mit.edu	37	7	128527409	128527410	+	Intron	DEL	CA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128527409_128527410delCA	uc011kor.1	-							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	128900636	128900638	+	Intron	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128900636_128900638delTTT	uc011kov.1	+						AHCYL2_uc003vot.2_Intron	NM_015328	NP_056143			S-adenosylhomocysteine hydrolase-like 2 isoform						one-carbon metabolic process		adenosylhomocysteinase activity			ovary(2)	2																		---	---	---	---
NRF1	4899	broad.mit.edu	37	7	129289538	129289539	+	Intron	DEL	AG	-	-	rs35298794		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129289538_129289539delAG	uc003voz.2	+						NRF1_uc003vpa.2_Intron|NRF1_uc011kpa.1_Intron|NRF1_uc003vpb.2_Intron	NM_005011	NP_005002			nuclear respiratory factor 1						generation of precursor metabolites and energy|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1																		---	---	---	---
KLHDC10	23008	broad.mit.edu	37	7	129761051	129761051	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129761051delC	uc003vpj.1	+						KLHDC10_uc003vpk.1_Intron|KLHDC10_uc010lmb.1_Intron	NM_014997	NP_055812			kelch domain containing 10												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	129862002	129862003	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129862002_129862003delTT								C7orf45 (5319 upstream) : CPA2 (44700 downstream)																																			---	---	---	---
FLJ43663	378805	broad.mit.edu	37	7	130651000	130651001	+	Intron	INS	-	A	A	rs78839119		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130651000_130651001insA	uc011kpk.1	-						FLJ43663_uc003vqo.1_Intron|FLJ43663_uc003vqp.2_Intron|FLJ43663_uc003vqq.2_Intron	NR_024153				Homo sapiens cDNA FLJ43663 fis, clone SYNOV4005989.												0																		---	---	---	---
FLJ43663	378805	broad.mit.edu	37	7	130658862	130658862	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130658862delG	uc011kpk.1	-						FLJ43663_uc003vqo.1_Intron|FLJ43663_uc003vqp.2_Intron|FLJ43663_uc003vqq.2_Intron	NR_024153				Homo sapiens cDNA FLJ43663 fis, clone SYNOV4005989.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	131286271	131286273	+	IGR	DEL	AAA	-	-	rs72416933		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131286271_131286273delAAA								PODXL (44895 upstream) : PLXNA4 (521819 downstream)																																			---	---	---	---
PLXNA4	91584	broad.mit.edu	37	7	132296015	132296015	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:132296015delC	uc003vrb.2	-							NM_181775	NP_861440			plexin A4 isoform 2							integral to membrane|intracellular|plasma membrane				ovary(1)	1																		---	---	---	---
CHCHD3	54927	broad.mit.edu	37	7	132657212	132657212	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:132657212delA	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	133006028	133006028	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:133006028delT	uc003vrk.2	+						EXOC4_uc011kpo.1_Intron|EXOC4_uc003vri.2_Intron|EXOC4_uc003vrj.2_Intron	NM_021807	NP_068579			SEC8 protein isoform a						vesicle docking involved in exocytosis	exocyst	protein N-terminus binding			ovary(4)|large_intestine(3)|upper_aerodigestive_tract(1)|skin(1)	9		Esophageal squamous(399;0.129)																---	---	---	---
Unknown	0	broad.mit.edu	37	7	134434863	134434870	+	IGR	DEL	AAACAAAC	-	-	rs111400308		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134434863_134434870delAAACAAAC								BPGM (70298 upstream) : CALD1 (29301 downstream)																																	OREG0018338	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
NUP205	23165	broad.mit.edu	37	7	135294228	135294228	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135294228delA	uc003vsw.2	+							NM_015135	NP_055950			nucleoporin 205kDa						carbohydrate metabolic process|glucose transport|mRNA transport|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear pore	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	135473730	135473735	+	IGR	DEL	TGTGTA	-	-	rs66491975		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135473730_135473735delTGTGTA								FAM180A (40136 upstream) : LUZP6 (137770 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	136526854	136526854	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:136526854delA								LUZP6 (864650 upstream) : CHRM2 (26545 downstream)																																			---	---	---	---
PTN	5764	broad.mit.edu	37	7	136938377	136938377	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:136938377delT	uc003vtq.2	-	3	486	c.123delA	c.(121-123)AAAfs	p.K41fs	PTN_uc010lmx.2_Frame_Shift_Del_p.K41fs|PTN_uc003vtr.1_Frame_Shift_Del_p.K41fs	NM_002825	NP_002816	P21246	PTN_HUMAN	pleiotrophin	41					nervous system development|positive regulation of cell division|positive regulation of cell proliferation|transmembrane receptor protein tyrosine phosphatase signaling pathway	endoplasmic reticulum|extracellular space	growth factor activity|heparin binding|protein phosphatase inhibitor activity			upper_aerodigestive_tract(1)|pancreas(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	137064156	137064156	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:137064156delT								PTN (35610 upstream) : DGKI (10230 downstream)																																			---	---	---	---
DGKI	9162	broad.mit.edu	37	7	137154481	137154482	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:137154481_137154482insT	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																		---	---	---	---
DGKI	9162	broad.mit.edu	37	7	137233773	137233773	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:137233773delA	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																		---	---	---	---
DGKI	9162	broad.mit.edu	37	7	137389222	137389222	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:137389222delA	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	137704611	137704612	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:137704611_137704612insT	uc011kqb.1	+						AKR1D1_uc011kqc.1_Intron|AKR1D1_uc011kqd.1_Intron	NM_005989	NP_005980			aldo-keto reductase family 1, member D1						androgen metabolic process|bile acid biosynthetic process|bile acid catabolic process|C21-steroid hormone metabolic process|cholesterol catabolic process|digestion	cytosol	aldo-keto reductase (NADP) activity|delta4-3-oxosteroid 5beta-reductase activity|steroid binding			skin(1)	1																		---	---	---	---
TRIM24	8805	broad.mit.edu	37	7	138154077	138154077	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138154077delT	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																		---	---	---	---
TTC26	79989	broad.mit.edu	37	7	138862939	138862939	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138862939delT	uc003vus.2	+						TTC26_uc011kqn.1_Intron|TTC26_uc011kqo.1_Intron|TTC26_uc011kqp.1_Intron|TTC26_uc003vut.2_Intron|TTC26_uc011kqq.1_Intron	NM_024926	NP_079202			tetratricopeptide repeat domain 26 isoform 1								binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	139003136	139003136	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139003136delT								UBN2 (10155 upstream) : LUC7L2 (21969 downstream)																																			---	---	---	---
CLEC2L	154790	broad.mit.edu	37	7	139229341	139229342	+	3'UTR	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139229341_139229342delAC	uc010lnd.2	+	5						NM_001080511	NP_001073980			C-type lectin domain family 2, member L							integral to membrane	sugar binding				0	Melanoma(164;0.233)																	---	---	---	---
HIPK2	28996	broad.mit.edu	37	7	139280211	139280211	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139280211delG	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)																	---	---	---	---
HIPK2	28996	broad.mit.edu	37	7	139325398	139325398	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139325398delT	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)																	---	---	---	---
TBXAS1	6916	broad.mit.edu	37	7	139507968	139507968	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139507968delA	uc003vvh.2	+						TBXAS1_uc010lne.2_Intron	NM_001130966	NP_001124438			thromboxane A synthase 1, platelet isoform						hormone biosynthetic process|prostaglandin biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum lumen|endoplasmic reticulum membrane|integral to membrane	electron carrier activity|heme binding|monooxygenase activity|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen|thromboxane-A synthase activity			ovary(2)|breast(1)	3	Melanoma(164;0.0142)																	---	---	---	---
TBXAS1	6916	broad.mit.edu	37	7	139622272	139622272	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139622272delC	uc011kqv.1	+						TBXAS1_uc003vvh.2_Intron|TBXAS1_uc010lne.2_Intron|TBXAS1_uc011kqu.1_Intron|TBXAS1_uc003vvi.2_Intron|TBXAS1_uc003vvj.2_Intron|TBXAS1_uc011kqw.1_Intron	NM_001130966	NP_001124438			thromboxane A synthase 1, platelet isoform						hormone biosynthetic process|prostaglandin biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum lumen|endoplasmic reticulum membrane|integral to membrane	electron carrier activity|heme binding|monooxygenase activity|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen|thromboxane-A synthase activity			ovary(2)|breast(1)	3	Melanoma(164;0.0142)																	---	---	---	---
PARP12	64761	broad.mit.edu	37	7	139738671	139738671	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139738671delA	uc003vvl.1	-						PARP12_uc003vvk.1_Intron|PARP12_uc010lnf.1_Intron	NM_022750	NP_073587			poly ADP-ribose polymerase 12							nucleus	NAD+ ADP-ribosyltransferase activity|nucleic acid binding|zinc ion binding			ovary(3)	3	Melanoma(164;0.0142)																	---	---	---	---
JHDM1D	80853	broad.mit.edu	37	7	139854549	139854549	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139854549delT	uc003vvm.2	-							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)																	---	---	---	---
SLC37A3	84255	broad.mit.edu	37	7	140064052	140064052	+	Intron	DEL	G	-	-	rs66780610		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140064052delG	uc003vvo.2	-						SLC37A3_uc003vvp.2_Intron|SLC37A3_uc010lnh.2_Intron|SLC37A3_uc011kqz.1_Intron|SLC37A3_uc011kra.1_Intron|SLC37A3_uc011krb.1_Intron	NM_207113	NP_996996			solute carrier family 37 (glycerol-3-phosphate						carbohydrate transport|transmembrane transport	integral to membrane				ovary(3)	3	Melanoma(164;0.0142)																	---	---	---	---
RAB19	401409	broad.mit.edu	37	7	140122189	140122189	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140122189delA	uc010lni.2	+						RAB19_uc011krc.1_Intron	NM_001008749	NP_001008749			RAB19, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding				0	Melanoma(164;0.0142)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	141525607	141525607	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141525607delT								TAS2R5 (34441 upstream) : PRSS37 (10479 downstream)																																			---	---	---	---
MGAM	8972	broad.mit.edu	37	7	141703701	141703701	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141703701delA	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	142112109	142112110	+	Intron	INS	-	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142112109_142112110insC	uc011kro.1	+						uc011krp.1_Intron|uc011krr.1_Intron					SubName: Full=V_segment translation product; Flags: Fragment;																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	142854084	142854085	+	IGR	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142854084_142854085delTG								PIP (17250 upstream) : TAS2R39 (26427 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	143006533	143006537	+	IGR	DEL	AAAAC	-	-	rs80166998		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143006533_143006537delAAAAC								CASP2 (1749 upstream) : CLCN1 (6682 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	143287732	143287732	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143287732delT								LOC441294 (16489 upstream) : FAM115C (30313 downstream)																																			---	---	---	---
FAM115C	285966	broad.mit.edu	37	7	143343624	143343624	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143343624delA	uc003wdf.2	+						FAM115C_uc003wdg.2_Intron|FAM115C_uc011ktk.1_Intron|FAM115C_uc003wdh.2_Intron|FAM115C_uc011ktm.1_Intron|uc011ktn.1_Intron|uc011kto.1_Intron|uc011ktp.1_Intron|LOC154761_uc011ktq.1_Intron|LOC154761_uc011ktr.1_Intron|LOC154761_uc011kts.1_Intron	NM_001130025	NP_001123497			hypothetical protein LOC285966 isoform A												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	143430430	143430432	+	Intron	DEL	AAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143430430_143430432delAAA	uc011ktn.1	+						uc011kto.1_Intron|uc011ktp.1_Intron|LOC154761_uc011ktq.1_Intron|LOC154761_uc011ktr.1_Intron|LOC154761_uc011kts.1_Intron|LOC154761_uc003wdj.1_Intron	NM_001130026	NP_001123498			hypothetical protein LOC285966 isoform B																														---	---	---	---
FAM115A	9747	broad.mit.edu	37	7	143568369	143568369	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143568369delA	uc003wdo.1	-						FAM115A_uc011ktu.1_Intron|FAM115A_uc003wdp.1_Intron	NM_014719	NP_055534			hypothetical protein LOC9747												0	Melanoma(164;0.0903)																	---	---	---	---
OR2A9P	441295	broad.mit.edu	37	7	144028708	144028708	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:144028708delT	uc003wec.1	-											SubName: Full=Seven transmembrane helix receptor;												0																		---	---	---	---
TPK1	27010	broad.mit.edu	37	7	144518573	144518574	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:144518573_144518574delTT	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	144519913	144519922	+	Intron	DEL	GTGTGTGTGT	-	-	rs138267598		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:144519913_144519922delGTGTGTGTGT	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	144532720	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:144532719_144532720delAA	uc003weq.2	-						TPK1_uc003wer.2_Intron|TPK1_uc003wes.2_Intron	NM_022445	NP_071890			thiamin pyrophosphokinase 1 isoform a						thiamine diphosphate biosynthetic process	cytosol	ATP binding|kinase activity|thiamine diphosphokinase activity			ovary(2)	2					Thiamine(DB00152)													---	---	---	---
Unknown	0	broad.mit.edu	37	7	144648066	144648066	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:144648066delT								TPK1 (114920 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	145644467	145644467	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:145644467delA								None (None upstream) : CNTNAP2 (168986 downstream)																																			---	---	---	---
CNTNAP2	26047	broad.mit.edu	37	7	146282840	146282843	+	Intron	DEL	GAAG	-	-	rs66482340	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:146282840_146282843delGAAG	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	146425704	146425705	+	Intron	DEL	AA	-	-	rs71525967		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:146425704_146425705delAA	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	146924421	146924421	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:146924421delA	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	147107830	147107833	+	Intron	DEL	CATA	-	-	rs66740966		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:147107830_147107833delCATA	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	147382085	147382085	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:147382085delT	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	147847642	147847642	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:147847642delA	uc003weu.1	+							NM_014141	NP_054860			cell recognition molecule Caspr2 precursor						behavior|cell adhesion|clustering of voltage-gated potassium channels|limbic system development|neuron recognition|signal transduction|striatum development|superior temporal gyrus development|thalamus development|transmission of nerve impulse	axolemma|cell body fiber|dendrite|juxtaparanode region of axon|voltage-gated potassium channel complex	receptor binding			ovary(9)|central_nervous_system(1)|pancreas(1)	11	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)												HNSCC(39;0.1)			---	---	---	---
CUL1	8454	broad.mit.edu	37	7	148468177	148468177	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148468177delT	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	148626360	148626360	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148626360delC								EZH2 (44946 upstream) : MIR1975 (12220 downstream)																																			---	---	---	---
PDIA4	9601	broad.mit.edu	37	7	148713619	148713622	+	Intron	DEL	TTTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148713619_148713622delTTTT	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)															---	---	---	---
ZNF398	57541	broad.mit.edu	37	7	148841680	148841680	+	5'Flank	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148841680delT	uc003wfl.2	+						ZNF398_uc011kul.1_Intron	NM_170686	NP_733787			zinc finger 398 isoform a						positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00143)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	149820702	149820703	+	IGR	DEL	AA	-	-	rs72445326		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149820702_149820703delAA								ATP6V0E2 (242916 upstream) : ACTR3C (123599 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	150204087	150204087	+	IGR	DEL	A	-	-	rs79782467		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150204087delA								GIMAP8 (27605 upstream) : GIMAP7 (7858 downstream)																																			---	---	---	---
ABP1	26	broad.mit.edu	37	7	150532172	150532172	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150532172delA	uc003why.1	+							NM_001091	NP_001082			amiloride binding protein 1 precursor						amine metabolic process	extracellular space|peroxisome	copper ion binding|diamine oxidase activity|heparin binding|histamine oxidase activity|methylputrescine oxidase activity|primary amine oxidase activity|propane-1,3-diamine oxidase activity|quinone binding			ovary(2)|breast(2)|skin(2)	6	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Amiloride(DB00594)|Spermine(DB00127)													---	---	---	---
PRKAG2	51422	broad.mit.edu	37	7	151448185	151448187	+	Intron	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151448185_151448187delTTT	uc003wkk.2	-						PRKAG2_uc003wkj.2_Intron|PRKAG2_uc010lqe.1_Intron|PRKAG2_uc003wkm.1_Intron	NM_016203	NP_057287			AMP-activated protein kinase gamma2 subunit						ATP biosynthetic process|carnitine shuttle|cell cycle arrest|fatty acid biosynthetic process|glycogen metabolic process|insulin receptor signaling pathway|intracellular protein kinase cascade|positive regulation of peptidyl-threonine phosphorylation|positive regulation of protein kinase activity|regulation of fatty acid biosynthetic process|regulation of fatty acid oxidation|regulation of glucose import|regulation of glycolysis|sterol biosynthetic process	AMP-activated protein kinase complex|cytosol|nucleoplasm	ADP binding|ATP binding|cAMP-dependent protein kinase inhibitor activity|cAMP-dependent protein kinase regulator activity|phosphorylase kinase regulator activity|protein kinase activator activity|protein kinase binding			breast(1)|kidney(1)	2	all_neural(206;0.187)	all_hematologic(28;0.0605)	OV - Ovarian serous cystadenocarcinoma(82;0.00252)	UCEC - Uterine corpus endometrioid carcinoma (81;0.185)														---	---	---	---
MLL3	58508	broad.mit.edu	37	7	152026662	152026662	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152026662delA	uc003wla.2	-							NM_170606	NP_733751			myeloid/lymphoid or mixed-lineage leukemia 3						intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)				N		medulloblastoma								---	---	---	---
MLL3	58508	broad.mit.edu	37	7	152085813	152085814	+	Intron	DEL	TA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152085813_152085814delTA	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	152085836	152085836	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152085836delT	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	153291592	153291592	+	IGR	DEL	A	-	-	rs114070122	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:153291592delA								ACTR3B (739129 upstream) : DPP6 (292827 downstream)																																			---	---	---	---
DPP6	1804	broad.mit.edu	37	7	154447138	154447138	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154447138delT	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)															---	---	---	---
RBM33	155435	broad.mit.edu	37	7	155534924	155534926	+	Intron	DEL	TTT	-	-	rs72456061		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155534924_155534926delTTT	uc010lqk.1	+						RBM33_uc011kvv.1_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	155912253	155912253	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155912253delA								SHH (307286 upstream) : C7orf4 (420932 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	155971662	155971662	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155971662delC								SHH (366695 upstream) : C7orf4 (361523 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	155973453	155973453	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155973453delA								SHH (368486 upstream) : C7orf4 (359732 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	156247559	156247559	+	IGR	DEL	A	-	-	rs11315836		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:156247559delA								SHH (642592 upstream) : C7orf4 (85626 downstream)																																			---	---	---	---
NOM1	64434	broad.mit.edu	37	7	156754449	156754449	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:156754449delA	uc003wmy.2	+						NOM1_uc010lqp.1_5'Flank	NM_138400	NP_612409			nucleolar protein with MIF4G domain 1						RNA metabolic process	nucleolus	protein binding				0	Ovarian(565;0.218)	all_hematologic(28;0.0749)	OV - Ovarian serous cystadenocarcinoma(82;0.00301)	UCEC - Uterine corpus endometrioid carcinoma (81;0.169)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	157279059	157279060	+	IGR	DEL	GT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157279059_157279060delGT								DNAJB6 (68927 upstream) : PTPRN2 (52691 downstream)																																			---	---	---	---
PTPRN2	5799	broad.mit.edu	37	7	157360228	157360228	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157360228delT	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	157464651	157464651	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157464651delG	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	157515521	157515521	+	Intron	DEL	T	-	-	rs13231216	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157515521delT	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	159024963	159024963	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:159024963delT								VIPR2 (87314 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	541056	541056	+	IGR	DEL	A	-	-	rs34599962		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:541056delA								C8orf42 (45725 upstream) : ERICH1 (23693 downstream)																																			---	---	---	---
ERICH1	157697	broad.mit.edu	37	8	645108	645109	+	Intron	INS	-	A	A	rs143069283	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:645108_645109insA	uc003wph.2	-						ERICH1_uc011kwh.1_Intron|ERICH1_uc003wpe.1_Intron	NM_207332	NP_997215			glutamate-rich 1											large_intestine(2)	2		Colorectal(14;0.158)|Ovarian(12;0.17)|Myeloproliferative disorder(644;0.185)|Hepatocellular(245;0.236)		Epithelial(5;3.29e-14)|BRCA - Breast invasive adenocarcinoma(11;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(5;3.65e-06)|READ - Rectum adenocarcinoma(1;0.0325)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	696683	696683	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:696683delT	uc003wpj.1	+											Homo sapiens cDNA clone IMAGE:4824304.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	1067127	1067159	+	Intron	DEL	TTGGAAAACCCAACACCGTCTCTTTGACCTGTC	-	-	rs36231284		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1067127_1067159delTTGGAAAACCCAACACCGTCTCTTTGACCTGTC	uc003wpj.1	+											Homo sapiens cDNA clone IMAGE:4824304.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	1313992	1313992	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1313992delG								ERICH1 (632766 upstream) : DLGAP2 (135577 downstream)																																			---	---	---	---
ARHGEF10	9639	broad.mit.edu	37	8	1859456	1859456	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1859456delT	uc003wpr.2	+						ARHGEF10_uc003wpq.1_Intron|ARHGEF10_uc003wps.2_Intron|ARHGEF10_uc003wpv.2_Intron|ARHGEF10_uc010lre.2_Intron	NM_014629	NP_055444			Rho guanine nucleotide exchange factor 10						centrosome duplication|myelination in peripheral nervous system|positive regulation of GTP catabolic process|positive regulation of stress fiber assembly|regulation of Rho protein signal transduction|spindle assembly involved in mitosis	centrosome|cytosol|soluble fraction	kinesin binding|Rho guanyl-nucleotide exchange factor activity			large_intestine(1)	1		Colorectal(14;3.46e-05)|Renal(68;0.000518)|Ovarian(12;0.00409)|Myeloproliferative disorder(644;0.0255)|Hepatocellular(245;0.0834)		COAD - Colon adenocarcinoma(149;1.62e-05)|BRCA - Breast invasive adenocarcinoma(11;1.68e-05)|KIRC - Kidney renal clear cell carcinoma(542;0.00361)|READ - Rectum adenocarcinoma(644;0.0718)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	1973286	1973286	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1973286delG								KBTBD11 (18178 upstream) : MYOM2 (19872 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	2195494	2195495	+	IGR	INS	-	G	G	rs111274980		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2195494_2195495insG								MYOM2 (102115 upstream) : CSMD1 (597381 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	2296360	2296361	+	IGR	INS	-	GA	GA			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2296360_2296361insGA								MYOM2 (202981 upstream) : CSMD1 (496515 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	2499811	2499815	+	IGR	DEL	TTATT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2499811_2499815delTTATT								MYOM2 (406432 upstream) : CSMD1 (293061 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	2730788	2730788	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2730788delA								MYOM2 (637409 upstream) : CSMD1 (62088 downstream)																																			---	---	---	---
CSMD1	64478	broad.mit.edu	37	8	2821034	2821034	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2821034delA	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	2849956	2849956	+	Intron	DEL	T	-	-	rs79659187		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2849956delT	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	3054764	3054764	+	Intron	DEL	T	-	-	rs34895955		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3054764delT	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	3071688	3071689	+	Intron	DEL	GA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3071688_3071689delGA	uc011kwk.1	-						CSMD1_uc011kwj.1_Intron|CSMD1_uc003wqe.2_Intron	NM_033225	NP_150094			CUB and Sushi multiple domains 1 precursor							integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)														---	---	---	---
CSMD1	64478	broad.mit.edu	37	8	3246419	3246444	+	Intron	DEL	ACACACACACACACACACACACACAC	-	-	rs6150441		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3246419_3246444delACACACACACACACACACACACACAC	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	4154469	4154470	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4154469_4154470insA	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	4215073	4215073	+	Intron	DEL	A	-	-	rs35981216		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4215073delA	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	4218956	4218956	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4218956delA	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	4923117	4923118	+	IGR	INS	-	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4923117_4923118insC								CSMD1 (70789 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	6004053	6004054	+	IGR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6004053_6004054insA								None (None upstream) : MCPH1 (260067 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	6083770	6083770	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6083770delT								None (None upstream) : MCPH1 (180351 downstream)																																			---	---	---	---
XKR5	389610	broad.mit.edu	37	8	6673270	6673271	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6673270_6673271delAA	uc003wqp.2	-						XKR5_uc003wqq.2_Intron|XKR5_uc003wqr.1_Intron	NM_207411	NP_997294			XK-related protein 5a							integral to membrane					0			STAD - Stomach adenocarcinoma(24;0.0984)	READ - Rectum adenocarcinoma(644;0.137)|COAD - Colon adenocarcinoma(149;0.166)												OREG0018511	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
DEFB1	1672	broad.mit.edu	37	8	6736663	6736664	+	5'Flank	DEL	AG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6736663_6736664delAG	uc003wqs.2	-							NM_005218	NP_005209			defensin, beta 1 preproprotein						chemotaxis|defense response to bacterium|G-protein coupled receptor protein signaling pathway|innate immune response	extracellular region					0			STAD - Stomach adenocarcinoma(24;0.0984)	COAD - Colon adenocarcinoma(149;0.0162)|READ - Rectum adenocarcinoma(644;0.128)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	7347247	7347247	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:7347247delT								DEFB105A (175 upstream) : DEFB107A (6121 downstream)																																			---	---	---	---
DEFB104A	140596	broad.mit.edu	37	8	7696225	7696226	+	Intron	INS	-	AC	AC	rs79367841		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:7696225_7696226insAC	uc003wrv.2	+							NM_080389	NP_525128			defensin, beta 104A precursor						defense response to bacterium	extracellular region					0				COAD - Colon adenocarcinoma(149;0.0162)|READ - Rectum adenocarcinoma(644;0.236)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	8125596	8125605	+	IGR	DEL	GTGTGTGTGT	-	-	rs72127068		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8125596_8125605delGTGTGTGTGT								FLJ10661 (23210 upstream) : SGK223 (49654 downstream)																																			---	---	---	---
SGK223	157285	broad.mit.edu	37	8	8205101	8205102	+	Intron	DEL	CT	-	-	rs35950762		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8205101_8205102delCT	uc003wsh.3	-							NM_001080826	NP_001074295			pragmin								ATP binding|non-membrane spanning protein tyrosine kinase activity				0																		---	---	---	---
SGK223	157285	broad.mit.edu	37	8	8232303	8232303	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8232303delA	uc003wsh.3	-							NM_001080826	NP_001074295			pragmin								ATP binding|non-membrane spanning protein tyrosine kinase activity				0																		---	---	---	---
MFHAS1	9258	broad.mit.edu	37	8	8689965	8689966	+	Intron	DEL	AG	-	-	rs71219092		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8689965_8689966delAG	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	8837883	8837888	+	IGR	DEL	GTGTGC	-	-	rs138511028	by1000genomes;by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8837883_8837888delGTGTGC								MFHAS1 (86752 upstream) : ERI1 (22426 downstream)																																			---	---	---	---
ERI1	90459	broad.mit.edu	37	8	8874059	8874059	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8874059delA	uc011kwu.1	+						ERI1_uc003wsk.2_Intron	NM_153332	NP_699163			three prime histone mRNA exonuclease 1						gene silencing by RNA|rRNA 3'-end processing	cytoplasm|histone pre-mRNA 3'end processing complex|nucleolus	3'-5' exonuclease activity|histone pre-mRNA stem-loop binding|metal ion binding|ribosome binding|rRNA binding				0					Adenosine monophosphate(DB00131)													---	---	---	---
Unknown	0	broad.mit.edu	37	8	9043355	9043356	+	IGR	DEL	TT	-	-	rs10088196	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9043355_9043356delTT								PPP1R3B (34271 upstream) : TNKS (370089 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	9058224	9058224	+	Intron	DEL	T	-	-	rs77062444		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9058224delT	uc003wsp.1	+											Homo sapiens cDNA clone IMAGE:4096591, partial cds.																														---	---	---	---
TNKS	8658	broad.mit.edu	37	8	9539053	9539053	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9539053delT	uc003wss.2	+						TNKS_uc011kwv.1_Intron|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	9646102	9646105	+	IGR	DEL	TTTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9646102_9646105delTTTT								TNKS (6247 upstream) : LOC157627 (111469 downstream)																																			---	---	---	---
LOC157627	157627	broad.mit.edu	37	8	9762919	9762919	+	5'Flank	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9762919delG	uc003wsu.2	-						uc003wsw.1_5'Flank|MIR124-1_hsa-mir-124-1|MI0000443_5'Flank	NR_024281				Homo sapiens clone 23687 mRNA sequence.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	9815758	9815759	+	IGR	INS	-	TCCTGT	TCCTGT	rs145278049	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9815758_9815759insTCCTGT								MIR124-1 (54776 upstream) : MSRA (96071 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	9820776	9820779	+	IGR	DEL	TGTG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9820776_9820779delTGTG								MIR124-1 (59794 upstream) : MSRA (91051 downstream)																																			---	---	---	---
MSRA	4482	broad.mit.edu	37	8	9969543	9969544	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9969543_9969544delTT	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	8	10414012	10414012	+	IGR	DEL	A	-	-	rs80033715		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10414012delA								PRSS55 (11305 upstream) : RP1L1 (49850 downstream)																																			---	---	---	---
RP1L1	94137	broad.mit.edu	37	8	10470757	10470757	+	Frame_Shift_Del	DEL	G	-	-	rs74594406	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10470757delG	uc003wtc.2	-	4	1080	c.851delC	c.(850-852)CCGfs	p.P284fs		NM_178857	NP_849188	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	284					intracellular signal transduction					ovary(4)|breast(3)|central_nervous_system(1)	8				COAD - Colon adenocarcinoma(149;0.0811)														---	---	---	---
C8orf12	83656	broad.mit.edu	37	8	11249521	11249521	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11249521delT	uc003wtu.2	+						C8orf12_uc003wtv.2_5'Flank	NR_026814				Homo sapiens mRNA for hypothetical protein (C8orf12 gene).												0																		---	---	---	---
BLK	640	broad.mit.edu	37	8	11391112	11391114	+	Intron	DEL	AGA	-	-	rs67934857		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11391112_11391114delAGA	uc003wty.2	+						BLK_uc003wtz.2_Intron	NM_001715	NP_001706			B lymphoid tyrosine kinase						intracellular protein kinase cascade|positive regulation of insulin secretion		ATP binding|non-membrane spanning protein tyrosine kinase activity			large_intestine(1)|stomach(1)|ovary(1)	3			STAD - Stomach adenocarcinoma(15;0.00391)	COAD - Colon adenocarcinoma(149;0.207)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	11469229	11469230	+	IGR	INS	-	T	T	rs144587072	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11469229_11469230insT								BLK (47122 upstream) : GATA4 (65238 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	11735784	11735784	+	IGR	DEL	G	-	-	rs144830361		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11735784delG								CTSB (10138 upstream) : DEFB136 (95664 downstream)																																			---	---	---	---
FAM66D	100132923	broad.mit.edu	37	8	12415248	12415250	+	Intron	DEL	AAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12415248_12415250delAAA	uc011kxp.1	+						uc003wvm.1_Intron|uc003wvw.1_Intron|uc003wvx.1_Intron|uc003wvy.3_Intron					Homo sapiens cDNA FLJ37098 fis, clone BRACE2019004.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	12444115	12444116	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12444115_12444116insA	uc003wvy.3	-											Homo sapiens cDNA FLJ42906 fis, clone BRHIP3016213.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	12704055	12704055	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12704055delG								LOC340357 (35145 upstream) : C8orf79 (99096 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	12796915	12796915	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12796915delT								LOC340357 (128005 upstream) : C8orf79 (6236 downstream)																																			---	---	---	---
C8orf79	57604	broad.mit.edu	37	8	12842497	12842498	+	Intron	DEL	CT	-	-	rs71207110		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12842497_12842498delCT	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	12943086	12943087	+	3'UTR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12943086_12943087delTT	uc003wwm.2	-	18					DLC1_uc003wwk.1_3'UTR|DLC1_uc003wwl.1_3'UTR|DLC1_uc011kxx.1_3'UTR	NM_182643	NP_872584			deleted in liver cancer 1 isoform 1						actin cytoskeleton organization|activation of caspase activity|focal adhesion assembly|forebrain development|heart morphogenesis|hindbrain morphogenesis|induction of apoptosis|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of Rho protein signal transduction|negative regulation of stress fiber assembly|neural tube closure|positive regulation of protein dephosphorylation|regulation of cell shape|small GTPase mediated signal transduction	caveola|cytosol|focal adhesion|nucleus	Rho GTPase activator activity|SH2 domain binding			ovary(3)|pancreas(2)|lung(1)|kidney(1)	7																		---	---	---	---
SGCZ	137868	broad.mit.edu	37	8	14414416	14414416	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:14414416delT	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)														---	---	---	---
TUSC3	7991	broad.mit.edu	37	8	15535553	15535553	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:15535553delA	uc003wwt.2	+						TUSC3_uc003wwr.2_Intron|TUSC3_uc003wws.2_Intron|TUSC3_uc003wwu.2_Intron|TUSC3_uc003wwv.2_Intron|TUSC3_uc003www.2_Intron|TUSC3_uc003wwx.2_Intron|TUSC3_uc003wwy.2_Intron	NM_006765	NP_006756			tumor suppressor candidate 3 isoform a						cell redox homeostasis|post-translational protein modification|protein N-linked glycosylation via asparagine	integral to membrane|oligosaccharyltransferase complex				ovary(2)|central_nervous_system(1)	3				Colorectal(111;0.113)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	15682260	15682261	+	IGR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:15682260_15682261insA								TUSC3 (60267 upstream) : MSR1 (283127 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	15705382	15705382	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:15705382delT								TUSC3 (83389 upstream) : MSR1 (260006 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	15880117	15880117	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:15880117delA								TUSC3 (258124 upstream) : MSR1 (85271 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	16281262	16281262	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:16281262delT								MSR1 (230962 upstream) : FGF20 (569072 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	16333536	16333536	+	IGR	DEL	G	-	-	rs68149806		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:16333536delG								MSR1 (283236 upstream) : FGF20 (516798 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	16500396	16500397	+	IGR	DEL	AT	-	-	rs11777135		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:16500396_16500397delAT								MSR1 (450096 upstream) : FGF20 (349937 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	16622481	16622481	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:16622481delT								MSR1 (572181 upstream) : FGF20 (227853 downstream)																																			---	---	---	---
VPS37A	137492	broad.mit.edu	37	8	17142235	17142235	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17142235delT	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	17172817	17172818	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17172817_17172818insA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	17343600	17343601	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17343600_17343601delTT								MTMR7 (72560 upstream) : SLC7A2 (10999 downstream)																																			---	---	---	---
MTUS1	57509	broad.mit.edu	37	8	17614050	17614050	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17614050delG	uc003wxv.2	-						MTUS1_uc010lsy.2_5'Flank|MTUS1_uc003wxw.2_Intron|MTUS1_uc010lsz.2_Intron	NM_001001924	NP_001001924			mitochondrial tumor suppressor 1 isoform 1							Golgi apparatus|microtubule|microtubule organizing center|mitochondrion|nucleus|plasma membrane|spindle				ovary(1)|skin(1)	2				Colorectal(111;0.0778)														---	---	---	---
MTUS1	57509	broad.mit.edu	37	8	17641031	17641031	+	Intron	DEL	T	-	-	rs79875542		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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)														---	---	---	---
ASAH1	427	broad.mit.edu	37	8	17914872	17914873	+	3'UTR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17914872_17914873delAA	uc003wyl.2	-	14					ASAH1_uc010ltb.1_RNA|ASAH1_uc003wym.2_3'UTR|ASAH1_uc003wyn.2_3'UTR|ASAH1_uc003wyo.2_3'UTR	NM_177924	NP_808592			N-acylsphingosine amidohydrolase 1 isoform a						ceramide metabolic process	lysosome	ceramidase activity				0				Colorectal(111;0.0646)|COAD - Colon adenocarcinoma(73;0.228)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	19060081	19060081	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19060081delT								PSD3 (188885 upstream) : SH2D4A (111126 downstream)																																			---	---	---	---
CSGALNACT1	55790	broad.mit.edu	37	8	19558665	19558668	+	Intron	DEL	TTTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19558665_19558668delTTTT	uc011kyp.1	-							NM_018371	NP_060841			chondroitin sulfate						anatomical structure morphogenesis|cell proliferation|cell recognition|chondroitin sulfate biosynthetic process|chondroitin sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|dermatan sulfate proteoglycan biosynthetic process|extracellular matrix organization|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|heparin biosynthetic process|nervous system development|UDP-glucuronate metabolic process|UDP-N-acetylgalactosamine metabolic process	Golgi cisterna membrane|integral to Golgi membrane|soluble fraction	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|glucuronosyltransferase activity|glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|metal ion binding|peptidoglycan glycosyltransferase activity			central_nervous_system(2)|ovary(1)	3				Colorectal(111;0.182)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	20227227	20227229	+	IGR	DEL	AAA	-	-	rs74484560		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20227227_20227229delAAA								LZTS1 (114424 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	20227310	20227317	+	IGR	DEL	TCCTTCCT	-	-	rs10566124		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20227310_20227317delTCCTTCCT								LZTS1 (114507 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	20243894	20243897	+	IGR	DEL	CAAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20243894_20243897delCAAA								LZTS1 (131091 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	20406999	20406999	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20406999delG								LZTS1 (294196 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	20547882	20547882	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20547882delA								LZTS1 (435079 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	20871509	20871512	+	IGR	DEL	CACA	-	-	rs148527384		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20871509_20871512delCACA								LZTS1 (758706 upstream) : GFRA2 (678018 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	20881432	20881432	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20881432delA								LZTS1 (768629 upstream) : GFRA2 (668098 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	21468856	21468857	+	IGR	INS	-	TC	TC	rs149679268	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21468856_21468857insTC								None (None upstream) : GFRA2 (80673 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	21548828	21548829	+	IGR	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21548828_21548829delAC								None (None upstream) : GFRA2 (701 downstream)																																			---	---	---	---
GFRA2	2675	broad.mit.edu	37	8	21576530	21576530	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21576530delC	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)														---	---	---	---
GFRA2	2675	broad.mit.edu	37	8	21578508	21578508	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21578508delA	uc003wzu.1	-						GFRA2_uc003wzv.1_Intron|GFRA2_uc003wzw.1_Intron|DOK2_uc003wzx.1_Intron	NM_001495	NP_001486			GDNF family receptor alpha 2 isoform a							anchored to membrane|extrinsic to membrane|plasma membrane	glial cell-derived neurotrophic factor receptor activity				0				Colorectal(74;0.0189)|COAD - Colon adenocarcinoma(73;0.0727)														---	---	---	---
GFRA2	2675	broad.mit.edu	37	8	21594881	21594881	+	Intron	DEL	A	-	-	rs79713947		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21594881delA	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)														---	---	---	---
EPB49	2039	broad.mit.edu	37	8	21932809	21932810	+	Intron	INS	-	CCTCCT	CCTCCT	rs145121822	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21932809_21932810insCCTCCT	uc011kyt.1	+						EPB49_uc010ltl.2_Intron|EPB49_uc011kys.1_Intron|EPB49_uc010ltn.2_Intron|EPB49_uc011kyu.1_Intron|EPB49_uc011kyv.1_Intron|EPB49_uc010ltq.2_Intron	NM_001114136	NP_001107608			erythrocyte membrane protein band 4.9 isoform 1						actin filament bundle assembly|actin filament capping	actin cytoskeleton|nucleus	actin binding			central_nervous_system(1)	1				Colorectal(74;9.05e-05)|READ - Rectum adenocarcinoma(5;0.0276)|COAD - Colon adenocarcinoma(73;0.0631)														---	---	---	---
LGI3	203190	broad.mit.edu	37	8	22008953	22008953	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22008953delC	uc003xav.2	-						LGI3_uc010ltu.2_Intron	NM_139278	NP_644807			leucine-rich repeat LGI family, member 3						exocytosis	cell junction|extracellular region|synaptic vesicle|synaptosome				ovary(1)	1				Colorectal(74;0.00189)|COAD - Colon adenocarcinoma(73;0.0612)|READ - Rectum adenocarcinoma(644;0.0999)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	22985382	22985382	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22985382delC								TNFRSF10C (10434 upstream) : TNFRSF10D (7722 downstream)																																			---	---	---	---
NKX2-6	137814	broad.mit.edu	37	8	23563333	23563333	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23563333delG	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																		---	---	---	---
STC1	6781	broad.mit.edu	37	8	23709570	23709571	+	Intron	DEL	TG	-	-	rs113294965		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23709570_23709571delTG	uc003xdw.1	-							NM_003155	NP_003146			stanniocalcin 1 precursor						cell surface receptor linked signaling pathway|cell-cell signaling|cellular calcium ion homeostasis		hormone activity			skin(3)|upper_aerodigestive_tract(1)	4		Prostate(55;0.055)|Breast(100;0.116)		Colorectal(74;0.0155)|COAD - Colon adenocarcinoma(73;0.0632)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	23764140	23764140	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23764140delA								STC1 (51820 upstream) : ADAM28 (387440 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	23791620	23791620	+	IGR	DEL	T	-	-	rs72122672		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23791620delT								STC1 (79300 upstream) : ADAM28 (359960 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	24074278	24074278	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24074278delA								STC1 (361958 upstream) : ADAM28 (77302 downstream)																																			---	---	---	---
ADAM7	8756	broad.mit.edu	37	8	24338577	24338580	+	Intron	DEL	AAAC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24338577_24338580delAAAC	uc003xeb.2	+						ADAM7_uc003xec.2_Intron	NM_003817	NP_003808			a disintegrin and metalloproteinase domain 7						proteolysis	integral to membrane	metalloendopeptidase activity|zinc ion binding			skin(3)|ovary(1)|kidney(1)	5		Prostate(55;0.0181)		Colorectal(74;0.0199)|COAD - Colon adenocarcinoma(73;0.0754)|BRCA - Breast invasive adenocarcinoma(99;0.182)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	24626606	24626606	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24626606delA								ADAM7 (242125 upstream) : NEFM (144668 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	24918336	24918336	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24918336delA								NEFL (104205 upstream) : DOCK5 (123951 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	24943438	24943438	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24943438delA								NEFL (129307 upstream) : DOCK5 (98849 downstream)																																			---	---	---	---
DOCK5	80005	broad.mit.edu	37	8	25076852	25076852	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25076852delT	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-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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)														---	---	---	---
DOCK5	80005	broad.mit.edu	37	8	25248335	25248335	+	Intron	DEL	T	-	-	rs77439889		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25248335delT	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	25400561	25400561	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25400561delA	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	25738406	25738406	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25738406delA	uc003xes.1	-						PPP2R2A_uc003xek.2_Intron|EBF2_uc010lug.1_Intron	NM_022659	NP_073150			early B-cell factor 2						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|metal ion binding			ovary(3)|skin(1)	4		all_cancers(63;0.0989)|Ovarian(32;2.74e-05)|all_epithelial(46;0.0608)|Prostate(55;0.0845)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0277)|Epithelial(17;3.29e-10)|Colorectal(74;0.00383)|COAD - Colon adenocarcinoma(73;0.00738)														---	---	---	---
EBF2	64641	broad.mit.edu	37	8	25857155	25857155	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25857155delT	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	26088593	26088593	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26088593delA	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	26228343	26228343	+	3'UTR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26228343delT	uc003xeu.2	+	10					PPP2R2A_uc003xek.2_3'UTR|PPP2R2A_uc011laf.1_3'UTR	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)														---	---	---	---
DPYSL2	1808	broad.mit.edu	37	8	26458054	26458054	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26458054delT	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	26470055	26470056	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26470055_26470056insA	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	26575215	26575217	+	IGR	DEL	TTT	-	-	rs894329		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26575215_26575217delTTT								DPYSL2 (59522 upstream) : ADRA1A (30450 downstream)																																			---	---	---	---
PTK2B	2185	broad.mit.edu	37	8	27238053	27238053	+	Intron	DEL	T	-	-	rs138097587		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27238053delT	uc003xfn.1	+						PTK2B_uc003xfo.1_Intron|PTK2B_uc003xfp.1_Intron|PTK2B_uc003xfq.1_Intron	NM_173174	NP_775266			PTK2B protein tyrosine kinase 2 beta isoform a						apoptosis|bone resorption|positive regulation of cell proliferation|signal complex assembly	cytosol	ATP binding|non-membrane spanning protein tyrosine kinase activity|signal transducer activity			lung(3)|ovary(1)|skin(1)	5		Ovarian(32;2.72e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|Epithelial(17;6.61e-10)|BRCA - Breast invasive adenocarcinoma(99;0.226)|Colorectal(74;0.229)														---	---	---	---
PBK	55872	broad.mit.edu	37	8	27690542	27690542	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	28064346	28064346	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28064346delA								ELP3 (15679 upstream) : PNOC (110303 downstream)																																			---	---	---	---
KIF13B	23303	broad.mit.edu	37	8	29038330	29038331	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29038330_29038331delTT	uc003xhh.3	-						KIF13B_uc003xhj.2_Intron|KIF13B_uc010lvf.1_Intron	NM_015254	NP_056069			kinesin family member 13B						microtubule-based movement|protein targeting|signal transduction|T cell activation	cytoplasm|microtubule	ATP binding|microtubule motor activity|protein kinase binding				0		Ovarian(32;0.000536)		KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	29151124	29151125	+	IGR	INS	-	G	G	rs147717682	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29151124_29151125insG								KIF13B (30514 upstream) : DUSP4 (42492 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	29213587	29213588	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29213587_29213588delTT								DUSP4 (5402 upstream) : C8orf75 (365190 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	29482514	29482514	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29482514delT								DUSP4 (274329 upstream) : C8orf75 (96264 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	29811890	29811890	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29811890delT								LOC286135 (769 upstream) : TMEM66 (108742 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	29895545	29895546	+	IGR	DEL	AA	-	-	rs78292321		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29895545_29895546delAA								LOC286135 (84424 upstream) : TMEM66 (25086 downstream)																																			---	---	---	---
DCTN6	10671	broad.mit.edu	37	8	30031847	30031848	+	Intron	DEL	TT	-	-	rs113335753		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30031847_30031848delTT	uc003xhy.2	+							NM_006571	NP_006562			dynactin 6							centrosome	transferase activity			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(542;0.099)|Kidney(114;0.119)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	30138997	30138999	+	IGR	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30138997_30138999delTTT								DCTN6 (97938 upstream) : RBPMS (102945 downstream)																																			---	---	---	---
UBXN8	7993	broad.mit.edu	37	8	30608867	30608867	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30608867delA	uc003xii.2	+						UBXN8_uc010lvi.2_Intron|UBXN8_uc011lbb.1_Intron|UBXN8_uc003xij.2_5'Flank	NM_005671	NP_005662			reproduction 8						single fertilization						0																		---	---	---	---
WRN	7486	broad.mit.edu	37	8	30985600	30985600	+	Intron	DEL	A	-	-	rs112773122		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30985600delA	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	31039801	31039801	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:31039801delT								WRN (8525 upstream) : NRG1 (457467 downstream)																																			---	---	---	---
NRG1	3084	broad.mit.edu	37	8	31818536	31818536	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:31818536delT	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	32221226	32221226	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32221226delT	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	32342116	32342116	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32342116delT	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	32412419	32412420	+	Intron	INS	-	GACT	GACT	rs150386926	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32412419_32412420insGACT	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	32436001	32436001	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32436001delG	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	33125884	33125884	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33125884delT								NRG1 (503326 upstream) : FUT10 (102462 downstream)																																			---	---	---	---
RNF122	79845	broad.mit.edu	37	8	33416652	33416652	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33416652delA	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)														---	---	---	---
RNF122	79845	broad.mit.edu	37	8	33426080	33426080	+	5'Flank	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33426080delA	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	33486413	33486413	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33486413delT								DUSP26 (28974 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	33824805	33824805	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33824805delT								DUSP26 (367366 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	33839778	33839782	+	IGR	DEL	TTTTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33839778_33839782delTTTTT								DUSP26 (382339 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	34006278	34006278	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:34006278delA								DUSP26 (548839 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	34181924	34181924	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:34181924delA								DUSP26 (724485 upstream) : UNC5D (911051 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	34372018	34372019	+	IGR	INS	-	CA	CA	rs141175504	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:34372018_34372019insCA								DUSP26 (914579 upstream) : UNC5D (720956 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	34573999	34574000	+	IGR	DEL	AC	-	-	rs71896694		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:34573999_34574000delAC								None (None upstream) : UNC5D (518975 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	34864665	34864666	+	IGR	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:34864665_34864666delTG								None (None upstream) : UNC5D (228309 downstream)																																			---	---	---	---
UNC5D	137970	broad.mit.edu	37	8	35296550	35296550	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:35296550delT	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	35307433	35307433	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:35307433delC	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	35455222	35455223	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:35455222_35455223insT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	35680745	35680745	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:35680745delA								UNC5D (28565 upstream) : KCNU1 (961097 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	35702876	35702877	+	IGR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:35702876_35702877insA								UNC5D (50696 upstream) : KCNU1 (938965 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	35707842	35707842	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:35707842delT								UNC5D (55662 upstream) : KCNU1 (934000 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	35731271	35731271	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:35731271delA								UNC5D (79091 upstream) : KCNU1 (910571 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	36038758	36038758	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:36038758delT								UNC5D (386578 upstream) : KCNU1 (603084 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	36417885	36417886	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:36417885_36417886delTT								UNC5D (765705 upstream) : KCNU1 (223956 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	36479787	36479787	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:36479787delA								UNC5D (827607 upstream) : KCNU1 (162055 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	36809710	36809710	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:36809710delA								KCNU1 (16069 upstream) : ZNF703 (743591 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	36859387	36859387	+	IGR	DEL	T	-	-	rs72129803		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:36859387delT								KCNU1 (65746 upstream) : ZNF703 (693914 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	36900009	36900009	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:36900009delA								KCNU1 (106368 upstream) : ZNF703 (653292 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	36949084	36949084	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:36949084delC								KCNU1 (155443 upstream) : ZNF703 (604217 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	37047421	37047421	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37047421delA								KCNU1 (253780 upstream) : ZNF703 (505880 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	37149095	37149095	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37149095delA								KCNU1 (355454 upstream) : ZNF703 (404206 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	37207230	37207230	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37207230delT								KCNU1 (413589 upstream) : ZNF703 (346071 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	37228183	37228184	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37228183_37228184delAA								KCNU1 (434542 upstream) : ZNF703 (325117 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	37437284	37437284	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37437284delA								KCNU1 (643643 upstream) : ZNF703 (116017 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	37442364	37442364	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37442364delA								KCNU1 (648723 upstream) : ZNF703 (110937 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	37451690	37451691	+	IGR	DEL	CT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37451690_37451691delCT								KCNU1 (658049 upstream) : ZNF703 (101610 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	37644244	37644249	+	IGR	DEL	GTGTGT	-	-	rs113342053		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37644244_37644249delGTGTGT								PROSC (6959 upstream) : GPR124 (10175 downstream)																																			---	---	---	---
GPR124	25960	broad.mit.edu	37	8	37695483	37695484	+	Intron	INS	-	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37695483_37695484insG	uc003xkj.2	+						GPR124_uc010lvy.2_Intron	NM_032777	NP_116166			G protein-coupled receptor 124 precursor						central nervous system development|endothelial cell migration|neuropeptide signaling pathway|regulation of angiogenesis|regulation of chemotaxis|sprouting angiogenesis	integral to membrane|plasma membrane	G-protein coupled receptor activity			large_intestine(2)|ovary(2)|skin(1)	5			BRCA - Breast invasive adenocarcinoma(5;2.75e-24)|LUSC - Lung squamous cell carcinoma(8;3.5e-10)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	37815780	37815781	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37815780_37815781insT								GOT1L1 (18133 upstream) : ADRB3 (4735 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	38075684	38075685	+	IGR	DEL	GT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38075684_38075685delGT								BAG4 (7147 upstream) : DDHD2 (13324 downstream)																																			---	---	---	---
DDHD2	23259	broad.mit.edu	37	8	38109272	38109272	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38109272delT	uc003xlb.2	+						DDHD2_uc003xlc.2_Intron|DDHD2_uc003xld.2_Intron	NM_015214	NP_056029			DDHD domain containing 2 isoform 1						lipid catabolic process	centrosome	hydrolase activity|metal ion binding			large_intestine(1)|ovary(1)	2	Colorectal(12;0.000442)	all_lung(54;0.0657)|Lung NSC(58;0.175)	BRCA - Breast invasive adenocarcinoma(5;3.76e-25)|COAD - Colon adenocarcinoma(9;0.0977)															---	---	---	---
WHSC1L1	54904	broad.mit.edu	37	8	38153187	38153187	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38153187delT	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								---	---	---	---
FGFR1	2260	broad.mit.edu	37	8	38307183	38307184	+	Intron	INS	-	CCATTCT	CCATTCT	rs138612053	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38307183_38307184insCCATTCT	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	38432163	38432163	+	IGR	DEL	T	-	-	rs67056103		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38432163delT								C8orf86 (45983 upstream) : RNF5P1 (25532 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	38560659	38560659	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38560659delA								RNF5P1 (101884 upstream) : TACC1 (25045 downstream)																																			---	---	---	---
PLEKHA2	59339	broad.mit.edu	37	8	38802022	38802023	+	Intron	INS	-	A	A	rs138755319	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38802022_38802023insA	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	38861741	38861741	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38861741delT	uc003xmr.2	+						ADAM9_uc011lcf.1_Intron|ADAM9_uc011lcg.1_Intron|ADAM9_uc010lwr.2_Intron|ADAM9_uc003xmo.1_Intron|ADAM9_uc003xmp.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	38971518	38971518	+	Intron	DEL	T	-	-	rs10707232		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38971518delT	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	39133405	39133406	+	Intron	DEL	TT	-	-	rs34870154		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39133405_39133406delTT	uc003xmt.3	+						ADAM32_uc011lch.1_Intron|ADAM32_uc003xmu.3_Intron|ADAM32_uc003xmv.2_Intron	NM_145004	NP_659441			a disintegrin and metalloprotease domain 32						proteolysis	integral to membrane	metalloendopeptidase activity|zinc ion binding			ovary(1)|lung(1)|kidney(1)	3		all_cancers(7;3e-05)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00771)|Breast(189;0.0503)	LUSC - Lung squamous cell carcinoma(45;6.2e-07)|Colorectal(1;0.00699)|READ - Rectum adenocarcinoma(1;0.146)															---	---	---	---
ADAM5P	255926	broad.mit.edu	37	8	39210724	39210724	+	Intron	DEL	A	-	-	rs146466389		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39210724delA	uc003xmx.1	+						ADAM5P_uc003xmy.1_Intron|ADAM5P_uc003xmz.1_Intron|ADAM5P_uc010lwt.1_Intron|ADAM5P_uc003xna.2_Intron|ADAM5P_uc003xnb.2_Intron|ADAM5P_uc003xnc.2_Intron	NR_001448				Homo sapiens mRNA for tMDC II, isoform [a].												0																		---	---	---	---
ADAM5P	255926	broad.mit.edu	37	8	39251869	39251869	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39251869delT	uc003xmx.1	+						ADAM5P_uc003xmy.1_Intron|ADAM5P_uc003xmz.1_Intron|ADAM5P_uc010lwt.1_Intron|ADAM5P_uc003xna.2_Intron|ADAM5P_uc003xnb.2_Intron|ADAM5P_uc003xnc.2_Intron|ADAM5P_uc010lwu.1_Intron	NR_001448				Homo sapiens mRNA for tMDC II, isoform [a].												0																		---	---	---	---
IDO2	169355	broad.mit.edu	37	8	39854527	39854528	+	Intron	INS	-	A	A	rs140446241	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39854527_39854528insA	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	39885022	39885023	+	IGR	INS	-	GT	GT	rs150724832	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39885022_39885023insGT								IDO2 (11112 upstream) : C8orf4 (125966 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	39953678	39953678	+	IGR	DEL	T	-	-	rs10709641		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39953678delT								IDO2 (79768 upstream) : C8orf4 (57311 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	40317642	40317642	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40317642delA								C8orf4 (304821 upstream) : ZMAT4 (70474 downstream)																																			---	---	---	---
ZMAT4	79698	broad.mit.edu	37	8	40405810	40405811	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40405810_40405811insA	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	40449131	40449131	+	Intron	DEL	A	-	-	rs140623217		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40449131delA	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	40458768	40458768	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40458768delT	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	40575420	40575422	+	Intron	DEL	TGT	-	-	rs147333799		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40575420_40575422delTGT	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	40861344	40861344	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40861344delT								ZMAT4 (106001 upstream) : SFRP1 (258135 downstream)																																			---	---	---	---
ANK1	286	broad.mit.edu	37	8	41660712	41660712	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41660712delA	uc003xom.2	-							NM_001142446	NP_001135918			ankyrin 1 isoform 9						axon guidance|cytoskeleton organization|exocytosis|maintenance of epithelial cell apical/basal polarity|signal transduction	basolateral plasma membrane|cytosol|sarcomere|sarcoplasmic reticulum|spectrin-associated cytoskeleton	cytoskeletal adaptor activity|enzyme binding|protein binding|spectrin binding|structural constituent of cytoskeleton			ovary(3)|central_nervous_system(3)|lung(2)|breast(1)	9	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)															---	---	---	---
MYST3	7994	broad.mit.edu	37	8	41799626	41799626	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41799626delA	uc010lxb.2	-						MYST3_uc010lxc.2_Intron|MYST3_uc003xon.3_Intron|MYST3_uc010lxd.2_3'UTR	NM_001099412	NP_001092882			MYST histone acetyltransferase (monocytic						histone H3 acetylation|myeloid cell differentiation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	MOZ/MORF histone acetyltransferase complex|nucleosome	DNA binding|histone acetyltransferase activity|transcription coactivator activity|transcription factor binding|zinc ion binding			ovary(4)|pancreas(1)|central_nervous_system(1)|skin(1)	7	all_epithelial(6;1.12e-27)|all_lung(13;3.94e-12)|Lung NSC(13;6.54e-11)|Ovarian(28;0.00744)|Prostate(17;0.0119)|Colorectal(14;0.0221)|Lung SC(25;0.211)	all_lung(54;0.000294)|Lung NSC(58;0.00105)|Hepatocellular(245;0.0524)|Esophageal squamous(32;0.0954)|Renal(179;0.0983)	Epithelial(1;2.82e-19)|all cancers(1;1.15e-16)|BRCA - Breast invasive adenocarcinoma(8;9.17e-11)|OV - Ovarian serous cystadenocarcinoma(14;9.4e-05)|Colorectal(10;0.000728)|Lung(22;0.00153)|LUSC - Lung squamous cell carcinoma(45;0.00741)|COAD - Colon adenocarcinoma(11;0.0171)															---	---	---	---
MYST3	7994	broad.mit.edu	37	8	41836072	41836072	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41836072delT	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)															---	---	---	---
PLAT	5327	broad.mit.edu	37	8	42058351	42058351	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42058351delT	uc003xos.2	-						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	42494217	42494220	+	IGR	DEL	GTGT	-	-	rs67426094		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42494217_42494220delGTGT								C8orf40 (86078 upstream) : CHRNB3 (58342 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	42521444	42521444	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42521444delT								C8orf40 (113305 upstream) : CHRNB3 (31118 downstream)																																			---	---	---	---
CHRNB3	1142	broad.mit.edu	37	8	42552905	42552905	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42552905delG	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)															---	---	---	---
CHRNA6	8973	broad.mit.edu	37	8	42610185	42610188	+	Intron	DEL	TTTT	-	-	rs36021741		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42610185_42610188delTTTT	uc003xpj.2	-						CHRNA6_uc011lcw.1_Intron	NM_004198	NP_004189			cholinergic receptor, nicotinic, alpha 6							cell junction|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity				0	all_lung(13;3.33e-12)|Lung NSC(13;9.17e-11)|Ovarian(28;0.01)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.00439)|Lung NSC(58;0.0124)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	Lung(22;0.0252)|LUSC - Lung squamous cell carcinoma(45;0.0869)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	42643871	42643871	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42643871delA								CHRNA6 (20252 upstream) : THAP1 (47947 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	42676851	42676854	+	IGR	DEL	AAAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42676851_42676854delAAAA								CHRNA6 (53232 upstream) : THAP1 (14964 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	42906248	42906253	+	IGR	DEL	TTTTTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42906248_42906253delTTTTTT								HOOK3 (20567 upstream) : FNTA (5189 downstream)																																			---	---	---	---
SGK196	84197	broad.mit.edu	37	8	42953744	42953745	+	Intron	DEL	GT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42953744_42953745delGT	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	43329721	43329721	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:43329721delA								POTEA (111393 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	43387076	43387076	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:43387076delT								POTEA (168748 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	43517627	43517627	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:43517627delT								POTEA (299299 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	43596989	43596989	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:43596989delT								POTEA (378661 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	43641581	43641581	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:43641581delA								POTEA (423253 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	43760842	43760842	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:43760842delA								POTEA (542514 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	43773565	43773565	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:43773565delT								POTEA (555237 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	47414365	47414365	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:47414365delT								None (None upstream) : BEYLA (338143 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	47588860	47588860	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:47588860delA								None (None upstream) : BEYLA (163648 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	47723674	47723674	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:47723674delA								None (None upstream) : BEYLA (28834 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	47879214	47879214	+	IGR	DEL	C	-	-	rs68193308		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:47879214delC								BEYLA (111807 upstream) : KIAA0146 (294328 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	47901473	47901474	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:47901473_47901474insT								BEYLA (134066 upstream) : KIAA0146 (272068 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	47952416	47952416	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:47952416delT								BEYLA (185009 upstream) : KIAA0146 (221126 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	48019852	48019852	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48019852delT								BEYLA (252445 upstream) : KIAA0146 (153690 downstream)																																			---	---	---	---
KIAA0146	23514	broad.mit.edu	37	8	48631068	48631069	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48631068_48631069delTT	uc003xqd.2	+						KIAA0146_uc011ldc.1_Intron|KIAA0146_uc011ldd.1_Intron|KIAA0146_uc003xqe.2_Intron|KIAA0146_uc003xqf.2_Intron|KIAA0146_uc010lxt.2_Intron|KIAA0146_uc011ldf.1_Intron|KIAA0146_uc011ldg.1_Intron|KIAA0146_uc003xqg.1_Intron	NM_001080394	NP_001073863			hypothetical protein LOC23514												0		Lung NSC(58;0.175)																---	---	---	---
KIAA0146	23514	broad.mit.edu	37	8	48661976	48661977	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48661976_48661977delAA	uc003xqg.1	+											Homo sapiens cDNA FLJ38459 fis, clone FEBRA2020566.												0		Lung NSC(58;0.175)																---	---	---	---
KIAA0146	23514	broad.mit.edu	37	8	48662533	48662534	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48662533_48662534delAA	uc003xqg.1	+											Homo sapiens cDNA FLJ38459 fis, clone FEBRA2020566.												0		Lung NSC(58;0.175)																---	---	---	---
PRKDC	5591	broad.mit.edu	37	8	48848624	48848624	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48848624delA	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	49137475	49137475	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49137475delT								UBE2V2 (163023 upstream) : EFCAB1 (485876 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	49242754	49242754	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49242754delT								UBE2V2 (268302 upstream) : EFCAB1 (380597 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	49293929	49293929	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49293929delC								UBE2V2 (319477 upstream) : EFCAB1 (329422 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	49303472	49303472	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49303472delA								UBE2V2 (329020 upstream) : EFCAB1 (319879 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	49345589	49345590	+	IGR	INS	-	C	C	rs139729891	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49345589_49345590insC								UBE2V2 (371137 upstream) : EFCAB1 (277761 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	49533848	49533848	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49533848delT								UBE2V2 (559396 upstream) : EFCAB1 (89503 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	49617119	49617119	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49617119delT								UBE2V2 (642667 upstream) : EFCAB1 (6232 downstream)																																			---	---	---	---
EFCAB1	79645	broad.mit.edu	37	8	49626432	49626432	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49626432delA	uc003xqn.3	-											Homo sapiens cDNA FLJ11767 fis, clone HEMBA1005737, weakly similar to CALCINEURIN B SUBUNIT.								calcium ion binding				0		all_epithelial(80;0.0134)|Lung NSC(129;0.0207)|all_lung(136;0.0464)																---	---	---	---
EFCAB1	79645	broad.mit.edu	37	8	49639430	49639433	+	Intron	DEL	ATCT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49639430_49639433delATCT	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	49676371	49676371	+	IGR	DEL	T	-	-	rs11319174		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49676371delT								EFCAB1 (28501 upstream) : SNAI2 (153868 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	50103432	50103433	+	IGR	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:50103432_50103433delTG								C8orf22 (114791 upstream) : SNTG1 (718916 downstream)																																			---	---	---	---
SNTG1	54212	broad.mit.edu	37	8	51396785	51396785	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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	51922982	51922982	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:51922982delT								SNTG1 (217555 upstream) : PXDNL (309162 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	52124544	52124545	+	IGR	DEL	CC	-	-	rs6984166	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52124544_52124545delCC								SNTG1 (419117 upstream) : PXDNL (107599 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	52164361	52164364	+	IGR	DEL	GTGT	-	-	rs71993348		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52164361_52164364delGTGT								SNTG1 (458934 upstream) : PXDNL (67780 downstream)																																			---	---	---	---
PXDNL	137902	broad.mit.edu	37	8	52656444	52656445	+	Intron	DEL	CT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52656444_52656445delCT	uc003xqu.3	-							NM_144651	NP_653252			peroxidasin homolog-like precursor						hydrogen peroxide catabolic process	extracellular space	heme binding|peroxidase activity			ovary(1)|pancreas(1)	2		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)																---	---	---	---
ST18	9705	broad.mit.edu	37	8	53093073	53093073	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53093073delT	uc003xqz.2	-						ST18_uc011ldq.1_Intron|ST18_uc011ldr.1_Intron|ST18_uc011lds.1_Intron|ST18_uc003xra.2_Intron|ST18_uc003xrb.2_Intron|ST18_uc010lyb.2_Intron	NM_014682	NP_055497			suppression of tumorigenicity 18							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)|skin(1)	5		Lung NSC(129;0.131)|all_epithelial(80;0.217)|all_lung(136;0.229)																---	---	---	---
ST18	9705	broad.mit.edu	37	8	53156453	53156454	+	Intron	DEL	GA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53156453_53156454delGA	uc003xra.2	-						ST18_uc003xrb.2_Intron|ST18_uc010lyb.2_Intron	NM_014682	NP_055497			suppression of tumorigenicity 18							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)|skin(1)	5		Lung NSC(129;0.131)|all_epithelial(80;0.217)|all_lung(136;0.229)																---	---	---	---
ST18	9705	broad.mit.edu	37	8	53183472	53183472	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53183472delT	uc003xra.2	-						ST18_uc003xrb.2_Intron|ST18_uc010lyb.2_Intron	NM_014682	NP_055497			suppression of tumorigenicity 18							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)|skin(1)	5		Lung NSC(129;0.131)|all_epithelial(80;0.217)|all_lung(136;0.229)																---	---	---	---
RB1CC1	9821	broad.mit.edu	37	8	53558455	53558455	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53558455delA	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	53683379	53683380	+	IGR	INS	-	TG	TG	rs142312023	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53683379_53683380insTG								RB1CC1 (56353 upstream) : NPBWR1 (169088 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	53903788	53903788	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53903788delA								NPBWR1 (50335 upstream) : OPRK1 (234488 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	54054179	54054179	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54054179delC								NPBWR1 (200726 upstream) : OPRK1 (84097 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	54061634	54061634	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54061634delT								NPBWR1 (208181 upstream) : OPRK1 (76642 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	54084476	54084477	+	IGR	INS	-	G	G	rs72532843	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54084476_54084477insG								NPBWR1 (231023 upstream) : OPRK1 (53799 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	54303880	54303880	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54303880delA								OPRK1 (139686 upstream) : ATP6V1H (324236 downstream)																																			---	---	---	---
ATP6V1H	51606	broad.mit.edu	37	8	54674823	54674824	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54674823_54674824delAA	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)															---	---	---	---
TCEA1	6917	broad.mit.edu	37	8	54922593	54922593	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54922593delA	uc003xru.2	-						TCEA1_uc003xrv.2_Intron|TCEA1_uc011ldw.1_Intron|TCEA1_uc003xrw.1_Intron	NM_006756	NP_006747			transcription elongation factor A 1 isoform 1						positive regulation of viral transcription|regulation of transcription elongation, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription elongation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	nucleoplasm	DNA binding|translation elongation factor activity|zinc ion binding				0		Lung NSC(129;0.109)|all_epithelial(80;0.11)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;9.1e-07)|Epithelial(17;9.44e-05)|all cancers(17;0.000699)					T	PLAG1	salivary adenoma								---	---	---	---
Unknown	0	broad.mit.edu	37	8	55274597	55274598	+	IGR	INS	-	TG	TG			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55274597_55274598insTG								MRPL15 (213523 upstream) : SOX17 (95897 downstream)																																			---	---	---	---
RP1	6101	broad.mit.edu	37	8	55647090	55647090	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55647090delT	uc011ldy.1	+											SubName: Full=cDNA, FLJ79410, moderately similar to Oxygen-regulated protein 1;						axoneme assembly|intracellular signal transduction|photoreceptor cell maintenance|photoreceptor cell outer segment organization|phototransduction, visible light|retinal cone cell development|retinal rod cell development	cilium axoneme|cytoplasm|microtubule|microtubule associated complex|photoreceptor connecting cilium|photoreceptor inner segment|photoreceptor outer segment	microtubule binding			skin(7)|ovary(4)|pancreas(1)	12		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)															---	---	---	---
RP1	6101	broad.mit.edu	37	8	55658040	55658040	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55658040delA	uc011ldy.1	+											SubName: Full=cDNA, FLJ79410, moderately similar to Oxygen-regulated protein 1;						axoneme assembly|intracellular signal transduction|photoreceptor cell maintenance|photoreceptor cell outer segment organization|phototransduction, visible light|retinal cone cell development|retinal rod cell development	cilium axoneme|cytoplasm|microtubule|microtubule associated complex|photoreceptor connecting cilium|photoreceptor inner segment|photoreceptor outer segment	microtubule binding			skin(7)|ovary(4)|pancreas(1)	12		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	56006757	56006757	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56006757delC								RP1 (324226 upstream) : XKR4 (8260 downstream)																																			---	---	---	---
XKR4	114786	broad.mit.edu	37	8	56083203	56083204	+	Intron	INS	-	A	A	rs145895255	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56083203_56083204insA	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	56136363	56136364	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56136363_56136364insT	uc003xsf.2	+							NM_052898	NP_443130			XK, Kell blood group complex subunit-related							integral to membrane				pancreas(2)	2			Epithelial(17;0.000117)|all cancers(17;0.000836)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	56485453	56485453	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56485453delT								XKR4 (46745 upstream) : TMEM68 (165867 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	56559664	56559664	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56559664delT								XKR4 (120956 upstream) : TMEM68 (91656 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	56619946	56619946	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56619946delA								XKR4 (181238 upstream) : TMEM68 (31374 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	56745689	56745689	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56745689delT								TGS1 (7686 upstream) : LYN (46697 downstream)																																			---	---	---	---
LYN	4067	broad.mit.edu	37	8	56808188	56808188	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56808188delT	uc003xsk.3	+						LYN_uc003xsl.3_Intron	NM_002350	NP_002341			Yamaguchi sarcoma viral (v-yes-1) oncogene						erythrocyte differentiation|interspecies interaction between organisms|leukocyte migration|platelet activation|positive regulation of cellular component movement|positive regulation of stress-activated protein kinase signaling cascade|positive regulation of tyrosine phosphorylation of STAT protein|response to DNA damage stimulus|T cell costimulation	cytosol|Golgi apparatus|membrane raft|nucleus|perinuclear region of cytoplasm	ATP binding|ion channel binding|non-membrane spanning protein tyrosine kinase activity|receptor signaling protein tyrosine kinase activity			ovary(1)|breast(1)|central_nervous_system(1)	3		all_lung(136;0.0555)|Lung NSC(129;0.0726)|all_epithelial(80;0.0772)	Epithelial(17;0.000834)|all cancers(17;0.00598)															---	---	---	---
LYN	4067	broad.mit.edu	37	8	56910676	56910676	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56910676delT	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	56953230	56953230	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56953230delT								LYN (29294 upstream) : RPS20 (27509 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	56953632	56953633	+	IGR	DEL	AG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56953632_56953633delAG								LYN (29696 upstream) : RPS20 (27106 downstream)																																			---	---	---	---
PLAG1	5324	broad.mit.edu	37	8	57109347	57109348	+	Intron	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:57109347_57109348delTG	uc003xsr.3	-						PLAG1_uc010lyi.2_Intron|PLAG1_uc010lyj.2_Intron	NM_002655	NP_002646			pleiomorphic adenoma gene 1 isoform a							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding		CTNNB1/PLAG1(60)|FGFR1_ENST00000447712/PLAG1(28)|CHCHD7/PLAG1(12)|LIFR_ENST00000263409/PLAG1(10)|HAS2/PLAG1(10)|COL1A2/PLAG1(3)|TCEA1_ENST00000521604/PLAG1(3)	salivary_gland(113)|soft_tissue(13)|lung(1)|central_nervous_system(1)|breast(1)	129		all_lung(136;0.0548)|Lung NSC(129;0.0718)|all_epithelial(80;0.125)	Epithelial(17;0.00179)|all cancers(17;0.0125)					T	TCEA1|LIFR|CTNNB1|CHCHD7	salivary adenoma								---	---	---	---
Unknown	0	broad.mit.edu	37	8	58683106	58683106	+	IGR	DEL	A	-	-	rs139457979		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:58683106delA								C8orf71 (485818 upstream) : FAM110B (224007 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	58729292	58729292	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:58729292delA								C8orf71 (532004 upstream) : FAM110B (177821 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	58731290	58731290	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:58731290delA								C8orf71 (534002 upstream) : FAM110B (175823 downstream)																																			---	---	---	---
FAM110B	90362	broad.mit.edu	37	8	59055597	59055598	+	Intron	INS	-	GT	GT	rs142519692	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59055597_59055598insGT	uc003xtj.1	+							NM_147189	NP_671722			hypothetical protein LOC90362							microtubule organizing center|mitochondrion|nucleus				large_intestine(1)	1		all_epithelial(80;0.025)|all_lung(136;0.0274)|Lung NSC(129;0.0355)																---	---	---	---
Unknown	0	broad.mit.edu	37	8	59194949	59194950	+	IGR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59194949_59194950insA								FAM110B (132672 upstream) : UBXN2B (128873 downstream)																																			---	---	---	---
TOX	9760	broad.mit.edu	37	8	60003332	60003332	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:60003332delG	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	60021215	60021218	+	Intron	DEL	ACAC	-	-	rs72219254		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:60021215_60021218delACAC	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	60480821	60480824	+	IGR	DEL	GAGA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:60480821_60480824delGAGA								TOX (449054 upstream) : CA8 (620599 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	60571697	60571697	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:60571697delA								TOX (539930 upstream) : CA8 (529726 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	60743983	60743983	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:60743983delT								TOX (712216 upstream) : CA8 (357440 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	61099190	61099190	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61099190delA								None (None upstream) : CA8 (2233 downstream)																																			---	---	---	---
RAB2A	5862	broad.mit.edu	37	8	61462950	61462950	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61462950delT	uc003xud.1	+						RAB2A_uc011lef.1_Intron	NM_002865	NP_002856			RAB2A, member RAS oncogene family						ER to Golgi vesicle-mediated transport|protein transport|small GTPase mediated signal transduction	endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|Golgi membrane|melanosome	GDP binding|GTP binding|GTPase activity				0			BRCA - Breast invasive adenocarcinoma(89;0.0805)															---	---	---	---
RAB2A	5862	broad.mit.edu	37	8	61489001	61489001	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61489001delA	uc003xud.1	+						RAB2A_uc011lef.1_Intron	NM_002865	NP_002856			RAB2A, member RAS oncogene family						ER to Golgi vesicle-mediated transport|protein transport|small GTPase mediated signal transduction	endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|Golgi membrane|melanosome	GDP binding|GTP binding|GTPase activity				0			BRCA - Breast invasive adenocarcinoma(89;0.0805)															---	---	---	---
RAB2A	5862	broad.mit.edu	37	8	61503040	61503041	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61503040_61503041insA	uc003xud.1	+						RAB2A_uc011lef.1_Intron	NM_002865	NP_002856			RAB2A, member RAS oncogene family						ER to Golgi vesicle-mediated transport|protein transport|small GTPase mediated signal transduction	endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|Golgi membrane|melanosome	GDP binding|GTP binding|GTPase activity				0			BRCA - Breast invasive adenocarcinoma(89;0.0805)															---	---	---	---
RAB2A	5862	broad.mit.edu	37	8	61518273	61518273	+	Intron	DEL	C	-	-	rs603035	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61518273delC	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	61714076	61714076	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61714076delT	uc003xue.2	+							NM_017780	NP_060250			chromodomain helicase DNA binding protein 7						central nervous system development|chromatin modification|cognition|cranial nerve development|face development|heart morphogenesis|in utero embryonic development|inner ear morphogenesis|nose development|palate development|regulation of growth hormone secretion|regulation of transcription, DNA-dependent|retina development in camera-type eye|skeletal system development|T cell differentiation|transcription, DNA-dependent	nucleus	ATP binding|chromatin binding|DNA binding|helicase activity	p.556_871dup(1)		ovary(4)|large_intestine(1)|central_nervous_system(1)|lung(1)|breast(1)|pancreas(1)	9		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)															---	---	---	---
CHD7	55636	broad.mit.edu	37	8	61771697	61771697	+	Intron	DEL	T	-	-	rs34162663		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61771697delT	uc003xue.2	+							NM_017780	NP_060250			chromodomain helicase DNA binding protein 7						central nervous system development|chromatin modification|cognition|cranial nerve development|face development|heart morphogenesis|in utero embryonic development|inner ear morphogenesis|nose development|palate development|regulation of growth hormone secretion|regulation of transcription, DNA-dependent|retina development in camera-type eye|skeletal system development|T cell differentiation|transcription, DNA-dependent	nucleus	ATP binding|chromatin binding|DNA binding|helicase activity			ovary(4)|large_intestine(1)|central_nervous_system(1)|lung(1)|breast(1)|pancreas(1)	9		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	61809230	61809230	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61809230delA								CHD7 (29767 upstream) : CLVS1 (391295 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	61901081	61901081	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61901081delA								CHD7 (121618 upstream) : CLVS1 (299444 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	62121157	62121158	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62121157_62121158insT								CHD7 (341694 upstream) : CLVS1 (79367 downstream)																																			---	---	---	---
CLVS1	157807	broad.mit.edu	37	8	62412295	62412295	+	3'UTR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62412295delT	uc003xuh.2	+	6					CLVS1_uc003xui.2_RNA|CLVS1_uc010lyp.2_3'UTR	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	62538943	62538944	+	Intron	DEL	TT	-	-	rs78469859	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62538943_62538944delTT	uc003xuj.2	-						ASPH_uc011leg.1_Intron|ASPH_uc003xuo.2_Intron|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Intron|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Intron|ASPH_uc003xun.2_Intron|ASPH_uc011lek.1_Intron|ASPH_uc003xum.2_Intron	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	62970646	62970646	+	IGR	DEL	A	-	-	rs71559355		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62970646delA								ASPH (343447 upstream) : NKAIN3 (190855 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	64002485	64002486	+	IGR	DEL	AA	-	-	rs35464712		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:64002485_64002486delAA								TTPA (3873 upstream) : YTHDF3 (78635 downstream)																																			---	---	---	---
YTHDF3	253943	broad.mit.edu	37	8	64081982	64081982	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:64081982delT	uc003xuy.2	+						YTHDF3_uc010lys.2_Intron|YTHDF3_uc003xuz.2_Intron|YTHDF3_uc003xva.2_Intron|YTHDF3_uc011len.1_Intron	NM_152758	NP_689971			YTH domain family, member 3												0	Breast(64;0.0716)	all_cancers(86;0.169)|Lung NSC(129;0.0324)|all_lung(136;0.0593)|all_epithelial(80;0.146)	BRCA - Breast invasive adenocarcinoma(89;0.161)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	64165200	64165204	+	IGR	DEL	TTTTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:64165200_64165204delTTTTT								YTHDF3 (39855 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	64510977	64510977	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:64510977delA								YTHDF3 (385632 upstream) : MIR124-2 (780729 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	64535808	64535808	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:64535808delA								YTHDF3 (410463 upstream) : MIR124-2 (755898 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	65161072	65161072	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65161072delC								None (None upstream) : MIR124-2 (130634 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	65163885	65163885	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65163885delT								None (None upstream) : MIR124-2 (127821 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	65378152	65378152	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65378152delA								MIR124-2 (86338 upstream) : LOC401463 (108716 downstream)																																			---	---	---	---
CYP7B1	9420	broad.mit.edu	37	8	65528706	65528706	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65528706delT	uc003xvj.2	-	3	596	c.392delA	c.(391-393)AATfs	p.N131fs		NM_004820	NP_004811	O75881	CP7B1_HUMAN	cytochrome P450, family 7, subfamily B,	131					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	65895933	65895934	+	IGR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65895933_65895934insA								CYP7B1 (184585 upstream) : ARMC1 (619138 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	66430087	66430088	+	IGR	INS	-	AC	AC	rs138480843	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66430087_66430088insAC								CYP7B1 (718739 upstream) : ARMC1 (84984 downstream)																																			---	---	---	---
PDE7A	5150	broad.mit.edu	37	8	66662734	66662739	+	Intron	DEL	TGTGTC	-	-	rs67526512		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66662734_66662739delTGTGTC	uc003xvq.2	-						PDE7A_uc003xvr.2_Intron|PDE7A_uc003xvp.2_Intron	NM_002604	NP_002595			phosphodiesterase 7A isoform b							cell fraction|cytosol	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding				0			Epithelial(68;0.0509)|BRCA - Breast invasive adenocarcinoma(89;0.111)|all cancers(69;0.168)|OV - Ovarian serous cystadenocarcinoma(28;0.238)		Dyphylline(DB00651)|Ketotifen(DB00920)													---	---	---	---
Unknown	0	broad.mit.edu	37	8	66832907	66832907	+	IGR	DEL	A	-	-	rs79779601		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66832907delA								PDE7A (79152 upstream) : DNAJC5B (100884 downstream)																																			---	---	---	---
TRIM55	84675	broad.mit.edu	37	8	67044687	67044688	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67044687_67044688insA	uc003xvv.2	+						TRIM55_uc003xvu.2_Intron|TRIM55_uc003xvw.2_Intron|TRIM55_uc003xvx.2_Intron	NM_184085	NP_908973			tripartite motif-containing 55 isoform 1							cytoplasm|microtubule|nucleus	signal transducer activity|zinc ion binding			skin(3)|ovary(1)|central_nervous_system(1)	5		Lung NSC(129;0.138)|all_lung(136;0.221)	Epithelial(68;0.0136)|all cancers(69;0.0582)|BRCA - Breast invasive adenocarcinoma(89;0.0628)|OV - Ovarian serous cystadenocarcinoma(28;0.0904)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	67129573	67129573	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67129573delT								CRH (38875 upstream) : RRS1 (211690 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	67471324	67471324	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67471324delA								C8orf46 (40567 upstream) : MYBL1 (3087 downstream)																																			---	---	---	---
VCPIP1	80124	broad.mit.edu	37	8	67562563	67562563	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67562563delA	uc003xwn.2	-							NM_025054	NP_079330			valosin containing protein (p97)/p47 complex						protein ubiquitination	endoplasmic reticulum|Golgi stack	ubiquitin-specific protease activity			lung(2)|ovary(2)|central_nervous_system(1)|breast(1)|skin(1)|kidney(1)	8		Lung NSC(129;0.142)|all_lung(136;0.227)	Epithelial(68;0.000771)|OV - Ovarian serous cystadenocarcinoma(28;0.00248)|all cancers(69;0.00296)|BRCA - Breast invasive adenocarcinoma(89;0.149)															---	---	---	---
CSPP1	79848	broad.mit.edu	37	8	68035110	68035111	+	Intron	DEL	TG	-	-	rs34484092		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68035110_68035111delTG	uc003xxi.2	+						CSPP1_uc003xxg.1_Intron|CSPP1_uc003xxh.1_Intron|CSPP1_uc003xxj.2_Intron|CSPP1_uc003xxk.2_Intron	NM_001077204	NP_001070672			centrosome spindle pole associated protein 1							centrosome|microtubule|spindle				ovary(3)|breast(2)	5	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.00145)|OV - Ovarian serous cystadenocarcinoma(28;0.00589)|all cancers(69;0.0069)|BRCA - Breast invasive adenocarcinoma(89;0.153)															---	---	---	---
ARFGEF1	10565	broad.mit.edu	37	8	68195993	68195994	+	Intron	INS	-	AGTC	AGTC	rs145815352	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68195993_68195994insAGTC	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	68303309	68303310	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68303309_68303310delAA								ARFGEF1 (47397 upstream) : CPA6 (31096 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	68673456	68673456	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68673456delT								CPA6 (14836 upstream) : PREX2 (190892 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	68806909	68806909	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68806909delC								CPA6 (148289 upstream) : PREX2 (57439 downstream)																																			---	---	---	---
PREX2	80243	broad.mit.edu	37	8	68862206	68862207	+	5'Flank	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68862206_68862207delTT	uc003xxv.1	+						PREX2_uc003xxu.1_5'Flank|PREX2_uc011lez.1_5'Flank|PREX2_uc003xxt.2_5'Flank	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	68985247	68985248	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68985247_68985248insA	uc003xxv.1	+						PREX2_uc003xxu.1_Intron|PREX2_uc011lez.1_Intron	NM_024870	NP_079146			DEP domain containing 2 isoform a						G-protein coupled receptor protein signaling pathway|intracellular signal transduction	intracellular	protein binding|Rac GTPase activator activity|Rac guanyl-nucleotide exchange factor activity			skin(6)|large_intestine(4)|pancreas(3)|lung(2)|ovary(1)|kidney(1)	17																		---	---	---	---
PREX2	80243	broad.mit.edu	37	8	69113503	69113503	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69113503delT	uc003xxv.1	+							NM_024870	NP_079146			DEP domain containing 2 isoform a						G-protein coupled receptor protein signaling pathway|intracellular signal transduction	intracellular	protein binding|Rac GTPase activator activity|Rac guanyl-nucleotide exchange factor activity			skin(6)|large_intestine(4)|pancreas(3)|lung(2)|ovary(1)|kidney(1)	17																		---	---	---	---
C8orf34	116328	broad.mit.edu	37	8	69613749	69613749	+	Intron	DEL	T	-	-	rs11291622		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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	69956841	69956842	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69956841_69956842delTT	uc003xyc.1	-											Homo sapiens cDNA FLJ30952 fis, clone HCASM1000130.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	69959215	69959216	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69959215_69959216insA	uc003xyc.1	-											Homo sapiens cDNA FLJ30952 fis, clone HCASM1000130.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	70071583	70071583	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70071583delC								C8orf34 (340327 upstream) : SULF1 (307276 downstream)																																			---	---	---	---
SULF1	23213	broad.mit.edu	37	8	70514026	70514026	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70514026delT	uc010lza.1	+	10	1740	c.1023delT	c.(1021-1023)CCTfs	p.P341fs	SULF1_uc003xyd.2_Frame_Shift_Del_p.P341fs|SULF1_uc003xye.2_Frame_Shift_Del_p.P341fs|SULF1_uc003xyf.2_Frame_Shift_Del_p.P341fs|SULF1_uc003xyg.2_Frame_Shift_Del_p.P341fs|SULF1_uc003xyh.1_RNA	NM_015170	NP_055985	Q8IWU6	SULF1_HUMAN	sulfatase 1 precursor	341					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	70625679	70625680	+	Intron	DEL	TC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70625679_70625680delTC	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	70924009	70924009	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70924009delT								SLCO5A1 (176710 upstream) : PRDM14 (40016 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	70959889	70959889	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70959889delT								SLCO5A1 (212590 upstream) : PRDM14 (4136 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	70988247	70988248	+	IGR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70988247_70988248insA								PRDM14 (4685 upstream) : NCOA2 (36019 downstream)																																			---	---	---	---
NCOA2	10499	broad.mit.edu	37	8	71082394	71082394	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:71082394delG	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	71104564	71104564	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:71104564delA	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	71224755	71224756	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:71224755_71224756delTT	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								---	---	---	---
EYA1	2138	broad.mit.edu	37	8	72127508	72127508	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72127508delT	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	72715724	72715724	+	IGR	DEL	T	-	-	rs113569148		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72715724delT								EYA1 (441257 upstream) : MSC (38053 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	72932593	72932594	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72932593_72932594insA	uc011lff.1	+						uc003xyy.2_Intron					Homo sapiens cDNA FLJ41321 fis, clone BRAMY2045299.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	73217782	73217783	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:73217782_73217783insT	uc010lzg.2	-											Homo sapiens cDNA, FLJ99767.																														---	---	---	---
KCNB2	9312	broad.mit.edu	37	8	73598438	73598438	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:73598438delT	uc003xzb.2	+							NM_004770	NP_004761			potassium voltage-gated channel, Shab-related						regulation of smooth muscle contraction	voltage-gated potassium channel complex	delayed rectifier potassium channel activity|protein binding			skin(3)|large_intestine(1)|pancreas(1)|ovary(1)|central_nervous_system(1)	7	Breast(64;0.137)		Epithelial(68;0.105)															---	---	---	---
KCNB2	9312	broad.mit.edu	37	8	73675560	73675561	+	Intron	INS	-	T	T	rs138683471	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:73675560_73675561insT	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	74172771	74172771	+	5'Flank	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74172771delA	uc010lzh.1	-						uc010lzi.1_5'Flank|uc010lzj.1_5'Flank					Homo sapiens cDNA clone IMAGE:40127465.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	74303344	74303344	+	IGR	DEL	A	-	-	rs113855513		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74303344delA								RDH10 (65830 upstream) : STAU2 (29262 downstream)																																			---	---	---	---
STAU2	27067	broad.mit.edu	37	8	74356085	74356087	+	Intron	DEL	AAA	-	-	rs72463744		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74356085_74356087delAAA	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	74453060	74453060	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74453060delT	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	74507122	74507122	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74507122delA	uc003xzm.2	-						STAU2_uc011lfg.1_Intron|STAU2_uc003xzn.2_Intron|STAU2_uc011lfh.1_Intron|STAU2_uc003xzo.2_Intron|STAU2_uc003xzp.2_Intron|STAU2_uc011lfi.1_Intron|STAU2_uc003xzq.2_Intron|STAU2_uc010lzk.2_Intron|STAU2_uc010lzl.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	74648976	74648976	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74648976delA	uc003xzm.2	-						STAU2_uc011lfg.1_Intron|STAU2_uc003xzn.2_Intron|STAU2_uc011lfh.1_Intron|STAU2_uc003xzo.2_Intron|STAU2_uc003xzp.2_Intron|STAU2_uc011lfi.1_Intron|STAU2_uc003xzq.2_Intron|STAU2_uc010lzk.2_Intron|STAU2_uc010lzl.1_Intron|STAU2_uc003xzs.2_Intron|STAU2_uc003xzr.2_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)															---	---	---	---
UBE2W	55284	broad.mit.edu	37	8	74742889	74742889	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	74843843	74843843	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74843843delA								UBE2W (52733 upstream) : TCEB1 (14791 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	74996094	74996094	+	IGR	DEL	T	-	-	rs113368652		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74996094delT								LY96 (54789 upstream) : JPH1 (150847 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	75527087	75527088	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75527087_75527088delTT	uc003yaj.1	+											Homo sapiens cDNA FLJ39080 fis, clone NT2RP7018197.																														---	---	---	---
CRISPLD1	83690	broad.mit.edu	37	8	75895146	75895146	+	5'Flank	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75895146delA	uc003yan.2	+							NM_031461	NP_113649			cysteine-rich secretory protein LCCL domain							extracellular region				ovary(1)|central_nervous_system(1)	2	Breast(64;0.0799)		Epithelial(68;0.155)|BRCA - Breast invasive adenocarcinoma(89;0.161)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	76131065	76131066	+	IGR	INS	-	GGAA	GGAA	rs148982283	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:76131065_76131066insGGAA								CRISPLD1 (184274 upstream) : HNF4G (189117 downstream)																																			---	---	---	---
HNF4G	3174	broad.mit.edu	37	8	76399240	76399240	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:76399240delA	uc003yaq.2	+						HNF4G_uc003yap.1_Intron	NM_004133	NP_004124			hepatocyte nuclear factor 4, gamma						endocrine pancreas development|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)	1	Breast(64;0.0448)		BRCA - Breast invasive adenocarcinoma(89;0.161)															---	---	---	---
HNF4G	3174	broad.mit.edu	37	8	76463542	76463542	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:76463542delA	uc003yaq.2	+						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	77505759	77505759	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77505759delG								None (None upstream) : LOC100192378 (17356 downstream)																																			---	---	---	---
PEX2	5828	broad.mit.edu	37	8	77912120	77912120	+	Intron	DEL	A	-	-	rs146550182	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77912120delA	uc003yax.2	-						PEX2_uc003yay.2_Intron|PEX2_uc003yaz.2_Intron|PEX2_uc010lzn.1_Frame_Shift_Del_p.F52fs	NM_000318	NP_000309			peroxin 2						peroxisome organization	integral to peroxisomal membrane	protein binding|zinc ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	78294171	78294171	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:78294171delA								PEX2 (381647 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	78600181	78600182	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:78600181_78600182insT								PEX2 (687657 upstream) : PKIA (828154 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	78712430	78712430	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:78712430delC								PEX2 (799906 upstream) : PKIA (715906 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	78924702	78924705	+	IGR	DEL	CTTC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:78924702_78924705delCTTC								None (None upstream) : PKIA (503631 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	79065043	79065043	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:79065043delC								None (None upstream) : PKIA (363293 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	79152376	79152376	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:79152376delA								None (None upstream) : PKIA (275960 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	79345222	79345223	+	IGR	DEL	AA	-	-	rs79211174		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:79345222_79345223delAA								None (None upstream) : PKIA (83113 downstream)																																			---	---	---	---
PKIA	5569	broad.mit.edu	37	8	79501511	79501511	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:79501511delA	uc003yba.2	+						PKIA_uc003ybb.2_Intron|PKIA_uc010lzo.2_5'Flank	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	80144464	80144465	+	IGR	DEL	AA	-	-	rs146562190		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:80144464_80144465delAA								IL7 (426706 upstream) : STMN2 (378915 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	80174693	80174693	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:80174693delG								IL7 (456935 upstream) : STMN2 (348687 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	80824193	80824194	+	IGR	DEL	AA	-	-	rs34732424		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:80824193_80824194delAA								HEY1 (144095 upstream) : MRPS28 (6902 downstream)																																			---	---	---	---
TPD52	7163	broad.mit.edu	37	8	80999371	80999371	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:80999371delT	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	81504989	81504992	+	IGR	DEL	AAAA	-	-	rs67010834		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81504989_81504992delAAAA								ZBTB10 (70381 upstream) : ZNF704 (45777 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	81523178	81523178	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81523178delA								ZBTB10 (88570 upstream) : ZNF704 (27591 downstream)																																			---	---	---	---
ZNF704	619279	broad.mit.edu	37	8	81632829	81632829	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81632829delT	uc003yby.1	-							NM_001033723	NP_001028895			zinc finger protein 704							intracellular	zinc ion binding				0	all_cancers(3;8.53e-08)|all_epithelial(4;4.59e-10)|Breast(3;2.56e-06)|Lung NSC(7;2.58e-06)|all_lung(9;9.4e-06)		BRCA - Breast invasive adenocarcinoma(6;0.00401)|Epithelial(68;0.00448)|all cancers(69;0.0277)															---	---	---	---
ZNF704	619279	broad.mit.edu	37	8	81664550	81664550	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81664550delA	uc003yby.1	-							NM_001033723	NP_001028895			zinc finger protein 704							intracellular	zinc ion binding				0	all_cancers(3;8.53e-08)|all_epithelial(4;4.59e-10)|Breast(3;2.56e-06)|Lung NSC(7;2.58e-06)|all_lung(9;9.4e-06)		BRCA - Breast invasive adenocarcinoma(6;0.00401)|Epithelial(68;0.00448)|all cancers(69;0.0277)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	81856483	81856483	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81856483delT								ZNF704 (69467 upstream) : PAG1 (23565 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	81871483	81871484	+	IGR	INS	-	GT	GT	rs147587663	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81871483_81871484insGT								ZNF704 (84467 upstream) : PAG1 (8564 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	82054474	82054474	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82054474delT								PAG1 (30171 upstream) : FABP5 (138311 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	82163965	82163965	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82163965delA								PAG1 (139662 upstream) : FABP5 (28820 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	82293991	82293991	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82293991delT								FABP5 (96983 upstream) : PMP2 (58573 downstream)																																			---	---	---	---
FABP12	646486	broad.mit.edu	37	8	82444179	82444180	+	5'Flank	DEL	CA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82444179_82444180delCA	uc011lfp.1	-						FABP12_uc003ycg.3_5'Flank	NM_001105281	NP_001098751			fatty acid binding protein 12								lipid binding|transporter activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	82530375	82530375	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82530375delT								FABP12 (86825 upstream) : IMPA1 (38776 downstream)																																			---	---	---	---
IMPA1	3612	broad.mit.edu	37	8	82577133	82577133	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82577133delA	uc003ych.2	-						IMPA1_uc011lfq.1_Intron|IMPA1_uc011lfr.1_Intron	NM_005536	NP_005527			inositol(myo)-1(or 4)-monophosphatase 1 isoform						inositol phosphate dephosphorylation|phosphatidylinositol biosynthetic process|signal transduction	cytoplasm	inositol-1(or 4)-monophosphatase activity|metal ion binding|protein homodimerization activity			skin(1)	1					Lithium(DB01356)													---	---	---	---
IMPA1	3612	broad.mit.edu	37	8	82590361	82590361	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82590361delA	uc003ych.2	-						IMPA1_uc011lfq.1_Intron|IMPA1_uc011lfr.1_Intron	NM_005536	NP_005527			inositol(myo)-1(or 4)-monophosphatase 1 isoform						inositol phosphate dephosphorylation|phosphatidylinositol biosynthetic process|signal transduction	cytoplasm	inositol-1(or 4)-monophosphatase activity|metal ion binding|protein homodimerization activity			skin(1)	1					Lithium(DB01356)													---	---	---	---
Unknown	0	broad.mit.edu	37	8	82790373	82790374	+	IGR	INS	-	T	T	rs142041158	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82790373_82790374insT								SNX16 (35852 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	83116512	83116512	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:83116512delA								SNX16 (361991 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	83577831	83577831	+	IGR	DEL	A	-	-	rs111518211		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:83577831delA								SNX16 (823310 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	83744049	83744049	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:83744049delT								SNX16 (989528 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	84515633	84515634	+	IGR	INS	-	A	A	rs138569811	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:84515633_84515634insA								None (None upstream) : RALYL (579819 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	84720518	84720518	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:84720518delT								None (None upstream) : RALYL (374935 downstream)																																			---	---	---	---
RALYL	138046	broad.mit.edu	37	8	85748085	85748085	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:85748085delT	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																		---	---	---	---
RALYL	138046	broad.mit.edu	37	8	85833110	85833110	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:85833110delT	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																		---	---	---	---
CA13	377677	broad.mit.edu	37	8	86196369	86196369	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86196369delT	uc003ydf.1	+											Homo sapiens cDNA FLJ36434 fis, clone THYMU2012002.						one-carbon metabolic process		carbonate dehydratase activity|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	86498127	86498129	+	IGR	DEL	TTT	-	-	rs71720439		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86498127_86498129delTTT								CA2 (104406 upstream) : REXO1L1 (70435 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	87100614	87100614	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87100614delT								PSKH2 (18763 upstream) : ATP6V0D2 (10525 downstream)																																			---	---	---	---
WWP1	11059	broad.mit.edu	37	8	87421139	87421139	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87421139delA	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																		---	---	---	---
WWP1	11059	broad.mit.edu	37	8	87476299	87476299	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87476299delA	uc003ydt.2	+							NM_007013	NP_008944			WW domain containing E3 ubiquitin protein ligase						central nervous system development|entry of virus into host cell|negative regulation of transcription, DNA-dependent|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|signal transduction	cytoplasm|nucleus|plasma membrane|ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity			lung(1)|liver(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	87806449	87806450	+	IGR	INS	-	T	T	rs138146503	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87806449_87806450insT								CNGB3 (50548 upstream) : CNBD1 (72226 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	87866612	87866613	+	IGR	DEL	TT	-	-	rs71556415		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87866612_87866613delTT								CNGB3 (110711 upstream) : CNBD1 (12063 downstream)																																			---	---	---	---
CNBD1	168975	broad.mit.edu	37	8	88210713	88210713	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:88210713delA	uc003ydy.2	+							NM_173538	NP_775809			cyclic nucleotide binding domain containing 1											ovary(3)	3																		---	---	---	---
MMP16	4325	broad.mit.edu	37	8	89147206	89147206	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:89147206delA	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	89803992	89803992	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:89803992delA								MMP16 (464275 upstream) : RIPK2 (965983 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	90591898	90591898	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:90591898delA								None (None upstream) : RIPK2 (178077 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	90811110	90811110	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:90811110delA								RIPK2 (7819 upstream) : OSGIN2 (102986 downstream)																																			---	---	---	---
OSGIN2	734	broad.mit.edu	37	8	90924973	90924974	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:90924973_90924974delAA	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	91141251	91141252	+	IGR	DEL	AA	-	-	rs909190	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:91141251_91141252delAA								CALB1 (33564 upstream) : TMEM64 (492971 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	91193620	91193620	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:91193620delT								CALB1 (85933 upstream) : TMEM64 (440603 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	91369218	91369218	+	IGR	DEL	A	-	-	rs67971352		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:91369218delA								CALB1 (261531 upstream) : TMEM64 (265005 downstream)																																			---	---	---	---
NECAB1	64168	broad.mit.edu	37	8	91884332	91884332	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:91884332delT	uc011lgg.1	+							NM_022351	NP_071746			N-terminal EF-hand calcium binding protein 1						antibiotic biosynthetic process	cytoplasm	calcium ion binding|oxidoreductase activity			central_nervous_system(1)	1			BRCA - Breast invasive adenocarcinoma(11;0.0499)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	92957239	92957239	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:92957239delA								SLC26A7 (546859 upstream) : RUNX1T1 (13913 downstream)																																			---	---	---	---
RUNX1T1	862	broad.mit.edu	37	8	92996986	92996986	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:92996986delT	uc003yfd.2	-						RUNX1T1_uc003yfc.1_Intron|RUNX1T1_uc003yfe.1_Intron|RUNX1T1_uc010mao.2_Intron|RUNX1T1_uc011lgi.1_Intron|RUNX1T1_uc010man.1_Intron|RUNX1T1_uc003yfb.1_Intron	NM_175634	NP_783552			acute myelogenous leukemia 1 translocation 1						generation of precursor metabolites and energy	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(9)|large_intestine(3)|breast(2)|central_nervous_system(1)|pancreas(1)	16			BRCA - Breast invasive adenocarcinoma(11;0.0141)															---	---	---	---
RUNX1T1	862	broad.mit.edu	37	8	93088386	93088386	+	5'Flank	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93088386delA	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	93097034	93097035	+	Intron	DEL	GA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93097034_93097035delGA	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	93151581	93151581	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93151581delT								RUNX1T1 (43875 upstream) : C8orf83 (744284 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	93186792	93186792	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93186792delA								RUNX1T1 (79086 upstream) : C8orf83 (709073 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	93282475	93282475	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93282475delT								RUNX1T1 (174769 upstream) : C8orf83 (613390 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	93474396	93474396	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93474396delT								RUNX1T1 (366690 upstream) : C8orf83 (421469 downstream)																																			---	---	---	---
C8orf83	286144	broad.mit.edu	37	8	93976122	93976122	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93976122delA	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|C8orf83_uc003yfs.2_Intron	NR_015339				RecName: Full=UPF0599 protein C8orf83;							endoplasmic reticulum membrane|integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	94462035	94462035	+	IGR	DEL	A	-	-	rs77531634		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94462035delA								C8orf83 (432134 upstream) : FAM92A1 (250738 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	94514652	94514652	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94514652delT								C8orf83 (484751 upstream) : FAM92A1 (198121 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	94625618	94625618	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94625618delT								C8orf83 (595717 upstream) : FAM92A1 (87155 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	94641807	94641807	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94641807delG								C8orf83 (611906 upstream) : FAM92A1 (70966 downstream)																																			---	---	---	---
RBM12B	389677	broad.mit.edu	37	8	94745548	94745548	+	3'UTR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94745548delA	uc003yfz.2	-	3						NM_203390	NP_976324			RNA binding motif protein 12B								nucleotide binding|RNA binding				0	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.0168)															---	---	---	---
TMEM67	91147	broad.mit.edu	37	8	94777890	94777890	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94777890delT	uc011lgk.1	+						TMEM67_uc010mat.1_Intron|TMEM67_uc010maw.2_Intron|TMEM67_uc003yga.3_Intron	NM_153704	NP_714915			meckelin isoform 1						cilium assembly|ER-associated protein catabolic process|negative regulation of centrosome duplication	centrosome|cilium membrane|cytoplasmic vesicle membrane|endoplasmic reticulum membrane|integral to membrane|microtubule basal body	unfolded protein binding			ovary(2)	2	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.00896)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	94913324	94913325	+	IGR	INS	-	GT	GT	rs150256813	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94913324_94913325insGT								TMEM67 (82978 upstream) : PDP1 (15758 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	94969529	94969529	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94969529delT								PDP1 (31235 upstream) : CDH17 (169865 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	95094334	95094335	+	IGR	DEL	GA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95094334_95094335delGA								PDP1 (156040 upstream) : CDH17 (45059 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	95294742	95294742	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95294742delA								GEM (20185 upstream) : RAD54B (89447 downstream)																																			---	---	---	---
RAD54B	25788	broad.mit.edu	37	8	95488358	95488358	+	5'Flank	DEL	A	-	-	rs77567058		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95488358delA	uc003ygk.2	-						RAD54B_uc003ygl.1_5'Flank|RAD54B_uc003ygn.1_5'Flank	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	95558283	95558283	+	Intron	DEL	A	-	-	rs79927793		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95558283delA	uc003ygo.1	-						KIAA1429_uc003ygp.2_Intron	NM_015496	NP_056311			hypothetical protein LOC25962 isoform 1						mRNA processing|RNA splicing	nucleus				ovary(1)|skin(1)	2	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)															---	---	---	---
DPY19L4	286148	broad.mit.edu	37	8	95759954	95759954	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95759954delT	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	95805088	95805089	+	3'UTR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95805088_95805089insA	uc003ygx.2	+	19						NM_181787	NP_861452			dpy-19-like 4							integral to membrane				ovary(2)	2	Breast(36;3.85e-06)																	---	---	---	---
C8orf37	157657	broad.mit.edu	37	8	96261885	96261887	+	Intron	DEL	AAA	-	-	rs76478327		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96261885_96261887delAAA	uc003yho.1	-							NM_177965	NP_808880			hypothetical protein LOC157657												0	Breast(36;3.41e-05)																	---	---	---	---
Unknown	0	broad.mit.edu	37	8	96420190	96420190	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96420190delC								C8orf37 (138753 upstream) : GDF6 (734370 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	96749367	96749367	+	IGR	DEL	G	-	-	rs137885552		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96749367delG								C8orf37 (467930 upstream) : GDF6 (405193 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	96917457	96917457	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96917457delA								C8orf37 (636020 upstream) : GDF6 (237103 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	96977957	96977964	+	IGR	DEL	AGGGAAGG	-	-	rs67336860		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96977957_96977964delAGGGAAGG								C8orf37 (696520 upstream) : GDF6 (176596 downstream)																																			---	---	---	---
PTDSS1	9791	broad.mit.edu	37	8	97319052	97319053	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97319052_97319053insT	uc003yht.1	+						PTDSS1_uc003yhu.1_Intron	NM_014754	NP_055569			phosphatidylserine synthase 1						phosphatidylserine biosynthetic process	integral to membrane	transferase activity			ovary(1)	1	Breast(36;6.18e-05)				Phosphatidylserine(DB00144)													---	---	---	---
Unknown	0	broad.mit.edu	37	8	97452638	97452638	+	IGR	DEL	A	-	-	rs35358515		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97452638delA								PTDSS1 (105864 upstream) : SDC2 (53244 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	97492575	97492575	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97492575delT								PTDSS1 (145801 upstream) : SDC2 (13307 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	97629818	97629818	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97629818delT								SDC2 (5781 upstream) : PGCP (27681 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	97639975	97639975	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97639975delT								SDC2 (15938 upstream) : PGCP (17524 downstream)																																			---	---	---	---
PGCP	10404	broad.mit.edu	37	8	97936038	97936038	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97936038delA	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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	8	98211025	98211025	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98211025delA								PGCP (55304 upstream) : TSPYL5 (74690 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	98240142	98240143	+	IGR	INS	-	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98240142_98240143insG								PGCP (84421 upstream) : TSPYL5 (45572 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	98274985	98274985	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98274985delG								PGCP (119264 upstream) : TSPYL5 (10730 downstream)																																			---	---	---	---
MTDH	92140	broad.mit.edu	37	8	98697990	98697992	+	Intron	DEL	AAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98697990_98697992delAAA	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)															---	---	---	---
MTDH	92140	broad.mit.edu	37	8	98698791	98698791	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98698791delT	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)															---	---	---	---
MTDH	92140	broad.mit.edu	37	8	98730755	98730755	+	Intron	DEL	T	-	-	rs111793423		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98730755delT	uc003yhz.2	+						MTDH_uc010mbf.2_Intron	NM_178812	NP_848927			metadherin						lipopolysaccharide-mediated signaling pathway|negative regulation of apoptosis|negative regulation of transcription from RNA polymerase II promoter|positive regulation of angiogenesis|positive regulation of autophagy|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of protein kinase B signaling cascade	apical plasma membrane|endoplasmic reticulum membrane|integral to membrane|intercellular canaliculus|nuclear body|nuclear membrane|nucleolus|perinuclear region of cytoplasm|tight junction	NF-kappaB binding|RNA polymerase II transcription factor binding|transcription coactivator activity			liver(1)|central_nervous_system(1)	2	Breast(36;2.56e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.178)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	98870481	98870486	+	IGR	DEL	TTTTTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98870481_98870486delTTTTTT								LAPTM4B (5652 upstream) : MATN2 (10825 downstream)																																			---	---	---	---
MATN2	4147	broad.mit.edu	37	8	98927391	98927391	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98927391delT	uc003yic.2	+						MATN2_uc003yib.1_Intron|MATN2_uc010mbh.1_Intron|MATN2_uc003yid.2_Intron|MATN2_uc003yie.1_Intron	NM_002380	NP_002371			matrilin 2 isoform a precursor							proteinaceous extracellular matrix	calcium ion binding			ovary(2)	2	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)															---	---	---	---
POP1	10940	broad.mit.edu	37	8	99148630	99148631	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99148630_99148631delAA	uc003yij.3	+						POP1_uc011lgv.1_Intron|POP1_uc003yik.2_Intron	NM_001145860	NP_001139332			processing of precursor 1						tRNA 5'-leader removal|tRNA catabolic process	nucleolar ribonuclease P complex|ribonuclease MRP complex	identical protein binding|ribonuclease MRP activity|ribonuclease P activity			ovary(1)|breast(1)	2	Breast(36;1.78e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.145)															---	---	---	---
NIPAL2	79815	broad.mit.edu	37	8	99279556	99279558	+	Intron	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99279556_99279558delTTT	uc003yil.1	-						NIPAL2_uc003yim.1_Intron	NM_024759	NP_079035			NIPA-like domain containing 2							integral to membrane					0																		---	---	---	---
NIPAL2	79815	broad.mit.edu	37	8	99282250	99282250	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99282250delT	uc003yil.1	-						NIPAL2_uc003yim.1_Intron	NM_024759	NP_079035			NIPA-like domain containing 2							integral to membrane					0																		---	---	---	---
STK3	6788	broad.mit.edu	37	8	99607998	99607998	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99607998delA	uc003yip.2	-						STK3_uc003yio.2_Intron|STK3_uc010mbm.1_Intron	NM_006281	NP_006272			serine/threonine kinase 3						apoptosis|hippo signaling cascade|intracellular protein kinase cascade|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of apoptosis	cytoplasm|nucleus	ATP binding|magnesium ion binding|protein dimerization activity|protein serine/threonine kinase activator activity|protein serine/threonine kinase activity			lung(3)|ovary(1)	4	Breast(36;2.4e-06)	Breast(495;0.106)	OV - Ovarian serous cystadenocarcinoma(57;0.0382)	KIRC - Kidney renal clear cell carcinoma(542;9.44e-06)														---	---	---	---
STK3	6788	broad.mit.edu	37	8	99771869	99771870	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99771869_99771870delAA	uc003yip.2	-						STK3_uc003yio.2_Intron|STK3_uc010mbm.1_Intron	NM_006281	NP_006272			serine/threonine kinase 3						apoptosis|hippo signaling cascade|intracellular protein kinase cascade|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of apoptosis	cytoplasm|nucleus	ATP binding|magnesium ion binding|protein dimerization activity|protein serine/threonine kinase activator activity|protein serine/threonine kinase activity			lung(3)|ovary(1)	4	Breast(36;2.4e-06)	Breast(495;0.106)	OV - Ovarian serous cystadenocarcinoma(57;0.0382)	KIRC - Kidney renal clear cell carcinoma(542;9.44e-06)														---	---	---	---
STK3	6788	broad.mit.edu	37	8	99944414	99944414	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99944414delA	uc003yio.2	-							NM_006281	NP_006272			serine/threonine kinase 3						apoptosis|hippo signaling cascade|intracellular protein kinase cascade|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of apoptosis	cytoplasm|nucleus	ATP binding|magnesium ion binding|protein dimerization activity|protein serine/threonine kinase activator activity|protein serine/threonine kinase activity			lung(3)|ovary(1)	4	Breast(36;2.4e-06)	Breast(495;0.106)	OV - Ovarian serous cystadenocarcinoma(57;0.0382)	KIRC - Kidney renal clear cell carcinoma(542;9.44e-06)														---	---	---	---
VPS13B	157680	broad.mit.edu	37	8	100267284	100267284	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100267284delT	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	100611140	100611140	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100611140delA	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	100827189	100827189	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100827189delA	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	100832521	100832521	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100832521delT	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	100918990	100918993	+	IGR	DEL	TTTC	-	-	rs143602870	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100918990_100918993delTTTC								COX6C (13095 upstream) : RGS22 (54283 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	101425296	101425298	+	IGR	DEL	TTT	-	-	rs10714702		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101425296_101425298delTTT								RNF19A (102969 upstream) : ANKRD46 (96689 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	101438731	101438733	+	IGR	DEL	TGT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101438731_101438733delTGT								RNF19A (116404 upstream) : ANKRD46 (83254 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	101439017	101439018	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101439017_101439018insT								RNF19A (116690 upstream) : ANKRD46 (82969 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	101865786	101865786	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101865786delA								PABPC1 (131471 upstream) : YWHAZ (65018 downstream)																																			---	---	---	---
YWHAZ	7534	broad.mit.edu	37	8	101942277	101942278	+	Intron	INS	-	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101942277_101942278insG	uc011lhe.1	-						YWHAZ_uc003yjv.2_Intron|YWHAZ_uc011lhf.1_Intron|YWHAZ_uc003yjw.2_Intron|YWHAZ_uc010mbq.2_Intron|YWHAZ_uc011lhg.1_Intron|YWHAZ_uc010mbr.2_Intron|YWHAZ_uc003yjx.2_Intron|YWHAZ_uc003yjy.2_Intron	NM_001135702	NP_001129174			tyrosine 3/tryptophan 5 -monooxygenase						anti-apoptosis|mRNA metabolic process|platelet activation|signal transduction	cytosol|melanosome	transcription factor binding				0	all_cancers(14;7.43e-06)|all_epithelial(15;2.77e-08)|Lung NSC(17;6.08e-05)|all_lung(17;0.000197)		Epithelial(11;2.79e-11)|all cancers(13;5.45e-09)|OV - Ovarian serous cystadenocarcinoma(57;4.75e-05)		Ginkgo biloba(DB01381)													---	---	---	---
Unknown	0	broad.mit.edu	37	8	102010440	102010441	+	IGR	INS	-	TAC	TAC	rs145278492	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102010440_102010441insTAC								YWHAZ (44817 upstream) : ZNF706 (198827 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	102487861	102487861	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102487861delA								NACAP1 (102926 upstream) : GRHL2 (16807 downstream)																																			---	---	---	---
GRHL2	79977	broad.mit.edu	37	8	102636764	102636778	+	Intron	DEL	AGTACACAGTAGGAC	-	-	rs72219256		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102636764_102636778delAGTACACAGTAGGAC	uc010mbu.2	+							NM_024915	NP_079191			transcription factor CP2-like 3							cytoplasm|nucleus	DNA binding			ovary(2)|skin(1)	3	all_cancers(14;4.39e-08)|all_epithelial(15;4.09e-10)|Lung NSC(17;7.11e-06)|all_lung(17;1.44e-05)		Epithelial(11;5.81e-09)|all cancers(13;3.81e-07)|OV - Ovarian serous cystadenocarcinoma(57;0.000213)															---	---	---	---
NCALD	83988	broad.mit.edu	37	8	102840837	102840837	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102840837delT	uc003ykf.2	-						NCALD_uc003ykg.2_Intron|NCALD_uc003ykh.2_Intron|NCALD_uc003yki.2_Intron|NCALD_uc003ykj.2_Intron|NCALD_uc003ykk.2_Intron|NCALD_uc003ykl.2_Intron	NM_001040628	NP_001035718			neurocalcin delta						synaptic transmission|vesicle-mediated transport	clathrin coat of trans-Golgi network vesicle|cytosol	actin binding|calcium ion binding|clathrin binding|tubulin binding				0	all_cancers(14;8.94e-08)|all_epithelial(15;7.03e-10)|Lung NSC(17;1.36e-05)|all_lung(17;2.7e-05)		all cancers(13;1.09e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000699)															---	---	---	---
NCALD	83988	broad.mit.edu	37	8	103112308	103112308	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103112308delA	uc003ykf.2	-						NCALD_uc003ykg.2_Intron|NCALD_uc003ykh.2_Intron|NCALD_uc003yki.2_Intron|NCALD_uc003ykj.2_Intron|NCALD_uc003ykk.2_Intron|NCALD_uc003ykl.2_Intron	NM_001040628	NP_001035718			neurocalcin delta						synaptic transmission|vesicle-mediated transport	clathrin coat of trans-Golgi network vesicle|cytosol	actin binding|calcium ion binding|clathrin binding|tubulin binding				0	all_cancers(14;8.94e-08)|all_epithelial(15;7.03e-10)|Lung NSC(17;1.36e-05)|all_lung(17;2.7e-05)		all cancers(13;1.09e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000699)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	103187912	103187919	+	IGR	DEL	GAGAGAGA	-	-	rs113960971		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103187912_103187919delGAGAGAGA								NCALD (50777 upstream) : RRM2B (28813 downstream)																																			---	---	---	---
UBR5	51366	broad.mit.edu	37	8	103270059	103270060	+	Intron	INS	-	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103270059_103270060insG	uc003ykr.1	-						UBR5_uc003yks.1_Intron|UBR5_uc003ykq.2_Intron	NM_015902	NP_056986			ubiquitin protein ligase E3 component n-recognin						cell proliferation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of catenin import into nucleus|positive regulation of protein import into nucleus, translocation|progesterone receptor signaling pathway|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to DNA damage stimulus	nucleus|soluble fraction	protein binding|RNA binding|ubiquitin-ubiquitin ligase activity|zinc ion binding			lung(16)|ovary(4)|large_intestine(3)|breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)	28	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000442)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	103477862	103477863	+	IGR	INS	-	T	T	rs149183226	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103477862_103477863insT								UBR5 (53367 upstream) : ODF1 (85985 downstream)																																			---	---	---	---
ODF1	4956	broad.mit.edu	37	8	103568656	103568663	+	Intron	DEL	TTGTTGTT	-	-	rs141819674	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103568656_103568663delTTGTTGTT	uc003ykt.2	+							NM_024410	NP_077721			outer dense fiber of sperm tails 1						cell differentiation|multicellular organismal development|spermatogenesis	outer dense fiber	structural molecule activity			ovary(2)	2	all_cancers(14;2.76e-05)|all_epithelial(15;4.54e-08)|Lung NSC(17;4.08e-05)|all_lung(17;9.15e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000125)|STAD - Stomach adenocarcinoma(118;0.0826)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	103708471	103708471	+	IGR	DEL	C	-	-	rs78994539	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103708471delC								KLF10 (40488 upstream) : AZIN1 (130066 downstream)																																			---	---	---	---
ATP6V1C1	528	broad.mit.edu	37	8	104037272	104037275	+	Intron	DEL	GTGT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104037272_104037275delGTGT	uc003ykz.3	+						ATP6V1C1_uc010mbz.2_Intron|ATP6V1C1_uc003yla.2_Intron|ATP6V1C1_uc011lhl.1_Intron	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)															---	---	---	---
ATP6V1C1	528	broad.mit.edu	37	8	104044077	104044077	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104044077delA	uc003ykz.3	+						ATP6V1C1_uc010mbz.2_Intron|ATP6V1C1_uc003yla.2_Intron|ATP6V1C1_uc011lhl.1_Intron	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)															---	---	---	---
DCAF13	25879	broad.mit.edu	37	8	104439487	104439487	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	104456354	104456354	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104456354delT								DCAF13 (676 upstream) : RIMS2 (56622 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	104474180	104474181	+	5'Flank	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104474180_104474181delTT	uc010mce.1	+											Homo sapiens mRNA; cDNA DKFZp686E23222 (from clone DKFZp686E23222).																														---	---	---	---
RIMS2	9699	broad.mit.edu	37	8	105008524	105008524	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105008524delA	uc003yls.2	+						RIMS2_uc003ylp.2_Intron|RIMS2_uc003ylw.2_Intron|RIMS2_uc003ylq.2_Intron|RIMS2_uc003ylr.2_Intron	NM_014677	NP_055492			regulating synaptic membrane exocytosis 2						intracellular protein transport	cell junction|presynaptic membrane	metal ion binding|Rab GTPase binding			ovary(6)|lung(2)|breast(2)|skin(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	15			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)												HNSCC(12;0.0054)			---	---	---	---
RIMS2	9699	broad.mit.edu	37	8	105170345	105170345	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105170345delA	uc003yls.2	+						RIMS2_uc003ylp.2_Intron|RIMS2_uc003ylw.2_Intron|RIMS2_uc003ylq.2_Intron|RIMS2_uc003ylr.2_Intron	NM_014677	NP_055492			regulating synaptic membrane exocytosis 2						intracellular protein transport	cell junction|presynaptic membrane	metal ion binding|Rab GTPase binding			ovary(6)|lung(2)|breast(2)|skin(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	15			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)												HNSCC(12;0.0054)			---	---	---	---
DPYS	1807	broad.mit.edu	37	8	105404154	105404154	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105404154delA	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	105545310	105545310	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105545310delA	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	105798208	105798208	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105798208delA								LRP12 (196988 upstream) : ZFPM2 (532939 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	105822243	105822244	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105822243_105822244insT								LRP12 (221023 upstream) : ZFPM2 (508903 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	105843533	105843533	+	IGR	DEL	A	-	-	rs75368349		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105843533delA								LRP12 (242313 upstream) : ZFPM2 (487614 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	106007876	106007877	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:106007876_106007877delTT								LRP12 (406656 upstream) : ZFPM2 (323270 downstream)																																			---	---	---	---
ZFPM2	23414	broad.mit.edu	37	8	106477366	106477366	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:106477366delA	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	106663694	106663694	+	Intron	DEL	A	-	-	rs35055314		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:106663694delA	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	106721426	106721426	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:106721426delT	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	106740182	106740183	+	Intron	INS	-	A	A	rs74437452		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:106740182_106740183insA	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	106825025	106825025	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:106825025delA								ZFPM2 (8260 upstream) : OXR1 (457448 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	107028544	107028544	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:107028544delA								ZFPM2 (211779 upstream) : OXR1 (253929 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	107064229	107064234	+	IGR	DEL	CACACG	-	-	rs66805605		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:107064229_107064234delCACACG								ZFPM2 (247464 upstream) : OXR1 (218239 downstream)																																			---	---	---	---
OXR1	55074	broad.mit.edu	37	8	107384636	107384636	+	Intron	DEL	T	-	-	rs113406678		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:107384636delT	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	107410277	107410278	+	Intron	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:107410277_107410278delTG	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	107697925	107697926	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:107697925_107697926delAA	uc011lht.1	+						OXR1_uc003ymf.2_Intron|OXR1_uc011lhu.1_Intron|OXR1_uc010mcg.2_Intron|OXR1_uc003ymg.1_Intron|OXR1_uc003ymi.1_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	107938347	107938347	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:107938347delT								ABRA (155875 upstream) : ANGPT1 (323364 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	108169729	108169730	+	IGR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:108169729_108169730insA								ABRA (387257 upstream) : ANGPT1 (91981 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	108600300	108600300	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:108600300delG								ANGPT1 (90046 upstream) : RSPO2 (311245 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	108814878	108814879	+	IGR	INS	-	A	A	rs34121729		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:108814878_108814879insA								ANGPT1 (304624 upstream) : RSPO2 (96666 downstream)																																			---	---	---	---
RSPO2	340419	broad.mit.edu	37	8	108937051	108937054	+	Intron	DEL	CACA	-	-	rs146856025		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:108937051_108937054delCACA	uc003yms.2	-						RSPO2_uc003ymq.2_Intron|RSPO2_uc003ymr.2_Intron	NM_178565	NP_848660			R-spondin family, member 2 precursor						Wnt receptor signaling pathway	extracellular region	heparin binding			skin(3)|ovary(2)|pancreas(1)|lung(1)	7			OV - Ovarian serous cystadenocarcinoma(57;1.55e-09)															---	---	---	---
RSPO2	340419	broad.mit.edu	37	8	109013980	109013980	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109013980delA	uc003yms.2	-						RSPO2_uc003ymq.2_Intron|RSPO2_uc003ymr.2_Intron	NM_178565	NP_848660			R-spondin family, member 2 precursor						Wnt receptor signaling pathway	extracellular region	heparin binding			skin(3)|ovary(2)|pancreas(1)|lung(1)	7			OV - Ovarian serous cystadenocarcinoma(57;1.55e-09)															---	---	---	---
RSPO2	340419	broad.mit.edu	37	8	109054809	109054809	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109054809delA	uc003yms.2	-						RSPO2_uc003ymq.2_Intron|RSPO2_uc003ymr.2_Intron	NM_178565	NP_848660			R-spondin family, member 2 precursor						Wnt receptor signaling pathway	extracellular region	heparin binding			skin(3)|ovary(2)|pancreas(1)|lung(1)	7			OV - Ovarian serous cystadenocarcinoma(57;1.55e-09)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	109211743	109211743	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109211743delG								RSPO2 (115830 upstream) : EIF3E (2230 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	109540755	109540756	+	IGR	DEL	GA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109540755_109540756delGA								TTC35 (41619 upstream) : TMEM74 (78324 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	110051501	110051502	+	IGR	DEL	TG	-	-	rs72321831		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110051501_110051502delTG								TMEM74 (251731 upstream) : TRHR (48237 downstream)																																			---	---	---	---
PKHD1L1	93035	broad.mit.edu	37	8	110397975	110397975	+	Intron	DEL	T	-	-	rs11987766	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110397975delT	uc003yne.2	+							NM_177531	NP_803875			fibrocystin L precursor						immune response	cytosol|extracellular space|integral to membrane	receptor activity			ovary(9)|central_nervous_system(2)|large_intestine(1)|breast(1)|pancreas(1)	14			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)												HNSCC(38;0.096)			---	---	---	---
Unknown	0	broad.mit.edu	37	8	110737847	110737848	+	IGR	DEL	CG	-	-	rs71513064		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110737847_110737848delCG								SYBU (33827 upstream) : KCNV1 (241387 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	110758405	110758405	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110758405delA								SYBU (54385 upstream) : KCNV1 (220830 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	110801504	110801504	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110801504delT								SYBU (97484 upstream) : KCNV1 (177731 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	111509791	111509791	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:111509791delA								KCNV1 (521715 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	111632346	111632347	+	IGR	DEL	TG	-	-	rs150973904		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:111632346_111632347delTG								KCNV1 (644270 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	111698128	111698129	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:111698128_111698129delTT								KCNV1 (710052 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	111723594	111723595	+	IGR	INS	-	AA	AA			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:111723594_111723595insAA								KCNV1 (735518 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	111954511	111954514	+	IGR	DEL	AAAC	-	-	rs150269040		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:111954511_111954514delAAAC								KCNV1 (966435 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	112382149	112382150	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:112382149_112382150delTT								None (None upstream) : CSMD3 (853011 downstream)																																			---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	114037010	114037010	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:114037010delT	uc003ynu.2	-						CSMD3_uc003ynt.2_Intron|CSMD3_uc011lhx.1_Intron|CSMD3_uc010mcx.1_Intron	NM_198123	NP_937756			CUB and Sushi multiple domains 3 isoform 1							integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63															HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			---	---	---	---
Unknown	0	broad.mit.edu	37	8	114878268	114878269	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:114878268_114878269delAA								CSMD3 (429026 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	115004581	115004582	+	IGR	INS	-	TTTAAG	TTTAAG	rs148741003	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:115004581_115004582insTTTAAG								CSMD3 (555339 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	115172822	115172823	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:115172822_115172823delTT								CSMD3 (723580 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	115215302	115215302	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:115215302delA								CSMD3 (766060 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	115672711	115672711	+	IGR	DEL	T	-	-	rs5894213		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:115672711delT								None (None upstream) : TRPS1 (748014 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	115707891	115707892	+	IGR	DEL	GA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:115707891_115707892delGA								None (None upstream) : TRPS1 (712833 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	116070760	116070761	+	IGR	INS	-	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116070760_116070761insC								None (None upstream) : TRPS1 (349964 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	116168152	116168152	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116168152delA								None (None upstream) : TRPS1 (252573 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	116276162	116276163	+	IGR	DEL	AA	-	-	rs5894246		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116276162_116276163delAA								None (None upstream) : TRPS1 (144562 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	116372053	116372053	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116372053delT								None (None upstream) : TRPS1 (48672 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	116392212	116392218	+	IGR	DEL	AAAAAAG	-	-	rs79550875	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116392212_116392218delAAAAAAG								None (None upstream) : TRPS1 (28507 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	116873024	116873025	+	IGR	DEL	AC	-	-	rs58844559		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116873024_116873025delAC								TRPS1 (191796 upstream) : EIF3H (784031 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	117018825	117018825	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117018825delA								TRPS1 (337597 upstream) : EIF3H (638231 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	117056361	117056361	+	IGR	DEL	C	-	-	rs58369737	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117056361delC								TRPS1 (375133 upstream) : EIF3H (600695 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	117356352	117356352	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117356352delT								TRPS1 (675124 upstream) : EIF3H (300704 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	117362185	117362185	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117362185delA								TRPS1 (680957 upstream) : EIF3H (294871 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	117569056	117569056	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117569056delA								TRPS1 (887828 upstream) : EIF3H (88000 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	117805027	117805027	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117805027delA								UTP23 (18108 upstream) : RAD21 (53147 downstream)																																			---	---	---	---
RAD21	5885	broad.mit.edu	37	8	117858533	117858533	+	3'UTR	DEL	T	-	-	rs16918579		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117858533delT	uc003yod.2	-	14						NM_006265	NP_006256			RAD21 homolog						apoptosis|cell division|chromosome segregation|double-strand break repair|mitotic metaphase/anaphase transition|mitotic prometaphase|protein localization to chromatin|reciprocal meiotic recombination|regulation of transcription from RNA polymerase II promoter	chromosome, centromeric region|cohesin complex|nuclear chromosome|nucleoplasm	protein binding			lung(1)|skin(1)	2	all_cancers(13;1.21e-21)|Lung NSC(37;0.000134)|Ovarian(258;0.0172)																	---	---	---	---
SLC30A8	169026	broad.mit.edu	37	8	118042715	118042715	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118042715delT	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	118044021	118044021	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118044021delC	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	118128812	118128812	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118128812delG	uc010mcz.2	+						SLC30A8_uc011lia.1_Intron|SLC30A8_uc003yog.2_Intron	NM_173851	NP_776250			solute carrier family 30 member 8						insulin secretion|positive regulation of insulin secretion|regulation of sequestering of zinc ion|regulation of vesicle-mediated transport|response to glucose stimulus|sequestering of zinc ion	integral to membrane|plasma membrane|secretory granule membrane|transport vesicle membrane	protein homodimerization activity|zinc ion transmembrane transporter activity			ovary(2)|skin(2)	4	all_cancers(13;2.11e-22)|Lung NSC(37;6.08e-05)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.203)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	118209820	118209820	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118209820delA								SLC30A8 (20868 upstream) : MED30 (323145 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	118357147	118357147	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118357147delA								SLC30A8 (168195 upstream) : MED30 (175818 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	118430582	118430582	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118430582delA								SLC30A8 (241630 upstream) : MED30 (102383 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	118717182	118717183	+	IGR	INS	-	C	C	rs149588030	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118717182_118717183insC								MED30 (164683 upstream) : EXT1 (94419 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	118808897	118808897	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118808897delT								MED30 (256398 upstream) : EXT1 (2705 downstream)																																			---	---	---	---
EXT1	2131	broad.mit.edu	37	8	118994111	118994111	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118994111delA	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	119001872	119001872	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119001872delT	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	119191679	119191679	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119191679delA								EXT1 (67621 upstream) : SAMD12 (10016 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	119201652	119201653	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119201652_119201653insT								EXT1 (77594 upstream) : SAMD12 (42 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	119900279	119900279	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119900279delA								SAMD12 (266045 upstream) : TNFRSF11B (35518 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	120445432	120445432	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120445432delA								NOV (8754 upstream) : ENPP2 (123887 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	120457966	120457966	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120457966delC								NOV (21288 upstream) : ENPP2 (111353 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	120462698	120462698	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120462698delA								NOV (26020 upstream) : ENPP2 (106621 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	120724690	120724690	+	IGR	DEL	A	-	-	rs71571623		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120724690delA								ENPP2 (73584 upstream) : TAF2 (18325 downstream)																																			---	---	---	---
DSCC1	79075	broad.mit.edu	37	8	120856823	120856823	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120856823delT	uc003yov.2	-							NM_024094	NP_076999			defective in sister chromatid cohesion 1						DNA replication|maintenance of mitotic sister chromatid cohesion|post-translational protein acetylation|regulation of DNA replication	chromatin|chromosome, centromeric region|nucleoplasm	DNA binding|protein binding			pancreas(1)	1	Lung NSC(37;9.35e-07)|Ovarian(258;0.011)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)															---	---	---	---
DEPDC6	64798	broad.mit.edu	37	8	120942014	120942014	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120942014delT	uc003yow.3	+						DEPDC6_uc011lid.1_Intron	NM_022783	NP_073620			DEP domain containing 6						intracellular signal transduction|negative regulation of cell size|negative regulation of protein kinase activity|negative regulation of TOR signaling cascade|regulation of apoptosis	intracellular	protein binding				0	Lung NSC(37;9.35e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)															---	---	---	---
DEPDC6	64798	broad.mit.edu	37	8	120944388	120944388	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120944388delT	uc003yow.3	+						DEPDC6_uc011lid.1_Intron	NM_022783	NP_073620			DEP domain containing 6						intracellular signal transduction|negative regulation of cell size|negative regulation of protein kinase activity|negative regulation of TOR signaling cascade|regulation of apoptosis	intracellular	protein binding				0	Lung NSC(37;9.35e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)															---	---	---	---
DEPDC6	64798	broad.mit.edu	37	8	120985185	120985186	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120985185_120985186delTT	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	121298403	121298403	+	Intron	DEL	T	-	-	rs77603140	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121298403delT	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)															---	---	---	---
SNTB1	6641	broad.mit.edu	37	8	121816990	121816990	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121816990delT	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	122116813	122116814	+	IGR	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122116813_122116814delTG								SNTB1 (292504 upstream) : HAS2 (508457 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	122253618	122253618	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122253618delA								SNTB1 (429309 upstream) : HAS2 (371653 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	122266796	122266797	+	IGR	INS	-	TC	TC			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122266796_122266797insTC								SNTB1 (442487 upstream) : HAS2 (358474 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	122664346	122664346	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122664346delA								HAS2AS (7413 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	122666544	122666544	+	IGR	DEL	T	-	-	rs36032424		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122666544delT								HAS2AS (9611 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	122740757	122740757	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122740757delC								HAS2AS (83824 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	123417079	123417080	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123417079_123417080insT								HAS2AS (760146 upstream) : ZHX2 (376821 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	123418923	123418924	+	IGR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123418923_123418924insA								HAS2AS (761990 upstream) : ZHX2 (374977 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	123683643	123683645	+	IGR	DEL	AAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123683643_123683645delAAA								None (None upstream) : ZHX2 (110256 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	123701400	123701401	+	IGR	DEL	AA	-	-	rs35065606		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123701400_123701401delAA								None (None upstream) : ZHX2 (92500 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	123758645	123758645	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123758645delT								None (None upstream) : ZHX2 (35256 downstream)																																			---	---	---	---
ZHX2	22882	broad.mit.edu	37	8	123934565	123934565	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123934565delT	uc003ypk.1	+							NM_014943	NP_055758			zinc fingers and homeoboxes 2							cytoplasm|nucleus|plasma membrane	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|skin(1)	2	Lung NSC(37;2e-09)|Ovarian(258;0.0205)|Hepatocellular(40;0.105)		STAD - Stomach adenocarcinoma(47;0.00527)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	124063929	124063929	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124063929delT								DERL1 (9281 upstream) : WDR67 (20991 downstream)																																			---	---	---	---
C8orf76	84933	broad.mit.edu	37	8	124249024	124249024	+	Intron	DEL	A	-	-	rs34417634		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124249024delA	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)															---	---	---	---
ATAD2	29028	broad.mit.edu	37	8	124388350	124388350	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124388350delA	uc003yqh.3	-						ATAD2_uc011lii.1_Intron|ATAD2_uc003yqi.3_Intron|ATAD2_uc003yqj.2_Intron	NM_014109	NP_054828			ATPase family, AAA domain containing 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	mitochondrion|nucleus	ATP binding|ATPase activity			ovary(2)	2	Lung NSC(37;1.25e-09)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	124475573	124475573	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124475573delT								WDYHV1 (21313 upstream) : FBXO32 (39786 downstream)																																			---	---	---	---
FER1L6	654463	broad.mit.edu	37	8	124895326	124895327	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124895326_124895327insA	uc003yqw.2	+							NM_001039112	NP_001034201			fer-1-like 6							integral to membrane				ovary(5)|skin(5)|central_nervous_system(1)	11	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)															---	---	---	---
FER1L6	654463	broad.mit.edu	37	8	124952596	124952596	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124952596delT	uc003yqw.2	+							NM_001039112	NP_001034201			fer-1-like 6							integral to membrane				ovary(5)|skin(5)|central_nervous_system(1)	11	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)															---	---	---	---
FER1L6	654463	broad.mit.edu	37	8	125072651	125072651	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125072651delA	uc003yqw.2	+						uc003yqy.1_RNA	NM_001039112	NP_001034201			fer-1-like 6							integral to membrane				ovary(5)|skin(5)|central_nervous_system(1)	11	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	125191890	125191891	+	IGR	INS	-	GTGT	GTGT	rs139741594	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125191890_125191891insGTGT								FER1L6 (59589 upstream) : TMEM65 (131270 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	125245012	125245012	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125245012delA								FER1L6 (112711 upstream) : TMEM65 (78149 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	125416794	125416796	+	IGR	DEL	AAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125416794_125416796delAAA								TMEM65 (31854 upstream) : TRMT12 (46252 downstream)																																			---	---	---	---
TATDN1	83940	broad.mit.edu	37	8	125507787	125507787	+	Intron	DEL	A	-	-	rs35308504		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125507787delA	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	125709827	125709828	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125709827_125709828delAA	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	125727590	125727590	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125727590delT	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	125792889	125792892	+	IGR	DEL	TTTT	-	-	rs112804091		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125792889_125792892delTTTT								MTSS1 (52159 upstream) : LOC157381 (158992 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	125863656	125863657	+	IGR	INS	-	TG	TG	rs144053345	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125863656_125863657insTG								MTSS1 (122926 upstream) : LOC157381 (88227 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	125886775	125886776	+	IGR	INS	-	ATTTTAAAG	ATTTTAAAG	rs149134913	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125886775_125886776insATTTTAAAG								MTSS1 (146045 upstream) : LOC157381 (65108 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	125966728	125966729	+	IGR	INS	-	A	A	rs138527022	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125966728_125966729insA								LOC157381 (3391 upstream) : ZNF572 (18810 downstream)																																			---	---	---	---
NSMCE2	286053	broad.mit.edu	37	8	126163397	126163397	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126163397delT	uc003yrw.2	+						NSMCE2_uc003yrv.2_Intron	NM_173685	NP_775956			non-SMC element 2, MMS21 homolog						DNA recombination|DNA repair	nucleus	ligase activity|zinc ion binding			breast(1)	1	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)															---	---	---	---
NSMCE2	286053	broad.mit.edu	37	8	126288014	126288014	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126288014delT	uc003yrw.2	+							NM_173685	NP_775956			non-SMC element 2, MMS21 homolog						DNA recombination|DNA repair	nucleus	ligase activity|zinc ion binding			breast(1)	1	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)															---	---	---	---
NSMCE2	286053	broad.mit.edu	37	8	126317126	126317127	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126317126_126317127delAA	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)															---	---	---	---
TRIB1	10221	broad.mit.edu	37	8	126450058	126450058	+	3'UTR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126450058delA	uc003yrx.2	+	3					TRIB1_uc011lis.1_3'UTR|TRIB1_uc010mdn.2_3'UTR	NM_025195	NP_079471			G-protein-coupled receptor induced protein						JNK cascade|negative regulation of lipopolysaccharide-mediated signaling pathway|negative regulation of protein kinase activity|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of smooth muscle cell migration|negative regulation of smooth muscle cell proliferation|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|regulation of MAP kinase activity|response to lipopolysaccharide	cytoplasm|nucleus	ATP binding|mitogen-activated protein kinase kinase binding|protein kinase activity|protein kinase inhibitor activity|transcription factor binding|ubiquitin protein ligase binding|ubiquitin-protein ligase regulator activity			lung(1)	1	all_hematologic(1;4.97e-05)|Ovarian(258;0.00167)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	126637667	126637671	+	IGR	DEL	AAGGT	-	-	rs137901106		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126637667_126637671delAAGGT								TRIB1 (187025 upstream) : FAM84B (927016 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	126812658	126812659	+	IGR	INS	-	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126812658_126812659insC								TRIB1 (362016 upstream) : FAM84B (752028 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	126827767	126827767	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126827767delA								TRIB1 (377125 upstream) : FAM84B (736920 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	126900854	126900857	+	IGR	DEL	TTTT	-	-	rs142796809		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126900854_126900857delTTTT								TRIB1 (450212 upstream) : FAM84B (663830 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	126929978	126929979	+	IGR	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126929978_126929979delTG								TRIB1 (479336 upstream) : FAM84B (634708 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	127187021	127187021	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127187021delA								TRIB1 (736379 upstream) : FAM84B (377666 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	127753320	127753321	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127753320_127753321delTT								FAM84B (182854 upstream) : LOC727677 (548741 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	127978292	127978292	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127978292delT								FAM84B (407826 upstream) : LOC727677 (323770 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	128180908	128180908	+	IGR	DEL	T	-	-	rs2456457	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128180908delT								FAM84B (610442 upstream) : LOC727677 (121154 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	128762282	128762283	+	IGR	INS	-	TTCT	TTCT	rs150484845	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128762282_128762283insTTCT								MYC (8604 upstream) : PVT1 (44496 downstream)																																			---	---	---	---
PVT1	5820	broad.mit.edu	37	8	129000568	129000569	+	Intron	INS	-	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:129000568_129000569insG	uc010mdq.2	+						PVT1_uc003ysl.2_Intron	NR_003367				Homo sapiens Pvt1 oncogene (non-protein coding), mRNA (cDNA clone IMAGE:5517530), with apparent retained intron.												0																		---	---	---	---
PVT1	5820	broad.mit.edu	37	8	129015122	129015122	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:129015122delT	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	129133643	129133644	+	IGR	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:129133643_129133644delTG								PVT1 (20145 upstream) : MIR1208 (28718 downstream)																																			---	---	---	---
MIR1208	100302281	broad.mit.edu	37	8	129162432	129162433	+	RNA	INS	-	G	G	rs2648841	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:129162432_129162433insG	hsa-mir-1208|MI0006341	+			c.71_72insG																				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	129176955	129176956	+	IGR	INS	-	GT	GT	rs139560017	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:129176955_129176956insGT								MIR1208 (14521 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	129243651	129243652	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:129243651_129243652delTT								MIR1208 (81217 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	129600228	129600228	+	IGR	DEL	T	-	-	rs79948823		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:129600228delT								MIR1208 (437794 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	129970550	129970550	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:129970550delG								MIR1208 (808116 upstream) : GSDMC (789893 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	130564224	130564225	+	IGR	DEL	GT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:130564224_130564225delGT								None (None upstream) : GSDMC (196218 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	131063370	131063370	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131063370delT								FAM49B (34473 upstream) : ASAP1 (983 downstream)																																			---	---	---	---
ASAP1	50807	broad.mit.edu	37	8	131135834	131135837	+	Intron	DEL	AAAC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131135834_131135837delAAAC	uc003yta.1	-						ASAP1_uc003ysz.1_Intron|ASAP1_uc011liw.1_Intron	NM_018482	NP_060952			development and differentiation enhancing factor						cilium morphogenesis|filopodium assembly|regulation of ARF GTPase activity|signal transduction	cytoplasm|membrane	ARF GTPase activator activity|cytoskeletal adaptor activity|SH3 domain binding|zinc ion binding			ovary(4)	4																		---	---	---	---
ASAP1	50807	broad.mit.edu	37	8	131140419	131140420	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131140419_131140420delAA	uc003yta.1	-						ASAP1_uc003ysz.1_Intron|ASAP1_uc011liw.1_Intron	NM_018482	NP_060952			development and differentiation enhancing factor						cilium morphogenesis|filopodium assembly|regulation of ARF GTPase activity|signal transduction	cytoplasm|membrane	ARF GTPase activator activity|cytoskeletal adaptor activity|SH3 domain binding|zinc ion binding			ovary(4)	4																		---	---	---	---
ASAP1	50807	broad.mit.edu	37	8	131143120	131143120	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131143120delA	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	131219341	131219341	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131219341delT	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	131228170	131228171	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131228170_131228171insA	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	131258782	131258783	+	Intron	DEL	CT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131258782_131258783delCT	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	131307586	131307587	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131307586_131307587delTT	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	131311530	131311531	+	Intron	INS	-	AA	AA			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131311530_131311531insAA	uc003yta.1	-						ASAP1_uc011liw.1_Intron|ASAP1IT1_uc003ytc.1_5'Flank	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	131469126	131469132	+	IGR	DEL	TTTTTTT	-	-	rs139545712		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131469126_131469132delTTTTTTT								ASAP1 (54910 upstream) : ADCY8 (323416 downstream)																																			---	---	---	---
ADCY8	114	broad.mit.edu	37	8	131821143	131821145	+	Intron	DEL	CTC	-	-	rs140891148		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131821143_131821145delCTC	uc003ytd.3	-						ADCY8_uc010mds.2_Intron	NM_001115	NP_001106			adenylate cyclase 8						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|membrane fraction|plasma membrane	ATP binding|calcium- and calmodulin-responsive adenylate cyclase activity|metal ion binding			skin(4)|large_intestine(1)|central_nervous_system(1)	6	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)												HNSCC(32;0.087)			---	---	---	---
ADCY8	114	broad.mit.edu	37	8	131858890	131858891	+	Intron	INS	-	TCCT	TCCT	rs148542525	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131858890_131858891insTCCT	uc003ytd.3	-						ADCY8_uc010mds.2_Intron	NM_001115	NP_001106			adenylate cyclase 8						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|membrane fraction|plasma membrane	ATP binding|calcium- and calmodulin-responsive adenylate cyclase activity|metal ion binding			skin(4)|large_intestine(1)|central_nervous_system(1)	6	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)												HNSCC(32;0.087)			---	---	---	---
ADCY8	114	broad.mit.edu	37	8	131882263	131882264	+	Intron	INS	-	C	C	rs141165197	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131882263_131882264insC	uc003ytd.3	-						ADCY8_uc010mds.2_Intron	NM_001115	NP_001106			adenylate cyclase 8						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|membrane fraction|plasma membrane	ATP binding|calcium- and calmodulin-responsive adenylate cyclase activity|metal ion binding			skin(4)|large_intestine(1)|central_nervous_system(1)	6	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)												HNSCC(32;0.087)			---	---	---	---
ADCY8	114	broad.mit.edu	37	8	131888304	131888305	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131888304_131888305delTT	uc003ytd.3	-						ADCY8_uc010mds.2_Intron	NM_001115	NP_001106			adenylate cyclase 8						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|membrane fraction|plasma membrane	ATP binding|calcium- and calmodulin-responsive adenylate cyclase activity|metal ion binding			skin(4)|large_intestine(1)|central_nervous_system(1)	6	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)												HNSCC(32;0.087)			---	---	---	---
Unknown	0	broad.mit.edu	37	8	132099277	132099277	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:132099277delT								ADCY8 (46442 upstream) : EFR3A (817082 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	132160174	132160174	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:132160174delT								ADCY8 (107339 upstream) : EFR3A (756185 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	132580416	132580417	+	IGR	INS	-	T	T	rs61207230		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:132580416_132580417insT								ADCY8 (527581 upstream) : EFR3A (335942 downstream)																																			---	---	---	---
KCNQ3	3786	broad.mit.edu	37	8	133336082	133336082	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133336082delA	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	133388723	133388723	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133388723delT	uc003ytj.2	-						KCNQ3_uc010mdt.2_Intron	NM_004519	NP_004510			potassium voltage-gated channel KQT-like protein						axon guidance|synaptic transmission	voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(2)|breast(1)|central_nervous_system(1)|skin(1)	5	Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	133568946	133568947	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133568946_133568947delTT								KCNQ3 (75942 upstream) : HPYR1 (3798 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	133582158	133582158	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133582158delT								HPYR1 (8432 upstream) : LRRC6 (2290 downstream)																																			---	---	---	---
LRRC6	23639	broad.mit.edu	37	8	133590084	133590085	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133590084_133590085insT	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)															---	---	---	---
LRRC6	23639	broad.mit.edu	37	8	133638295	133638295	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133638295delT	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)															---	---	---	---
LRRC6	23639	broad.mit.edu	37	8	133680932	133680932	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133680932delC	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	133779725	133779728	+	IGR	DEL	TTTT	-	-	rs144086717		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133779725_133779728delTTTT								TMEM71 (6811 upstream) : PHF20L1 (7876 downstream)																																			---	---	---	---
TG	7038	broad.mit.edu	37	8	133950163	133950163	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133950163delT	uc003ytw.2	+						TG_uc010mdw.2_Intron|TG_uc011ljb.1_Intron	NM_003235	NP_003226			thyroglobulin precursor						hormone biosynthetic process|signal transduction|thyroid gland development|thyroid hormone generation	extracellular space	hormone activity			ovary(8)|breast(4)|pancreas(1)|central_nervous_system(1)|skin(1)	15	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)														---	---	---	---
TG	7038	broad.mit.edu	37	8	134011563	134011563	+	Intron	DEL	A	-	-	rs71518145		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134011563delA	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	134237718	134237718	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134237718delG	uc003yub.2	+	4	772	c.696delG	c.(694-696)CTGfs	p.L232fs	WISP1_uc003yuc.2_Frame_Shift_Del_p.L145fs|WISP1_uc010meb.2_Frame_Shift_Del_p.L60fs|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	232	TSP type-1.				cell adhesion|cell-cell signaling|regulation of cell growth|Wnt receptor signaling pathway	extracellular region|soluble fraction	insulin-like growth factor binding			central_nervous_system(1)|kidney(1)	2	all_epithelial(106;5.39e-23)|Lung NSC(106;7.26e-07)|all_lung(105;2.77e-06)|Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0107)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	134406181	134406182	+	IGR	DEL	CT	-	-	rs62518150		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134406181_134406182delCT								NDRG1 (96634 upstream) : ST3GAL1 (60909 downstream)																																			---	---	---	---
ST3GAL1	6482	broad.mit.edu	37	8	134510749	134510749	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134510749delT	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	134675695	134675695	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134675695delT								ST3GAL1 (91512 upstream) : ZFAT (814338 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	134680008	134680008	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134680008delT								ST3GAL1 (95825 upstream) : ZFAT (810025 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	134820596	134820599	+	IGR	DEL	TGTA	-	-	rs71997956		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134820596_134820599delTGTA								ST3GAL1 (236413 upstream) : ZFAT (669434 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	135406157	135406158	+	IGR	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135406157_135406158delAC								ST3GAL1 (821974 upstream) : ZFAT (83875 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	135418701	135418702	+	IGR	DEL	CT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135418701_135418702delCT								ST3GAL1 (834518 upstream) : ZFAT (71331 downstream)																																			---	---	---	---
ZFAT	57623	broad.mit.edu	37	8	135521633	135521633	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135521633delT	uc003yup.2	-						ZFAT_uc011ljj.1_Intron|ZFAT_uc003yun.2_Intron|ZFAT_uc003yuo.2_Intron|ZFAT_uc010meh.2_Intron|ZFAT_uc010mei.2_Intron|ZFAT_uc003yuq.2_Intron|ZFAT_uc010mej.2_Intron	NM_020863	NP_065914			zinc finger protein 406 isoform ZFAT-1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1	all_epithelial(106;8.26e-19)|Lung NSC(106;3.47e-07)|all_lung(105;1.39e-06)|Ovarian(258;0.0102)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0432)															---	---	---	---
ZFAT	57623	broad.mit.edu	37	8	135533266	135533266	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135533266delA	uc003yup.2	-						ZFAT_uc011ljj.1_Intron|ZFAT_uc003yun.2_Intron|ZFAT_uc003yuo.2_Intron|ZFAT_uc010meh.2_Intron|ZFAT_uc010mei.2_Intron|ZFAT_uc003yuq.2_Intron|ZFAT_uc010mej.2_Intron	NM_020863	NP_065914			zinc finger protein 406 isoform ZFAT-1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1	all_epithelial(106;8.26e-19)|Lung NSC(106;3.47e-07)|all_lung(105;1.39e-06)|Ovarian(258;0.0102)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0432)															---	---	---	---
ZFAT	57623	broad.mit.edu	37	8	135607586	135607586	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135607586delT	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|ZFATAS_uc003yus.1_5'Flank	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	135717139	135717139	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135717139delA	uc003yup.2	-						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)															---	---	---	---
KHDRBS3	10656	broad.mit.edu	37	8	136611027	136611027	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136611027delT	uc003yuv.2	+						KHDRBS3_uc003yuw.2_Intron|KHDRBS3_uc010mek.2_Intron	NM_006558	NP_006549			KH domain containing, RNA binding, signal						regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	nucleus	SH3 domain binding			ovary(2)	2	all_epithelial(106;2.85e-16)|all_neural(2;2.72e-06)|Lung NSC(106;3.95e-06)|all_lung(105;1.11e-05)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.247)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	136920301	136920301	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136920301delA								KHDRBS3 (260455 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	136926529	136926529	+	IGR	DEL	A	-	-	rs146635612	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136926529delA								KHDRBS3 (266683 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	137171300	137171300	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:137171300delG								KHDRBS3 (511454 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	137295707	137295707	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:137295707delA								KHDRBS3 (635861 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	137448354	137448354	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:137448354delC								KHDRBS3 (788508 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	137579554	137579554	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:137579554delA								KHDRBS3 (919708 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	138396861	138396861	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:138396861delA								None (None upstream) : FAM135B (745407 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	138494588	138494588	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:138494588delT								None (None upstream) : FAM135B (647680 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	138569951	138569952	+	IGR	INS	-	T	T	rs138847484	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:138569951_138569952insT								None (None upstream) : FAM135B (572316 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	138790846	138790846	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:138790846delT								None (None upstream) : FAM135B (351422 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	138791765	138791765	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:138791765delT								None (None upstream) : FAM135B (350503 downstream)																																			---	---	---	---
FAM135B	51059	broad.mit.edu	37	8	139393071	139393072	+	Intron	DEL	CA	-	-	rs143976086		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139393071_139393072delCA	uc003yuy.2	-						FAM135B_uc003yux.2_Intron|FAM135B_uc003yuz.2_Intron	NM_015912	NP_056996			hypothetical protein LOC51059											ovary(7)|skin(2)	9	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)												HNSCC(54;0.14)			---	---	---	---
COL22A1	169044	broad.mit.edu	37	8	139672833	139672833	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139672833delA	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-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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	139727812	139727821	+	Intron	DEL	TAAAAAAAAA	-	-	rs143920292		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139727812_139727821delTAAAAAAAAA	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	139781182	139781183	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139781182_139781183insA	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	139818559	139818560	+	Intron	DEL	GT	-	-	rs143822953	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139818559_139818560delGT	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	139840645	139840645	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139840645delG	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	140366306	140366306	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140366306delT								COL22A1 (440070 upstream) : KCNK9 (246776 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	140504130	140504130	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140504130delA								COL22A1 (577894 upstream) : KCNK9 (108952 downstream)																																			---	---	---	---
KCNK9	51305	broad.mit.edu	37	8	140709591	140709602	+	Intron	DEL	TGGATGGATGGA	-	-	rs111229425		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140709591_140709602delTGGATGGATGGA	uc003yvf.1	-						KCNK9_uc003yvg.1_Intron	NM_016601	NP_057685			potassium channel, subfamily K, member 9							integral to membrane|membrane fraction	potassium channel activity|voltage-gated ion channel activity			ovary(2)|lung(1)	3	all_cancers(97;3.94e-14)|all_epithelial(106;4.81e-13)|Lung NSC(106;8.18e-05)|all_lung(105;0.00015)|Ovarian(258;0.00235)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;0.134)	BRCA - Breast invasive adenocarcinoma(115;0.0855)															---	---	---	---
TRAPPC9	83696	broad.mit.edu	37	8	141056142	141056143	+	Intron	INS	-	A	A	rs143669048	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141056142_141056143insA	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	141066350	141066350	+	Intron	DEL	A	-	-	rs111833080		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141066350delA	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	141067947	141067947	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141067947delA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	142046946	142046946	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142046946delT								PTK2 (35614 upstream) : DENND3 (91774 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	142939867	142939869	+	IGR	DEL	ATC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142939867_142939869delATC								MIR1302-7 (72193 upstream) : NCRNA00051 (339848 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	142971308	142971309	+	IGR	DEL	GT	-	-	rs72368758		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142971308_142971309delGT								MIR1302-7 (103634 upstream) : NCRNA00051 (308408 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	143118145	143118145	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143118145delT								MIR1302-7 (250471 upstream) : NCRNA00051 (161572 downstream)																																			---	---	---	---
NCRNA00051	619434	broad.mit.edu	37	8	143280375	143280375	+	Intron	DEL	C	-	-	rs7813824	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143280375delC	uc011ljt.1	+							NR_024378				Homo sapiens chromosome 8 open reading frame 43, mRNA (cDNA clone IMAGE:3866356).												0																		---	---	---	---
TSNARE1	203062	broad.mit.edu	37	8	143354435	143354435	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143354435delG	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	143389771	143389771	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143389771delT	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)																	---	---	---	---
PSCA	8000	broad.mit.edu	37	8	143763562	143763562	+	3'UTR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143763562delC	uc003ywu.2	+	3					uc003ywt.1_5'Flank	NM_005672	NP_005663			prostate stem cell antigen preproprotein												0	all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)																	---	---	---	---
Unknown	0	broad.mit.edu	37	8	143891993	143891993	+	IGR	DEL	C	-	-	rs71901785		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143891993delC								LY6D (23985 upstream) : GML (24224 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	144013011	144013011	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144013011delA								CYP11B2 (13752 upstream) : LOC100133669 (50437 downstream)																																			---	---	---	---
C8orf31	286122	broad.mit.edu	37	8	144119817	144119818	+	5'Flank	INS	-	GAGG	GAGG	rs139423336	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144119817_144119818insGAGG	uc003yxp.1	+						C8orf31_uc003yxq.1_5'Flank|C8orf31_uc003yxr.1_5'Flank	NM_173687	NP_775958			hypothetical protein LOC286122											ovary(1)	1	all_cancers(97;1.89e-10)|all_epithelial(106;8.73e-09)|Lung NSC(106;0.000161)|all_lung(105;0.000447)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)																	---	---	---	---
LY6H	4062	broad.mit.edu	37	8	144240077	144240077	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144240077delG	uc011lka.1	-						LY6H_uc011lkb.1_Intron|LY6H_uc003yxt.2_Intron|LY6H_uc011lkc.1_Intron	NM_002347	NP_002338			lymphocyte antigen 6 complex, locus H isoform a						nervous system development|organ morphogenesis	anchored to membrane|plasma membrane					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)																	---	---	---	---
ZFP41	286128	broad.mit.edu	37	8	144330859	144330860	+	Intron	DEL	CA	-	-	rs71297485		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144330859_144330860delCA	uc003yxw.2	+						ZFP41_uc003yxv.2_Intron	NM_173832	NP_776193			zinc finger protein 41 homolog						cell differentiation|multicellular organismal development|regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	all_cancers(97;1.01e-10)|all_epithelial(106;4.6e-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)															---	---	---	---
ZFP41	286128	broad.mit.edu	37	8	144348804	144348804	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144348804delC	uc003yxv.2	+						GLI4_uc003yxx.2_5'Flank	NM_173832				zinc finger protein 41 homolog						cell differentiation|multicellular organismal development|regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	all_cancers(97;1.01e-10)|all_epithelial(106;4.6e-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)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	144361805	144361805	+	IGR	DEL	T	-	-	rs10708609		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144361805delT								ZFP41 (2706 upstream) : ZNF696 (11754 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	144502136	144502145	+	IGR	DEL	GCTGAGCTGG	-	-	rs137886440		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144502136_144502145delGCTGAGCTGG								RHPN1 (35747 upstream) : MAFA (9370 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	144835167	144835178	+	IGR	DEL	TTTTTTTTTTTT	-	-	rs113738497		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144835167_144835178delTTTTTTTTTTTT								FAM83H (19253 upstream) : SCRIB (37912 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	144868046	144868046	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144868046delA								FAM83H (52132 upstream) : SCRIB (5044 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	145129486	145129486	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145129486delT								OPLAH (13902 upstream) : EXOSC4 (4036 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	146132188	146132188	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:146132188delT								COMMD5 (5342 upstream) : ZNF16 (23558 downstream)																																			---	---	---	---
KANK1	23189	broad.mit.edu	37	9	710630	710630	+	Intron	DEL	C	-	-	rs68161748		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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)														---	---	---	---
KANK1	23189	broad.mit.edu	37	9	713812	713813	+	Intron	INS	-	A	A	rs142399753	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:713812_713813insA	uc003zgl.1	+						KANK1_uc003zgm.2_Intron|KANK1_uc003zgn.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	894792	894792	+	Intron	DEL	T	-	-	rs74774770		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:894792delT	uc003zgv.2	+						DMRT1_uc003zgu.1_3'UTR	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	1110615	1110615	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:1110615delT								DMRT2 (53062 upstream) : SMARCA2 (904727 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	1116620	1116621	+	IGR	INS	-	CTCCTCCTCCTT	CTCCTCCTCCTT	rs141460243	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:1116620_1116621insCTCCTCCTCCTT								DMRT2 (59067 upstream) : SMARCA2 (898721 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	1142432	1142433	+	IGR	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:1142432_1142433delTG								DMRT2 (84879 upstream) : SMARCA2 (872909 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	1151650	1151650	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:1151650delA								DMRT2 (94097 upstream) : SMARCA2 (863692 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	1608570	1608570	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:1608570delT								DMRT2 (551017 upstream) : SMARCA2 (406772 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	2906203	2906203	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2906203delT								KIAA0020 (62073 upstream) : RFX3 (318446 downstream)																																			---	---	---	---
RFX3	5991	broad.mit.edu	37	9	3303648	3303649	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:3303648_3303649delAA	uc003zhr.2	-						RFX3_uc010mhd.2_Intron|RFX3_uc003zhs.1_Intron|RFX3_uc003zht.1_Intron|RFX3_uc010mhe.1_Intron	NM_134428	NP_602304			regulatory factor X3 isoform b						cell maturation|ciliary cell motility|cilium assembly|cilium movement involved in determination of left/right asymmetry|endocrine pancreas development|negative regulation of transcription, DNA-dependent|positive regulation of transcription from RNA polymerase II promoter|positive regulation of type B pancreatic cell development|regulation of insulin secretion	nuclear chromatin	protein binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription regulatory region DNA binding			ovary(2)|central_nervous_system(1)|pancreas(1)	4				GBM - Glioblastoma multiforme(50;0.00124)|Lung(2;0.0337)														---	---	---	---
GLIS3	169792	broad.mit.edu	37	9	3982213	3982214	+	Intron	INS	-	TT	TT			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:3982213_3982214insTT	uc003zhw.1	-						GLIS3_uc003zhx.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)														---	---	---	---
C9orf68	55064	broad.mit.edu	37	9	4665999	4665999	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:4665999delA	uc011llz.1	-						C9orf68_uc003zik.2_Intron|C9orf68_uc003zil.2_Intron|C9orf68_uc010mhj.2_Intron|C9orf68_uc011lly.1_Intron|C9orf68_uc003zim.2_Intron	NM_001039395	NP_001034484			hypothetical protein LOC55064												0		Breast(48;0.0456)		GBM - Glioblastoma multiforme(50;0.0222)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	4770868	4770868	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:4770868delT								AK3 (28825 upstream) : RCL1 (21966 downstream)																																			---	---	---	---
RCL1	10171	broad.mit.edu	37	9	4850493	4850493	+	Intron	DEL	C	-	-	rs10974811		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:4850493delC	uc003zis.2	+						RCL1_uc003zit.2_Intron|RCL1_uc010mhk.1_Intron|RCL1_uc010mhl.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)														---	---	---	---
C9orf46	55848	broad.mit.edu	37	9	5504849	5504849	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5504849delA	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	5641097	5641099	+	Intron	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5641097_5641099delTTT	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	5688463	5688463	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5688463delT	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	5739770	5739770	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5739770delA	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)														---	---	---	---
KIAA2026	158358	broad.mit.edu	37	9	5987510	5987510	+	Intron	DEL	A	-	-	rs76506916		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5987510delA	uc003zjq.3	-							NM_001017969	NP_001017969			hypothetical protein LOC158358											ovary(2)|central_nervous_system(1)	3		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00155)|Lung(218;0.124)														---	---	---	---
IL33	90865	broad.mit.edu	37	9	6220141	6220141	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6220141delT	uc003zjt.2	+						IL33_uc011lmg.1_Intron|IL33_uc011lmh.1_Intron	NM_033439	NP_254274			interleukin 33 precursor						positive regulation of chemokine secretion|positive regulation of inflammatory response|positive regulation of macrophage activation|positive regulation of transcription from RNA polymerase II promoter	extracellular space	cytokine activity				0		Acute lymphoblastic leukemia(23;0.158)|Prostate(43;0.167)		GBM - Glioblastoma multiforme(50;0.0161)|Lung(218;0.105)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	6650487	6650487	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6650487delT								GLDC (4795 upstream) : KDM4C (66008 downstream)																																			---	---	---	---
KDM4C	23081	broad.mit.edu	37	9	7060216	7060216	+	Intron	DEL	T	-	-	rs76509457		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:7060216delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	7431169	7431170	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:7431169_7431170insT								KDM4C (255522 upstream) : C9orf123 (365323 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	8149334	8149334	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:8149334delA								C9orf123 (349535 upstream) : PTPRD (164913 downstream)																																			---	---	---	---
PTPRD	5789	broad.mit.edu	37	9	8494191	8494191	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:8494191delT	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	8897320	8897320	+	Intron	DEL	T	-	-	rs76473045	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:8897320delT	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	8920336	8920336	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:8920336delA	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	9126784	9126785	+	Intron	INS	-	TTTG	TTTG			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:9126784_9126785insTTTG	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	9428238	9428238	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:9428238delA	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	9457841	9457841	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:9457841delT	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	10159395	10159395	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:10159395delA	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	10882647	10882647	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:10882647delT								PTPRD (269924 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	13036695	13036698	+	IGR	DEL	TTTC	-	-	rs67820972		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:13036695_13036698delTTTC								C9orf150 (213637 upstream) : MPDZ (69011 downstream)																																			---	---	---	---
MPDZ	8777	broad.mit.edu	37	9	13244429	13244429	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:13244429delT	uc010mia.1	-						MPDZ_uc010mhy.2_Intron|MPDZ_uc010mhz.2_Intron|MPDZ_uc011lmn.1_Intron|MPDZ_uc003zlb.3_Intron	NM_003829	NP_003820			multiple PDZ domain protein						interspecies interaction between organisms	apical plasma membrane|dendrite|postsynaptic density|postsynaptic membrane|synaptosome|tight junction	protein C-terminus binding			ovary(5)|central_nervous_system(1)	6				GBM - Glioblastoma multiforme(50;2.03e-06)														---	---	---	---
MPDZ	8777	broad.mit.edu	37	9	13244909	13244909	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:13244909delA	uc010mia.1	-						MPDZ_uc010mhy.2_Intron|MPDZ_uc010mhz.2_Intron|MPDZ_uc011lmn.1_Intron|MPDZ_uc003zlb.3_Intron	NM_003829	NP_003820			multiple PDZ domain protein						interspecies interaction between organisms	apical plasma membrane|dendrite|postsynaptic density|postsynaptic membrane|synaptosome|tight junction	protein C-terminus binding			ovary(5)|central_nervous_system(1)	6				GBM - Glioblastoma multiforme(50;2.03e-06)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	13960211	13960212	+	IGR	DEL	GT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:13960211_13960212delGT								MPDZ (680648 upstream) : NFIB (121636 downstream)																																			---	---	---	---
FREM1	158326	broad.mit.edu	37	9	14789027	14789028	+	Frame_Shift_Del	DEL	GT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:14789027_14789028delGT	uc003zlm.2	-	23	4656_4657	c.4066_4067delAC	c.(4066-4068)ACCfs	p.T1356fs	FREM1_uc010mic.2_Intron	NM_144966	NP_659403	Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1 precursor	1356	CSPG 9.				cell communication|multicellular organismal development	basement membrane|integral to membrane	metal ion binding|sugar binding			ovary(2)|breast(2)|pancreas(1)	5				GBM - Glioblastoma multiforme(50;3.53e-06)														---	---	---	---
SNAPC3	6619	broad.mit.edu	37	9	15447515	15447516	+	Intron	INS	-	T	T	rs147086198	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:15447515_15447516insT	uc003zlt.2	+						SNAPC3_uc011lmt.1_Intron|SNAPC3_uc003zlu.2_Intron	NM_001039697	NP_001034786			small nuclear RNA activating complex,						regulation of transcription, DNA-dependent|snRNA transcription|transcription from RNA polymerase II promoter|transcription from RNA polymerase III promoter	nucleoplasm	DNA binding|protein binding				0				GBM - Glioblastoma multiforme(50;2.15e-06)														---	---	---	---
SNAPC3	6619	broad.mit.edu	37	9	15459986	15459986	+	3'UTR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:15459986delA	uc003zlt.2	+	9					SNAPC3_uc003zlu.2_RNA	NM_001039697	NP_001034786			small nuclear RNA activating complex,						regulation of transcription, DNA-dependent|snRNA transcription|transcription from RNA polymerase II promoter|transcription from RNA polymerase III promoter	nucleoplasm	DNA binding|protein binding				0				GBM - Glioblastoma multiforme(50;2.15e-06)														---	---	---	---
C9orf93	203238	broad.mit.edu	37	9	15570291	15570291	+	Intron	DEL	T	-	-	rs142904416		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:15570291delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	16315659	16315660	+	IGR	DEL	GT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:16315659_16315660delGT								C9orf93 (343764 upstream) : BNC2 (93842 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	16350015	16350016	+	IGR	INS	-	AG	AG	rs141841667	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:16350015_16350016insAG								C9orf93 (378120 upstream) : BNC2 (59486 downstream)																																			---	---	---	---
CNTLN	54875	broad.mit.edu	37	9	17201798	17201798	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:17201798delT	uc003zmz.2	+						CNTLN_uc003zmx.3_Intron|CNTLN_uc003zmy.2_Intron	NM_017738	NP_060208			centlein isoform 1							centriole|membrane	two-component sensor activity			pancreas(1)	1				GBM - Glioblastoma multiforme(50;6.14e-10)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	17855671	17855671	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:17855671delT								SH3GL2 (58551 upstream) : ADAMTSL1 (618433 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	17994089	17994090	+	IGR	DEL	TG	-	-	rs33979099		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:17994089_17994090delTG								SH3GL2 (196969 upstream) : ADAMTSL1 (480014 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	18102908	18102908	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:18102908delA								SH3GL2 (305788 upstream) : ADAMTSL1 (371196 downstream)																																			---	---	---	---
ADAMTSL1	92949	broad.mit.edu	37	9	18766086	18766086	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:18766086delG	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)														---	---	---	---
FAM154A	158297	broad.mit.edu	37	9	18957603	18957603	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:18957603delC	uc003zni.1	-						FAM154A_uc010mip.1_Intron	NM_153707	NP_714918			hypothetical protein LOC158297											pancreas(1)	1				GBM - Glioblastoma multiforme(50;6.53e-16)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	20632892	20632893	+	IGR	INS	-	A	A	rs34946794		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:20632892_20632893insA								MLLT3 (10378 upstream) : KIAA1797 (25416 downstream)																																			---	---	---	---
KIAA1797	54914	broad.mit.edu	37	9	20871203	20871203	+	Intron	DEL	A	-	-	rs78202769		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:20871203delA	uc003zog.1	+						KIAA1797_uc003zoh.1_Intron	NM_017794	NP_060264			hypothetical protein LOC54914							integral to membrane	binding			ovary(8)|breast(1)|kidney(1)	10				GBM - Glioblastoma multiforme(3;2.1e-125)|Lung(42;2.76e-14)|LUSC - Lung squamous cell carcinoma(42;1.99e-11)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	21051826	21051826	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:21051826delA								PTPLAD2 (20191 upstream) : IFNB1 (25279 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	21604731	21604731	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:21604731delA								LOC554202 (44899 upstream) : MTAP (197904 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	22890654	22890654	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:22890654delA								DMRTA1 (438182 upstream) : ELAVL2 (799451 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	22907443	22907444	+	IGR	DEL	AA	-	-	rs111290531		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:22907443_22907444delAA								DMRTA1 (454971 upstream) : ELAVL2 (782661 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	23331474	23331474	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:23331474delT								DMRTA1 (879002 upstream) : ELAVL2 (358631 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	23547500	23547500	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:23547500delT	uc003zpr.2	-											Homo sapiens mRNA; cDNA DKFZp781D1719 (from clone DKFZp781D1719).																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	23671067	23671067	+	Intron	DEL	A	-	-	rs147483341		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:23671067delA	uc003zpr.2	-											Homo sapiens mRNA; cDNA DKFZp781D1719 (from clone DKFZp781D1719).																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	24395324	24395324	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:24395324delC								ELAVL2 (569261 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	25333739	25333739	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:25333739delA								None (None upstream) : TUSC1 (342655 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	25459825	25459825	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:25459825delT								None (None upstream) : TUSC1 (216569 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	26553536	26553538	+	IGR	DEL	TTT	-	-	rs111397409		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:26553536_26553538delTTT								TUSC1 (874680 upstream) : C9orf82 (287146 downstream)																																			---	---	---	---
PLAA	9373	broad.mit.edu	37	9	26926684	26926684	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:26926684delT	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)														---	---	---	---
C9orf11	54586	broad.mit.edu	37	9	27293948	27293948	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27293948delA	uc003zql.2	-						C9orf11_uc011lnq.1_Intron|C9orf11_uc003zqm.2_Intron	NM_020641	NP_065692			Acr formation associated factor isoform 1							acrosomal membrane|integral to membrane				ovary(1)|central_nervous_system(1)	2				OV - Ovarian serous cystadenocarcinoma(39;7.39e-08)|Lung(218;1.26e-05)|LUSC - Lung squamous cell carcinoma(38;0.000106)														---	---	---	---
LINGO2	158038	broad.mit.edu	37	9	28704395	28704395	+	Intron	DEL	T	-	-	rs76982779		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:28704395delT	uc003zqv.1	-							NM_152570	NP_689783			leucine rich repeat and Ig domain containing 2							integral to membrane				upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3	Melanoma(11;0.242)	all_neural(11;2.78e-09)		UCEC - Uterine corpus endometrioid carcinoma (5;0.0818)|GBM - Glioblastoma multiforme(2;1.31e-34)|all cancers(2;2.37e-25)|Lung(2;7.48e-08)|LUSC - Lung squamous cell carcinoma(38;5.09e-07)|KIRC - Kidney renal clear cell carcinoma(2;0.0465)|Kidney(2;0.0604)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	30670501	30670501	+	IGR	DEL	A	-	-	rs151037108		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:30670501delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	30893157	30893157	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:30893157delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	31303162	31303164	+	IGR	DEL	TTT	-	-	rs76592133		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:31303162_31303164delTTT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	31303886	31303887	+	IGR	INS	-	TTGT	TTGT	rs141811258	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:31303886_31303887insTTGT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	31916941	31916941	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:31916941delT								None (None upstream) : ACO1 (467660 downstream)																																			---	---	---	---
ACO1	48	broad.mit.edu	37	9	32388527	32388527	+	Intron	DEL	A	-	-	rs77247114		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32388527delA	uc003zqw.3	+						ACO1_uc010mjh.1_Intron|ACO1_uc003zqx.3_Intron|ACO1_uc003zqy.3_Intron	NM_002197	NP_002188			aconitase 1						citrate metabolic process|response to iron(II) ion|tricarboxylic acid cycle	cytosol|endoplasmic reticulum|Golgi apparatus	4 iron, 4 sulfur cluster binding|aconitate hydratase activity|citrate hydro-lyase (cis-aconitate-forming) activity|iron-responsive element binding|isocitrate hydro-lyase (cis-aconitate-forming) activity|metal ion binding|protein binding				0			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;3.94e-06)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	32929960	32929960	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32929960delT								TMEM215 (140763 upstream) : APTX (42649 downstream)																																			---	---	---	---
B4GALT1	2683	broad.mit.edu	37	9	33135908	33135909	+	Intron	DEL	TA	-	-	rs34931533		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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)													---	---	---	---
CHMP5	51510	broad.mit.edu	37	9	33272798	33272798	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33272798delA	uc003zsl.3	+						SUGT1P1_uc010mjq.1_Intron|CHMP5_uc003zsm.3_Intron|CHMP5_uc011lnv.1_Intron	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	33313426	33313426	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33313426delA	uc003zsq.2	+						SUGT1P1_uc010mjq.1_Intron|NFX1_uc011lnw.1_Intron|NFX1_uc003zso.2_Intron|NFX1_uc003zsp.1_Intron|NFX1_uc010mjr.1_Intron|NFX1_uc003zsr.2_Intron	NM_002504	NP_002495			nuclear transcription factor, X-box binding 1						inflammatory response|interspecies interaction between organisms|negative regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	DNA binding|ligase activity|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1			LUSC - Lung squamous cell carcinoma(29;0.00506)	GBM - Glioblastoma multiforme(74;0.224)														---	---	---	---
NFX1	4799	broad.mit.edu	37	9	33317662	33317662	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33317662delA	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)														---	---	---	---
UBE2R2	54926	broad.mit.edu	37	9	33894272	33894272	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33894272delA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	34145593	34145595	+	IGR	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34145593_34145595delTTT								DCAF12 (18822 upstream) : UBAP1 (33416 downstream)																																			---	---	---	---
DNAI1	27019	broad.mit.edu	37	9	34501727	34501727	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34501727delC	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				---	---	---	---
CCL21	6366	broad.mit.edu	37	9	34710640	34710640	+	5'Flank	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34710640delT	uc003zvo.2	-							NM_002989	NP_002980			small inducible cytokine A21 precursor						activation of Rho GTPase activity|cell maturation|cell-cell signaling|dendritic cell chemotaxis|dendritic cell dendrite assembly|establishment of T cell polarity|immune response|immunological synapse formation|inflammatory response|mesangial cell-matrix adhesion|negative regulation of leukocyte apoptosis|positive regulation of actin filament polymerization|positive regulation of cell adhesion mediated by integrin|positive regulation of cell-matrix adhesion|positive regulation of dendritic cell antigen processing and presentation|positive regulation of ERK1 and ERK2 cascade|positive regulation of filopodium assembly|positive regulation of glycoprotein biosynthetic process|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of JNK cascade|positive regulation of myeloid dendritic cell chemotaxis|positive regulation of neutrophil chemotaxis|positive regulation of phosphatidylinositol 3-kinase activity|positive regulation of protein kinase activity|positive regulation of protein kinase B signaling cascade|positive regulation of pseudopodium assembly|positive regulation of receptor-mediated endocytosis|release of sequestered calcium ion into cytosol|response to prostaglandin E stimulus|ruffle organization|T cell costimulation	extracellular space	CCR7 chemokine receptor binding|chemokine activity				0	all_epithelial(49;0.0899)		STAD - Stomach adenocarcinoma(86;0.178)	GBM - Glioblastoma multiforme(74;0.173)														---	---	---	---
VCP	7415	broad.mit.edu	37	9	35066123	35066123	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35066123delA	uc003zvy.2	-						VCP_uc003zvz.2_Intron|VCP_uc010mkh.1_Intron|VCP_uc010mki.1_Intron	NM_007126	NP_009057			valosin-containing protein						activation of caspase activity|double-strand break repair|endoplasmic reticulum unfolded protein response|ER-associated protein catabolic process|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|protein ubiquitination|retrograde protein transport, ER to cytosol	cytosol|endoplasmic reticulum|microsome|nucleus|proteasome complex	ATP binding|ATPase activity|lipid binding|polyubiquitin binding|protein domain specific binding|protein phosphatase binding			upper_aerodigestive_tract(1)	1			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)															---	---	---	---
UNC13B	10497	broad.mit.edu	37	9	35193008	35193009	+	Intron	INS	-	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35193008_35193009insC	uc003zwq.2	+						UNC13B_uc010mkl.1_Intron|UNC13B_uc003zwr.2_Intron	NM_006377	NP_006368			UNC13 (C. elegans)-like						excretion|induction of apoptosis|intracellular signal transduction	cell junction|Golgi apparatus|synapse	metal ion binding|receptor activity			ovary(3)|large_intestine(1)|skin(1)	5	all_epithelial(49;0.212)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)|STAD - Stomach adenocarcinoma(86;0.194)															---	---	---	---
Unknown	0	broad.mit.edu	37	9	35776291	35776291	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35776291delT								MSMP (22019 upstream) : NPR2 (16115 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	35914226	35914229	+	IGR	DEL	GGTG	-	-	rs55727794	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35914226_35914229delGGTG								LOC158376 (2609 upstream) : OR2S2 (42877 downstream)																																			---	---	---	---
RECK	8434	broad.mit.edu	37	9	36064039	36064039	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36064039delT	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	9	36522526	36522526	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36522526delA								RNF38 (121331 upstream) : MELK (50379 downstream)																																			---	---	---	---
ZCCHC7	84186	broad.mit.edu	37	9	37200214	37200214	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37200214delT	uc003zzq.2	+						ZCCHC7_uc011lqh.1_Intron|ZCCHC7_uc011lqi.1_Intron|ZCCHC7_uc010mlt.2_Intron	NM_032226	NP_115602			zinc finger, CCHC domain containing 7								nucleic acid binding|zinc ion binding			ovary(1)|central_nervous_system(1)|skin(1)	3				GBM - Glioblastoma multiforme(29;0.0137)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	38371381	38371381	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:38371381delA								SHB (302171 upstream) : ALDH1B1 (21321 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	38634071	38634071	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:38634071delT								C9orf122 (10796 upstream) : CNTNAP3 (438695 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	40500071	40500071	+	3'UTR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:40500071delT	uc004abr.1	-	8										RecName: Full=Contactin-associated protein-like 3B; AltName: Full=Cell recognition molecule Caspr3b; Flags: Precursor;																														---	---	---	---
ANKRD20A3	441425	broad.mit.edu	37	9	43128186	43128186	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:43128186delT	uc004acw.1	-						ANKRD20A3_uc010mna.1_Intron	NM_001012421	NP_001012421			ankyrin repeat domain 20 family, member A2												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	43823712	43823713	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:43823712_43823713delAA	uc004acz.1	+											Homo sapiens cDNA FLJ30083 fis, clone BGGI12001097, weakly similar to Homo sapiens contactin associated protein (Caspr) mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	66333430	66333430	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66333430delA								FAM74A4 (839044 upstream) : LOC442421 (163040 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	66485321	66485322	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66485321_66485322delAA								FAM74A4 (990935 upstream) : LOC442421 (11148 downstream)																																			---	---	---	---
LOC442421	442421	broad.mit.edu	37	9	66502886	66502886	+	RNA	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66502886delT	uc004aed.1	+	3		c.2979delT								Homo sapiens similar to prostaglandin E receptor 4, subtype EP4; PGE receptor, EP4 subtype; prostaglandin E2 receptor, mRNA (cDNA clone IMAGE:5288780).												0																		---	---	---	---
AQP7P1	375719	broad.mit.edu	37	9	67276713	67276713	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:67276713delA	uc004aem.1	-						AQP7P1_uc004aen.1_Intron|AQP7P1_uc004aeo.1_Intron|AQP7P1_uc004aep.1_Intron					Homo sapiens aquaporin 7 pseudogene 1, mRNA (cDNA clone IMAGE:6191443).												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	67337092	67337092	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:67337092delT								AQP7P1 (47600 upstream) : FAM27B (455838 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	67912353	67912354	+	IGR	DEL	TA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:67912353_67912354delTA								FAM27B (118164 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	68361334	68361337	+	IGR	DEL	TTTG	-	-	rs141937536		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68361334_68361337delTTTG								FAM27B (567145 upstream) : MIR1299 (640902 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	68385894	68385894	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68385894delC								FAM27B (591705 upstream) : MIR1299 (616345 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	68426898	68426898	+	IGR	DEL	T	-	-	rs67299135		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68426898delT								FAM27B (632709 upstream) : MIR1299 (575341 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	68489055	68489056	+	IGR	INS	-	A	A	rs146831433		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68489055_68489056insA								FAM27B (694866 upstream) : MIR1299 (513183 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	68510411	68510411	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68510411delA								FAM27B (716222 upstream) : MIR1299 (491828 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	68999220	68999223	+	IGR	DEL	TGTT	-	-	rs145535214		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68999220_68999223delTGTT								None (None upstream) : MIR1299 (3016 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	69643067	69643067	+	Intron	DEL	C	-	-	rs145420014		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69643067delC	uc004afu.3	-											Homo sapiens aquaporin 7 pseudogene 2, mRNA (cDNA clone IMAGE:30406582).																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	69805068	69805069	+	IGR	DEL	TC	-	-	rs77193208		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69805068_69805069delTC								LOC100133920 (140119 upstream) : FOXD4L5 (370640 downstream)																																			---	---	---	---
FXN	2395	broad.mit.edu	37	9	71668387	71668388	+	Intron	INS	-	GATGGATG	GATGGATG	rs73647061	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71668387_71668388insGATGGATG	uc004aha.2	+						FXN_uc011lrr.1_Intron|FXN_uc004agz.2_Intron	NM_000144	NP_000135			frataxin isoform 1 preproprotein						cellular iron ion homeostasis|cellular response to hydrogen peroxide|heme biosynthetic process|ion transport|iron incorporation into metallo-sulfur cluster|negative regulation of apoptosis|negative regulation of release of cytochrome c from mitochondria|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of lyase activity|positive regulation of metalloenzyme activity|positive regulation of oxidoreductase activity|positive regulation of transferase activity|protein autoprocessing|regulation of ferrochelatase activity|response to iron ion	cytosol|mitochondrial matrix	2 iron, 2 sulfur cluster binding|ferric iron binding|ferrous iron binding|ferroxidase activity|iron chaperone activity|protein binding				0																		---	---	---	---
TJP2	9414	broad.mit.edu	37	9	71773342	71773342	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71773342delT	uc011lrs.1	+						TJP2_uc004ahb.1_Intron|TJP2_uc011lrt.1_Intron	NM_201629	NP_963923			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	71836476	71836476	+	Intron	DEL	T	-	-	rs113816166		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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																		---	---	---	---
TRPM3	80036	broad.mit.edu	37	9	73635062	73635062	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:73635062delA	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	74135623	74135623	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74135623delA								TRPM3 (73803 upstream) : TMEM2 (162659 downstream)																																			---	---	---	---
TMEM2	23670	broad.mit.edu	37	9	74382114	74382114	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74382114delT	uc011lsa.1	-						TMEM2_uc010mos.2_Intron|TMEM2_uc011lsb.1_Intron	NM_013390	NP_037522			transmembrane protein 2 isoform a							integral to membrane				ovary(2)	2		all_epithelial(88;4.56e-14)|Myeloproliferative disorder(762;0.0255)		GBM - Glioblastoma multiforme(74;7.45e-21)|OV - Ovarian serous cystadenocarcinoma(323;1.02e-16)														---	---	---	---
C9orf57	138240	broad.mit.edu	37	9	74677015	74677016	+	5'Flank	INS	-	GT	GT	rs144028506	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74677015_74677016insGT	uc004aip.2	-						C9orf57_uc011lsd.1_Intron	NM_001128618	NP_001122090			hypothetical protein LOC138240							integral to membrane					0																		---	---	---	---
ALDH1A1	216	broad.mit.edu	37	9	75563135	75563135	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:75563135delT	uc004ajd.2	-						ALDH1A1_uc011lsh.1_Intron	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)													---	---	---	---
ALDH1A1	216	broad.mit.edu	37	9	75631825	75631826	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:75631825_75631826insA	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	75920243	75920244	+	IGR	DEL	CA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:75920243_75920244delCA								ANXA1 (134936 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	76970889	76970890	+	IGR	DEL	AC	-	-	rs150391857		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:76970889_76970890delAC								None (None upstream) : RORB (141362 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	77806774	77806774	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77806774delT								OSTF1 (44661 upstream) : PCSK5 (698786 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	78015425	78015426	+	IGR	INS	-	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78015425_78015426insG								OSTF1 (253312 upstream) : PCSK5 (490134 downstream)																																			---	---	---	---
PCSK5	5125	broad.mit.edu	37	9	78655302	78655303	+	Intron	DEL	TC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78655302_78655303delTC	uc004ajz.2	+						PCSK5_uc004ajy.2_Intron|PCSK5_uc004aka.2_Intron	NM_006200	NP_006191			proprotein convertase subtilisin/kexin type 5						anterior/posterior pattern formation|cell-cell signaling|cytokine biosynthetic process|embryo implantation|embryonic digestive tract development|embryonic skeletal system development|heart development|kidney development|limb morphogenesis|nerve growth factor processing|nerve growth factor receptor signaling pathway|peptide biosynthetic process|renin secretion into blood stream|respiratory tube development|signal peptide processing|viral assembly, maturation, egress, and release	extracellular space|Golgi lumen|stored secretory granule	peptide binding|serine-type endopeptidase activity			ovary(2)|skin(1)	3																		---	---	---	---
PCSK5	5125	broad.mit.edu	37	9	78794417	78794417	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78794417delA	uc004ajz.2	+						PCSK5_uc004aka.2_Intron|PCSK5_uc004akb.2_5'Flank	NM_006200	NP_006191			proprotein convertase subtilisin/kexin type 5						anterior/posterior pattern formation|cell-cell signaling|cytokine biosynthetic process|embryo implantation|embryonic digestive tract development|embryonic skeletal system development|heart development|kidney development|limb morphogenesis|nerve growth factor processing|nerve growth factor receptor signaling pathway|peptide biosynthetic process|renin secretion into blood stream|respiratory tube development|signal peptide processing|viral assembly, maturation, egress, and release	extracellular space|Golgi lumen|stored secretory granule	peptide binding|serine-type endopeptidase activity			ovary(2)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	78916269	78916269	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78916269delA								PCSK5 (107931 upstream) : RFK (84164 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	78969205	78969205	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78969205delG	uc004akc.1	+											Homo sapiens cDNA FLJ16215 fis, clone CTONG2025610, moderately similar to PC6B.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	79162878	79162878	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79162878delT								GCNT1 (40548 upstream) : PRUNE2 (63415 downstream)																																			---	---	---	---
PRUNE2	158471	broad.mit.edu	37	9	79348482	79348483	+	Intron	DEL	TT	-	-	rs72071980		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79348482_79348483delTT	uc010mpk.2	-							NM_015225	NP_056040			prune homolog 2						apoptosis|G1 phase|induction of apoptosis	cytoplasm	metal ion binding|pyrophosphatase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	79532696	79532696	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79532696delT								PRUNE2 (11693 upstream) : FOXB2 (101875 downstream)																																			---	---	---	---
GNAQ	2776	broad.mit.edu	37	9	80339998	80339998	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:80339998delT	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	80524599	80524600	+	Intron	INS	-	A	A	rs71503231		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:80524599_80524600insA	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	80779281	80779282	+	IGR	INS	-	ATA	ATA	rs150104006	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:80779281_80779282insATA								GNAQ (133089 upstream) : CEP78 (71709 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	81122884	81122885	+	IGR	INS	-	T	T	rs150970891	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:81122884_81122885insT								PSAT1 (177877 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	81189200	81189200	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:81189200delT								PSAT1 (244193 upstream) : TLE4 (997678 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	81227108	81227111	+	IGR	DEL	TTTT	-	-	rs72176842		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:81227108_81227111delTTTT								PSAT1 (282101 upstream) : TLE4 (959767 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	81568746	81568746	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:81568746delA								PSAT1 (623739 upstream) : TLE4 (618132 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	81581376	81581381	+	IGR	DEL	ACACAC	-	-	rs3054634		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:81581376_81581381delACACAC								PSAT1 (636369 upstream) : TLE4 (605497 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	81847046	81847047	+	IGR	INS	-	G	G	rs72543016		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:81847046_81847047insG								PSAT1 (902039 upstream) : TLE4 (339831 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	82543442	82543442	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:82543442delT								TLE4 (201785 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	83556400	83556400	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:83556400delA								None (None upstream) : TLE1 (642200 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	84683132	84683133	+	IGR	INS	-	CAA	CAA	rs113407602		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84683132_84683133insCAA								FLJ46321 (72962 upstream) : RASEF (914184 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	85052129	85052129	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:85052129delT								FLJ46321 (441959 upstream) : RASEF (545188 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	85138997	85138997	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:85138997delT								FLJ46321 (528827 upstream) : RASEF (458320 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	85206774	85206777	+	IGR	DEL	ACAC	-	-	rs72074053		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:85206774_85206777delACAC								FLJ46321 (596604 upstream) : RASEF (390540 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	85359363	85359364	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:85359363_85359364delAA								FLJ46321 (749193 upstream) : RASEF (237953 downstream)																																			---	---	---	---
RASEF	158158	broad.mit.edu	37	9	85674278	85674278	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:85674278delA	uc004amo.1	-						RASEF_uc004amp.1_Intron	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																		---	---	---	---
FRMD3	257019	broad.mit.edu	37	9	85929968	85929968	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:85929968delT	uc004ams.1	-						FRMD3_uc004amr.1_Intron	NM_174938	NP_777598			FERM domain containing 3							cytoplasm|cytoskeleton|extrinsic to membrane|integral to membrane	cytoskeletal protein binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	86211265	86211265	+	IGR	DEL	A	-	-	rs66573960		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86211265delA								FRMD3 (57917 upstream) : C9orf103 (26701 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	86353554	86353554	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86353554delT								UBQLN1 (30386 upstream) : GKAP1 (783 downstream)																																			---	---	---	---
KIF27	55582	broad.mit.edu	37	9	86474788	86474788	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86474788delA	uc004ana.2	-						KIF27_uc010mpw.2_Intron|KIF27_uc010mpx.2_Intron	NM_017576	NP_060046			kinesin family member 27						cilium assembly|microtubule-based movement	cilium|cytoplasm|microtubule	ATP binding|microtubule motor activity			lung(4)|skin(1)	5																		---	---	---	---
C9orf64	84267	broad.mit.edu	37	9	86559615	86559615	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86559615delT	uc004anb.2	-						C9orf64_uc004anc.2_Intron	NM_032307	NP_115683			hypothetical protein LOC84267												0																		---	---	---	---
HNRNPK	3190	broad.mit.edu	37	9	86589414	86589414	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86589414delA	uc004ang.3	-						HNRNPK_uc011lsw.1_Intron|HNRNPK_uc004and.3_Intron|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	88455570	88455570	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88455570delT	uc004aog.1	+						uc004aoh.1_Intron					Homo sapiens cDNA FLJ42532 fis, clone BRACE3003004.																														---	---	---	---
NAA35	60560	broad.mit.edu	37	9	88564215	88564216	+	Intron	DEL	TT	-	-	rs28694713		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88564215_88564216delTT	uc004aoi.3	+						NAA35_uc004aoj.3_Intron|NAA35_uc004aok.1_Intron	NM_024635	NP_078911			corneal wound healing-related protein						smooth muscle cell proliferation	cytoplasm|nucleus|plasma membrane				skin(2)|central_nervous_system(1)	3																		---	---	---	---
ZCCHC6	79670	broad.mit.edu	37	9	88931992	88931993	+	Intron	INS	-	T	T	rs144085642	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88931992_88931993insT	uc004aoq.2	-						ZCCHC6_uc010mqe.2_Intron|ZCCHC6_uc011ltf.1_Intron|ZCCHC6_uc004aor.2_Intron|ZCCHC6_uc004aos.2_Intron|ZCCHC6_uc004aot.2_Intron|ZCCHC6_uc004aou.2_Intron	NM_024617	NP_078893			zinc finger, CCHC domain containing 6						RNA 3'-end processing		nucleic acid binding|RNA uridylyltransferase activity|zinc ion binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	89401599	89401599	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:89401599delA								ZCCHC6 (432221 upstream) : GAS1 (157680 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	89893003	89893003	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:89893003delG								C9orf170 (118362 upstream) : DAPK1 (219655 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	90415935	90415935	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90415935delT								CTSL3 (14136 upstream) : C9orf79 (81806 downstream)																																			---	---	---	---
C9orf79	286234	broad.mit.edu	37	9	90496184	90496184	+	5'Flank	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90496184delG	uc004app.3	+						C9orf79_uc004apo.1_5'Flank	NM_178828	NP_849150			chromosome 9 open reading frame 79							integral to membrane				ovary(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	90572810	90572811	+	IGR	DEL	AT	-	-	rs71507746		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90572810_90572811delAT								FAM75C1 (34239 upstream) : CDK20 (8550 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	90758492	90758495	+	IGR	DEL	TTTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90758492_90758495delTTTT								CDK20 (168825 upstream) : SPIN1 (244345 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	90939072	90939072	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90939072delC								CDK20 (349405 upstream) : SPIN1 (63768 downstream)																																			---	---	---	---
SEMA4D	10507	broad.mit.edu	37	9	92113277	92113278	+	5'Flank	INS	-	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:92113277_92113278insC	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	92179619	92179619	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:92179619delT								SEMA4D (66731 upstream) : GADD45G (40308 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	92455533	92455533	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:92455533delT								LOC100129066 (120859 upstream) : DIRAS2 (916581 downstream)																																			---	---	---	---
AUH	549	broad.mit.edu	37	9	93999972	93999972	+	Intron	DEL	T	-	-	rs34912309		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:93999972delT	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																		---	---	---	---
IARS	3376	broad.mit.edu	37	9	95024040	95024041	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95024040_95024041delTT	uc004art.1	-						IARS_uc004ars.1_Intron|IARS_uc004aru.3_Intron|IARS_uc010mqr.2_Intron|IARS_uc010mqt.2_Intron	NM_013417	NP_038203			isoleucine tRNA synthetase						isoleucyl-tRNA aminoacylation	cytosol|nucleus|soluble fraction	ATP binding|isoleucine-tRNA ligase activity|protein binding			ovary(1)|skin(1)	2					L-Isoleucine(DB00167)													---	---	---	---
FGD3	89846	broad.mit.edu	37	9	95790977	95790977	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95790977delT	uc004asw.2	+						FGD3_uc004asx.2_Intron|FGD3_uc004asz.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																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	95930923	95930923	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95930923delC								NINJ1 (34353 upstream) : WNK2 (16289 downstream)																																			---	---	---	---
WNK2	65268	broad.mit.edu	37	9	96073895	96073896	+	Intron	INS	-	TGTGTG	TGTGTG	rs138137559	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96073895_96073896insTGTGTG	uc004ati.1	+						WNK2_uc011lud.1_Intron|WNK2_uc004atj.2_Intron|WNK2_uc004atk.2_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																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	96159502	96159503	+	IGR	DEL	GA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96159502_96159503delGA								C9orf129 (50806 upstream) : FAM120AOS (39393 downstream)																																			---	---	---	---
PHF2	5253	broad.mit.edu	37	9	96385349	96385350	+	Intron	INS	-	T	T	rs151296781		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96385349_96385350insT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	96638759	96638759	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96638759delA								PHF2 (196892 upstream) : BARX1 (75152 downstream)																																			---	---	---	---
HIATL1	84641	broad.mit.edu	37	9	97218372	97218372	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97218372delA	uc004aur.2	+						HIATL1_uc011luh.1_Intron	NM_032558	NP_115947			hippocampus abundant transcript-like 1						transmembrane transport	integral to membrane|plasma membrane	protein binding|transporter activity			ovary(2)	2		Acute lymphoblastic leukemia(62;0.136)																---	---	---	---
Unknown	0	broad.mit.edu	37	9	97226978	97226978	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97226978delA								HIATL1 (3777 upstream) : FBP2 (94027 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	97244509	97244509	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97244509delT								HIATL1 (21308 upstream) : FBP2 (76496 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	97420213	97420213	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97420213delT								FBP1 (17682 upstream) : C9orf3 (68781 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	97473512	97473516	+	IGR	DEL	TTTTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97473512_97473516delTTTTT								FBP1 (70981 upstream) : C9orf3 (15478 downstream)																																			---	---	---	---
C9orf3	84909	broad.mit.edu	37	9	97555960	97555961	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97555960_97555961delAA	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	97684916	97684917	+	Intron	DEL	TT	-	-	rs113040711		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97684916_97684917delTT	uc004ava.2	+						C9orf3_uc004aux.1_Intron|C9orf3_uc004auy.2_Intron|C9orf3_uc004auz.1_Intron|C9orf3_uc004avc.2_Intron|uc004avb.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)														---	---	---	---
FANCC	2176	broad.mit.edu	37	9	98000832	98000832	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98000832delT	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	98825687	98825687	+	5'Flank	DEL	C	-	-	rs35459998		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98825687delC	uc004avy.3	+											Homo sapiens cDNA clone IMAGE:3638298.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	98893647	98893647	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98893647delA								NCRNA00092 (109610 upstream) : HSD17B3 (103942 downstream)																																			---	---	---	---
SLC35D2	11046	broad.mit.edu	37	9	99130723	99130723	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99130723delT	uc004awc.2	-						SLC35D2_uc010msd.2_Intron|SLC35D2_uc010mse.2_Intron|SLC35D2_uc010msf.2_Intron|SLC35D2_uc004awd.2_Intron|SLC35D2_uc004awe.2_Intron	NM_007001	NP_008932			solute carrier family 35, member D2							Golgi membrane|integral to membrane	nucleotide-sugar transmembrane transporter activity				0		Acute lymphoblastic leukemia(62;0.0167)																---	---	---	---
Unknown	0	broad.mit.edu	37	9	99433625	99433626	+	IGR	INS	-	G	G	rs150923383		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99433625_99433626insG								C9orf21 (16026 upstream) : LOC441455 (54477 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	99891268	99891269	+	Intron	INS	-	AC	AC	rs138767875	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99891268_99891269insAC	uc004aww.1	-											Homo sapiens cDNA FLJ34611 fis, clone KIDNE2014112.																														---	---	---	---
ANP32B	10541	broad.mit.edu	37	9	100767802	100767802	+	Intron	DEL	A	-	-	rs80277124		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100767802delA	uc004aya.2	+							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	101835334	101835339	+	IGR	DEL	TGTGTA	-	-	rs61503792		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101835334_101835339delTGTGTA								COL15A1 (2266 upstream) : TGFBR1 (32073 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	101857510	101857510	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101857510delT								COL15A1 (24442 upstream) : TGFBR1 (9902 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	102332951	102332951	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:102332951delT								SEC61B (340051 upstream) : NR4A3 (251186 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	103396276	103396277	+	IGR	DEL	TC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:103396276_103396277delTC								MURC (46105 upstream) : LPPR1 (394754 downstream)																																			---	---	---	---
LPPR1	54886	broad.mit.edu	37	9	104001235	104001238	+	Intron	DEL	TTTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104001235_104001238delTTTT	uc004bbb.2	+						LPPR1_uc011lvi.1_Intron|LPPR1_uc004bbc.2_Intron	NM_207299	NP_997182			plasticity related gene 3							integral to membrane	catalytic activity				0																		---	---	---	---
LPPR1	54886	broad.mit.edu	37	9	104071892	104071892	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104071892delC	uc004bbb.2	+						LPPR1_uc011lvi.1_Intron|LPPR1_uc004bbc.2_Intron|LPPR1_uc010mtc.2_Intron	NM_207299	NP_997182			plasticity related gene 3							integral to membrane	catalytic activity				0																		---	---	---	---
GRIN3A	116443	broad.mit.edu	37	9	104452026	104452027	+	Intron	DEL	AC	-	-	rs150030188		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104452026_104452027delAC	uc004bbp.1	-						GRIN3A_uc004bbq.1_Intron	NM_133445	NP_597702			glutamate receptor, ionotropic,						response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|neuron projection|neuronal cell body|outer membrane-bounded periplasmic space|postsynaptic density|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|glycine binding|identical protein binding|N-methyl-D-aspartate selective glutamate receptor activity|protein phosphatase 2A binding			ovary(4)|pancreas(1)|central_nervous_system(1)|skin(1)	7		Acute lymphoblastic leukemia(62;0.0568)			Acamprosate(DB00659)|Chloroprocaine(DB01161)|Dextromethorphan(DB00514)|Ethanol(DB00898)|Ethopropazine(DB00392)|Felbamate(DB00949)|Ketamine(DB01221)|L-Glutamic Acid(DB00142)|Memantine(DB01043)|Meperidine(DB00454)|Methadone(DB00333)|Orphenadrine(DB01173)|Procaine(DB00721)|Riluzole(DB00740)													---	---	---	---
Unknown	0	broad.mit.edu	37	9	104864856	104864857	+	IGR	INS	-	A	A	rs149348446	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104864856_104864857insA								GRIN3A (363994 upstream) : CYLC2 (892736 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	105160282	105160282	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:105160282delT								GRIN3A (659420 upstream) : CYLC2 (597311 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	106999274	106999274	+	IGR	DEL	A	-	-	rs145610734		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:106999274delA								SMC2 (95581 upstream) : OR13F1 (267270 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	107410707	107410707	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107410707delA								OR13C9 (30222 upstream) : OR13D1 (45996 downstream)																																			---	---	---	---
ABCA1	19	broad.mit.edu	37	9	107572811	107572811	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107572811delG	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	107618411	107618411	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107618411delA	uc004bcl.2	-							NM_005502	NP_005493			ATP-binding cassette, sub-family A member 1						Cdc42 protein signal transduction|cellular lipid metabolic process|cholesterol efflux|cholesterol homeostasis|cholesterol metabolic process|endosome transport|G-protein coupled receptor protein signaling pathway|high-density lipoprotein particle assembly|interleukin-1 beta secretion|intracellular cholesterol transport|lysosome organization|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|phospholipid efflux|phospholipid homeostasis|platelet dense granule organization|positive regulation of cAMP biosynthetic process|reverse cholesterol transport	integral to plasma membrane|membrane fraction|membrane raft|phagocytic vesicle	anion transmembrane transporter activity|apolipoprotein A-I receptor activity|ATP binding|ATPase activity|cholesterol transporter activity|phospholipid transporter activity|small GTPase binding|syntaxin-13 binding			large_intestine(4)|lung(4)|ovary(4)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	17				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)													---	---	---	---
Unknown	0	broad.mit.edu	37	9	107729929	107729929	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107729929delA								ABCA1 (39493 upstream) : SLC44A1 (277000 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	108988395	108988396	+	Intron	DEL	CT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:108988395_108988396delCT	uc004bcw.2	+											Homo sapiens, clone IMAGE:5538960, mRNA.																														---	---	---	---
ZNF462	58499	broad.mit.edu	37	9	109667052	109667052	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:109667052delT	uc004bcz.2	+							NM_021224	NP_067047			zinc finger protein 462						transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(5)	5																		---	---	---	---
ZNF462	58499	broad.mit.edu	37	9	109736291	109736291	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:109736291delT	uc004bcz.2	+						ZNF462_uc010mto.2_Intron|ZNF462_uc004bda.2_Intron|ZNF462_uc011lvz.1_Intron|ZNF462_uc004bdb.1_Intron	NM_021224	NP_067047			zinc finger protein 462						transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(5)	5																		---	---	---	---
RAD23B	5887	broad.mit.edu	37	9	110081279	110081279	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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	110264810	110264810	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110264810delA								KLF4 (12763 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	110706811	110706816	+	IGR	DEL	AAAAAC	-	-	rs71370259		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110706811_110706816delAAAAAC								KLF4 (454764 upstream) : ACTL7B (910055 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	111041207	111041207	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111041207delT								KLF4 (789160 upstream) : ACTL7B (575664 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	111115068	111115068	+	IGR	DEL	A	-	-	rs35623646		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111115068delA								KLF4 (863021 upstream) : ACTL7B (501803 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	111289524	111289525	+	IGR	DEL	AA	-	-	rs142756554		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111289524_111289525delAA								None (None upstream) : ACTL7B (327346 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	111293835	111293836	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111293835_111293836delAA								None (None upstream) : ACTL7B (323035 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	111593982	111593982	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111593982delG								None (None upstream) : ACTL7B (22889 downstream)																																			---	---	---	---
EPB41L4B	54566	broad.mit.edu	37	9	112018218	112018218	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112018218delA	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	112092314	112092315	+	IGR	INS	-	T	T	rs141606373	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112092314_112092315insT								EPB41L4B (9293 upstream) : PTPN3 (45659 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	112268750	112268751	+	IGR	INS	-	CCTT	CCTT	rs142108809	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112268750_112268751insCCTT								PTPN3 (8157 upstream) : PALM2 (134321 downstream)																																			---	---	---	---
PALM2-AKAP2	445815	broad.mit.edu	37	9	112724103	112724103	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112724103delT	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	112787067	112787068	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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																		---	---	---	---
SVEP1	79987	broad.mit.edu	37	9	113250986	113250987	+	Intron	INS	-	A	A	rs144779681	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113250986_113250987insA	uc010mtz.2	-						SVEP1_uc010mua.1_Intron|SVEP1_uc004beu.2_Intron	NM_153366	NP_699197			polydom						cell adhesion	cytoplasm|extracellular region|membrane	calcium ion binding			ovary(7)	7																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	113564505	113564505	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113564505delA								MUSK (1227 upstream) : LPAR1 (71551 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	113593936	113593936	+	IGR	DEL	A	-	-	rs143186781		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113593936delA								MUSK (30658 upstream) : LPAR1 (42120 downstream)																																			---	---	---	---
KIAA0368	23392	broad.mit.edu	37	9	114135312	114135312	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114135312delA	uc004bfe.1	-							NM_001080398	NP_001073867			KIAA0368 protein												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	114583404	114583408	+	IGR	DEL	AACAA	-	-	rs112359957		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114583404_114583408delAACAA								C9orf84 (26181 upstream) : UGCG (75798 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	114789697	114789697	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114789697delT								UGCG (94266 upstream) : SUSD1 (13365 downstream)																																			---	---	---	---
SUSD1	64420	broad.mit.edu	37	9	114837418	114837418	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114837418delT	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																		---	---	---	---
SUSD1	64420	broad.mit.edu	37	9	114923071	114923074	+	Intron	DEL	AGAC	-	-	rs141272933		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114923071_114923074delAGAC	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-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	115104356	115104356	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115104356delA								ROD1 (8412 upstream) : HSDL2 (37995 downstream)																																			---	---	---	---
HSDL2	84263	broad.mit.edu	37	9	115169698	115169698	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115169698delT	uc004bga.1	+						HSDL2_uc011lwv.1_Intron|HSDL2_uc004bgb.1_Intron|HSDL2_uc004bgc.1_Intron|HSDL2_uc011lww.1_Intron	NM_032303	NP_115679			hydroxysteroid dehydrogenase like 2							peroxisome	oxidoreductase activity|sterol binding				0																		---	---	---	---
KIAA1958	158405	broad.mit.edu	37	9	115257366	115257367	+	Intron	DEL	AT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115257366_115257367delAT	uc004bgf.1	+						KIAA1958_uc011lwx.1_Intron	NM_133465	NP_597722			hypothetical protein LOC158405											skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	115682590	115682590	+	IGR	DEL	A	-	-	rs71491068		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115682590delA								SLC46A2 (29397 upstream) : ZNF883 (76812 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	115908161	115908161	+	IGR	DEL	T	-	-	rs112104968		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115908161delT								C9orf109 (26037 upstream) : SLC31A2 (5077 downstream)																																			---	---	---	---
C9orf43	257169	broad.mit.edu	37	9	116186801	116186804	+	Intron	DEL	TTTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116186801_116186804delTTTT	uc004bho.3	+						C9orf43_uc004bhp.2_Intron	NM_152786	NP_689999			hypothetical protein LOC257169												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	116592460	116592460	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116592460delA								RGS3 (232443 upstream) : ZNF618 (46102 downstream)																																			---	---	---	---
AMBP	259	broad.mit.edu	37	9	116824436	116824437	+	Intron	INS	-	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116824436_116824437insC	uc004bie.3	-						AMBP_uc011lxk.1_Intron|AMBP_uc010mvc.1_Intron	NM_001633	NP_001624			alpha-1-microglobulin/bikunin preproprotein						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)													---	---	---	---
KIF12	113220	broad.mit.edu	37	9	116863480	116863481	+	5'Flank	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116863480_116863481insT	uc004bif.2	-						KIF12_uc004big.2_5'Flank	NM_138424	NP_612433			kinesin family member 12						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	116872087	116872088	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116872087_116872088delTT								KIF12 (10580 upstream) : COL27A1 (46143 downstream)																																			---	---	---	---
COL27A1	85301	broad.mit.edu	37	9	117038016	117038016	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117038016delC	uc011lxl.1	+	37	3685	c.3685delC	c.(3685-3687)CCCfs	p.P1229fs	COL27A1_uc004bii.2_RNA	NM_032888	NP_116277	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1 precursor	1229	Collagen-like 10.|Pro-rich.|Triple-helical region.				cell adhesion		extracellular matrix structural constituent			ovary(3)|skin(1)	4																		---	---	---	---
COL27A1	85301	broad.mit.edu	37	9	117047618	117047619	+	Intron	INS	-	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117047618_117047619insC	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	117339241	117339241	+	IGR	DEL	A	-	-	rs4978599	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117339241delA								DFNB31 (71511 upstream) : ATP6V1G1 (10753 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	117342929	117342931	+	IGR	DEL	GAA	-	-	rs35788739		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117342929_117342931delGAA								DFNB31 (75199 upstream) : ATP6V1G1 (7063 downstream)																																			---	---	---	---
TNFSF8	944	broad.mit.edu	37	9	117678053	117678054	+	Intron	INS	-	G	G	rs148692901	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117678053_117678054insG	uc004bji.1	-							NM_001244	NP_001235			tumor necrosis factor (ligand) superfamily,						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																		---	---	---	---
DEC1	50514	broad.mit.edu	37	9	118134990	118135001	+	Intron	DEL	GTGTGTGTGTGT	-	-	rs72181491		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:118134990_118135001delGTGTGTGTGTGT	uc004bjk.1	+						DEC1_uc004bjl.1_Intron	NM_017418	NP_059114			deleted in esophageal cancer 1						negative regulation of cell proliferation					ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	118908912	118908912	+	IGR	DEL	C	-	-	rs11336194		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:118908912delC								C9orf27 (221535 upstream) : PAPPA (7159 downstream)																																			---	---	---	---
ASTN2	23245	broad.mit.edu	37	9	119250090	119250090	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119250090delT	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_5'Flank	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	119311544	119311545	+	Intron	INS	-	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119311544_119311545insG	uc004bjs.1	-						ASTN2_uc004bjr.1_Intron|ASTN2_uc004bjt.1_Intron|ASTN2_uc004bjp.1_Intron|ASTN2_uc004bjq.1_Intron|ASTN2_uc011lxr.1_Intron|ASTN2_uc011lxs.1_Intron|ASTN2_uc011lxt.1_Intron|uc004bju.1_Intron	NM_198187	NP_937830			astrotactin 2 isoform c							integral to membrane				skin(4)|ovary(3)|breast(1)|kidney(1)	9																		---	---	---	---
ASTN2	23245	broad.mit.edu	37	9	119349105	119349110	+	Intron	DEL	ATACAT	-	-	rs111806063		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119349105_119349110delATACAT	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	119780823	119780823	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119780823delT	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	120491045	120491045	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:120491045delA								TLR4 (11281 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	120645431	120645432	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:120645431_120645432delAA								TLR4 (165667 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	121624988	121624988	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:121624988delT								None (None upstream) : DBC1 (303920 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	123078741	123078741	+	IGR	DEL	T	-	-	rs846822	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123078741delT								MIR147 (71413 upstream) : CDK5RAP2 (72407 downstream)																																			---	---	---	---
CDK5RAP2	55755	broad.mit.edu	37	9	123320950	123320951	+	Intron	INS	-	AAGCTCTT	AAGCTCTT			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123320950_123320951insAAGCTCTT	uc004bkf.2	-						CDK5RAP2_uc004bkg.2_Intron|CDK5RAP2_uc011lxw.1_Intron|CDK5RAP2_uc011lxx.1_Intron|CDK5RAP2_uc011lxy.1_Intron|CDK5RAP2_uc011lxz.1_Intron|CDK5RAP2_uc011lya.1_Intron|CDK5RAP2_uc004bkh.1_Intron	NM_018249	NP_060719			CDK5 regulatory subunit associated protein 2						brain development|centrosome organization|chromosome segregation|G2/M transition of mitotic cell cycle|microtubule bundle formation|negative regulation of centriole replication|positive regulation of transcription, DNA-dependent|regulation of neuron differentiation|regulation of spindle checkpoint	cytosol|Golgi apparatus|microtubule|pericentriolar material|perinuclear region of cytoplasm|spindle pole	calmodulin binding|microtubule binding|neuronal Cdc2-like kinase binding|transcription regulatory region DNA binding			ovary(2)|lung(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	123708287	123708287	+	IGR	DEL	A	-	-	rs34823362		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123708287delA								TRAF1 (16808 upstream) : C5 (6329 downstream)																																			---	---	---	---
CEP110	11064	broad.mit.edu	37	9	123927597	123927597	+	Intron	DEL	A	-	-	rs34558172		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123927597delA	uc004bkx.1	+						CEP110_uc004blb.1_Intron|CEP110_uc010mvp.1_Intron	NM_007018	NP_008949			centrosomal protein 110kDa						cell division|G2/M transition of mitotic cell cycle	centrosome|cytosol	protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	124204990	124204991	+	IGR	INS	-	GT	GT	rs148747239	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124204990_124204991insGT								STOM (72445 upstream) : GGTA1 (2278 downstream)																																			---	---	---	---
NDUFA8	4702	broad.mit.edu	37	9	124914835	124914836	+	Intron	DEL	TT	-	-	rs67198577		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124914835_124914836delTT	uc004blv.2	-							NM_014222	NP_055037			NADH dehydrogenase (ubiquinone) 1 alpha						mitochondrial electron transport, NADH to ubiquinone|transport	mitochondrial intermembrane space|mitochondrial respiratory chain complex I	NADH dehydrogenase (ubiquinone) activity			breast(1)	1					NADH(DB00157)													---	---	---	---
RABGAP1	23637	broad.mit.edu	37	9	125800013	125800014	+	Intron	DEL	TA	-	-	rs662117	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125800013_125800014delTA	uc011lzh.1	+						RABGAP1_uc004bnl.3_Intron|RABGAP1_uc011lzj.1_Intron	NM_012197	NP_036329			RAB GTPase activating protein 1						cell cycle	centrosome|cytosol|microtubule associated complex	Rab GTPase activator activity|tubulin binding			ovary(3)|kidney(2)	5																		---	---	---	---
RABGAP1	23637	broad.mit.edu	37	9	125811569	125811570	+	Intron	INS	-	TTG	TTG			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125811569_125811570insTTG	uc011lzh.1	+						RABGAP1_uc004bnl.3_Intron|RABGAP1_uc011lzj.1_Intron	NM_012197	NP_036329			RAB GTPase activating protein 1						cell cycle	centrosome|cytosol|microtubule associated complex	Rab GTPase activator activity|tubulin binding			ovary(3)|kidney(2)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	126051284	126051284	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126051284delT								STRBP (20441 upstream) : CRB2 (67164 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	126090467	126090467	+	IGR	DEL	G	-	-	rs34121345		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126090467delG								STRBP (59624 upstream) : CRB2 (27981 downstream)																																			---	---	---	---
DENND1A	57706	broad.mit.edu	37	9	126461357	126461357	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126461357delT	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																		---	---	---	---
GPR144	347088	broad.mit.edu	37	9	127224511	127224511	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127224511delT	uc010mwn.2	+						GPR144_uc004bom.1_Intron	NM_001161808	NP_001155280			G protein-coupled receptor 144						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	127596430	127596430	+	IGR	DEL	A	-	-	rs71492425		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127596430delA								OLFML2A (19273 upstream) : WDR38 (19325 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	128186931	128186931	+	IGR	DEL	T	-	-	rs80041036		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128186931delT								GAPVD1 (59642 upstream) : MAPKAP1 (12743 downstream)																																			---	---	---	---
MAPKAP1	79109	broad.mit.edu	37	9	128402392	128402392	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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																		---	---	---	---
MAPKAP1	79109	broad.mit.edu	37	9	128452502	128452502	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128452502delA	uc004bpv.2	-						MAPKAP1_uc004bpw.2_Intron|MAPKAP1_uc004bpx.2_Intron|MAPKAP1_uc004bpy.2_Intron|MAPKAP1_uc004bpz.2_Intron|MAPKAP1_uc010mxa.2_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																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	128803017	128803017	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128803017delT								PBX3 (73364 upstream) : FAM125B (286111 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	128813680	128813680	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128813680delA								PBX3 (84027 upstream) : FAM125B (275448 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	128897961	128897961	+	IGR	DEL	A	-	-	rs5900687		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128897961delA								PBX3 (168308 upstream) : FAM125B (191167 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	128944018	128944018	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128944018delT								PBX3 (214365 upstream) : FAM125B (145110 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	129038492	129038493	+	5'Flank	DEL	CT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129038492_129038493delCT	uc004bqf.1	-											Homo sapiens cDNA clone IMAGE:5259303.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	129323687	129323687	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129323687delT								FAM125B (49988 upstream) : LMX1B (53061 downstream)																																			---	---	---	---
ZBTB34	403341	broad.mit.edu	37	9	129633457	129633458	+	Intron	DEL	GG	-	-	rs10555630		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129633457_129633458delGG	uc004bqm.3	+							NM_001099270	NP_001092740			zinc finger and BTB domain containing 34						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	129651853	129651854	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129651853_129651854insT								ZBTB34 (3699 upstream) : RALGPS1 (25199 downstream)																																			---	---	---	---
LRSAM1	90678	broad.mit.edu	37	9	130234065	130234066	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130234065_130234066insA	uc004brb.1	+						LRSAM1_uc010mxk.1_Intron|LRSAM1_uc004brc.1_Intron|LRSAM1_uc004brd.1_Intron	NM_001005373	NP_001005373			leucine rich repeat and sterile alpha motif						negative regulation of endocytosis|non-lytic virus budding|protein autoubiquitination|protein catabolic process|protein polyubiquitination|protein transport|ubiquitin-dependent endocytosis	cytoplasm|extracellular region|membrane part	hormone activity|ubiquitin-protein ligase activity|zinc ion binding				0																		---	---	---	---
FAM129B	64855	broad.mit.edu	37	9	130326572	130326575	+	Intron	DEL	AAAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130326572_130326575delAAAA	uc004brh.2	-						FAM129B_uc004bri.2_Intron|FAM129B_uc004brj.3_Intron	NM_022833	NP_073744			hypothetical protein LOC64855 isoform 1								protein binding				0																		---	---	---	---
FPGS	2356	broad.mit.edu	37	9	130567170	130567170	+	Intron	DEL	T	-	-	rs72030539		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130567170delT	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)													---	---	---	---
ENG	2022	broad.mit.edu	37	9	130599076	130599076	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130599076delT	uc004bsj.3	-						ENG_uc011mam.1_Intron|ENG_uc004bsk.3_Intron	NM_001114753	NP_001108225			endoglin isoform 1 precursor						artery morphogenesis|BMP signaling pathway|cell adhesion|cell chemotaxis|central nervous system vasculogenesis|chronological cell aging|detection of hypoxia|extracellular matrix disassembly|heart looping|negative regulation of endothelial cell proliferation|negative regulation of nitric-oxide synthase activity|negative regulation of pathway-restricted SMAD protein phosphorylation|negative regulation of protein autophosphorylation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|patterning of blood vessels|positive regulation of BMP signaling pathway|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of systemic arterial blood pressure|positive regulation of transcription from RNA polymerase II promoter|regulation of cell adhesion|regulation of cell proliferation|regulation of transcription, DNA-dependent|regulation of transforming growth factor beta receptor signaling pathway|smooth muscle tissue development|transforming growth factor beta receptor signaling pathway|venous blood vessel morphogenesis|wound healing	cell surface|external side of plasma membrane|extracellular space|membrane fraction	activin binding|galactose binding|glycosaminoglycan binding|protein homodimerization activity|transforming growth factor beta binding|transforming growth factor beta receptor activity|transforming growth factor beta receptor, cytoplasmic mediator activity|transmembrane receptor activity|type I transforming growth factor beta receptor binding|type II transforming growth factor beta receptor binding				0														Juvenile_Polyposis|Hereditary_Hemorrhagic_Telangiectasia				---	---	---	---
SPTAN1	6709	broad.mit.edu	37	9	131322015	131322017	+	Intron	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131322015_131322017delTTT	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																		---	---	---	---
SH3GLB2	56904	broad.mit.edu	37	9	131775129	131775129	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131775129delC	uc004bwv.2	-						SH3GLB2_uc004bww.2_Intron|SH3GLB2_uc004bwx.1_Intron|SH3GLB2_uc011mbm.1_Intron	NM_020145	NP_064530			SH3-domain GRB2-like endophilin B2						filopodium assembly|signal transduction	cytoplasm|nucleus	cytoskeletal adaptor activity|SH3 domain binding				0																		---	---	---	---
PPP2R4	5524	broad.mit.edu	37	9	131893543	131893543	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131893543delT	uc004bxm.1	+						PPP2R4_uc004bxl.1_Intron|PPP2R4_uc011mbo.1_Intron|PPP2R4_uc010myr.1_Intron|PPP2R4_uc004bxn.1_Intron|PPP2R4_uc004bxo.1_Intron|PPP2R4_uc011mbp.1_Intron|PPP2R4_uc011mbq.1_Intron|PPP2R4_uc010mys.1_Intron	NM_178001	NP_821068			protein phosphatase 2A, regulatory subunit B'						ATP catabolic process|negative regulation of phosphoprotein phosphatase activity|negative regulation of protein dephosphorylation|positive regulation of apoptosis|positive regulation of phosphoprotein phosphatase activity|positive regulation of protein dephosphorylation	calcium channel complex|cytoplasm|nucleus|protein phosphatase type 2A complex|soluble fraction	ATP binding|peptidyl-prolyl cis-trans isomerase activity|protein heterodimerization activity|protein homodimerization activity|protein phosphatase 2A binding|protein phosphatase type 2A regulator activity|protein tyrosine phosphatase activator activity|receptor binding			ovary(1)|lung(1)|pancreas(1)	3		Medulloblastoma(224;0.235)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0178)												OREG0019530	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	132033196	132033196	+	IGR	DEL	T	-	-	rs5900840		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132033196delT								IER5L (92656 upstream) : C9orf106 (50099 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	132038489	132038492	+	IGR	DEL	TTTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132038489_132038492delTTTT								IER5L (97949 upstream) : C9orf106 (44803 downstream)																																			---	---	---	---
TOR1A	1861	broad.mit.edu	37	9	132576091	132576091	+	3'UTR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132576091delG	uc004byl.2	-	5					TOR1A_uc004bym.2_RNA	NM_000113	NP_000104			torsin A precursor						chaperone mediated protein folding requiring cofactor|response to unfolded protein	endoplasmic reticulum lumen|nuclear membrane	ATP binding|serine-type endopeptidase activity|unfolded protein binding			central_nervous_system(1)	1		Ovarian(14;0.00556)																---	---	---	---
FNBP1	23048	broad.mit.edu	37	9	132719836	132719836	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132719836delT	uc004byw.1	-						FNBP1_uc011mbv.1_Intron|FNBP1_uc011mbw.1_Intron|FNBP1_uc004bza.2_Intron|FNBP1_uc004byz.1_Intron|FNBP1_uc004byx.1_Intron|FNBP1_uc004byy.1_Intron	NM_015033	NP_055848			formin binding protein 1						endocytosis	cell cortex|cytoplasmic membrane-bounded vesicle|cytoskeleton|lysosome|plasma membrane	identical protein binding|lipid binding				0		Ovarian(14;0.000536)		GBM - Glioblastoma multiforme(294;0.0378)				T	MLL	AML								---	---	---	---
GPR107	57720	broad.mit.edu	37	9	132838832	132838832	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132838832delT	uc004bze.2	+						GPR107_uc004bzb.2_Intron|GPR107_uc004bzc.3_Intron|GPR107_uc011mbx.1_Intron|GPR107_uc004bzd.2_Intron	NM_001136557	NP_001130029			G protein-coupled receptor 107 isoform 1							integral to membrane				upper_aerodigestive_tract(1)	1		Ovarian(14;0.000531)																---	---	---	---
Unknown	0	broad.mit.edu	37	9	133386070	133386070	+	IGR	DEL	A	-	-	rs56246408	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133386070delA								ASS1 (9410 upstream) : LOC100272217 (66669 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	133436545	133436545	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133436545delA								ASS1 (59885 upstream) : LOC100272217 (16194 downstream)																																			---	---	---	---
ABL1	25	broad.mit.edu	37	9	133636056	133636057	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133636056_133636057delTT	uc004bzv.2	+							NM_007313	NP_009297			c-abl oncogene 1, receptor tyrosine kinase						actin cytoskeleton organization|axon guidance|blood coagulation|cell adhesion|DNA damage induced protein phosphorylation|DNA damage response, signal transduction resulting in induction of apoptosis|mismatch repair|muscle cell differentiation|negative regulation of protein serine/threonine kinase activity|peptidyl-tyrosine phosphorylation|positive regulation of muscle cell differentiation|positive regulation of oxidoreductase activity|regulation of transcription involved in S phase of mitotic cell cycle	cytoskeleton|cytosol|nuclear membrane|nucleolus|perinuclear region of cytoplasm	ATP binding|DNA binding|magnesium ion binding|manganese ion binding|mitogen-activated protein kinase binding|non-membrane spanning protein tyrosine kinase activity|proline-rich region binding|protein C-terminus binding|SH3 domain binding			haematopoietic_and_lymphoid_tissue(807)|lung(5)|stomach(2)|central_nervous_system(1)|breast(1)|skin(1)	817		all_hematologic(13;0.0361)|Acute lymphoblastic leukemia(5;0.0543)|Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.4e-05)	Adenosine triphosphate(DB00171)|Dasatinib(DB01254)|Imatinib(DB00619)			T|Mis	BCR|ETV6|NUP214	CML|ALL|T-ALL								---	---	---	---
Unknown	0	broad.mit.edu	37	9	133843442	133843442	+	IGR	DEL	T	-	-	rs113718802		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133843442delT								FIBCD1 (28987 upstream) : LAMC3 (41062 downstream)																																			---	---	---	---
LAMC3	10319	broad.mit.edu	37	9	133947527	133947528	+	Intron	INS	-	AGGGAGGG	AGGGAGGG	rs138234639	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133947527_133947528insAGGGAGGG	uc004caa.1	+							NM_006059	NP_006050			laminin, gamma 3 precursor						cell adhesion	basement membrane|membrane	structural molecule activity			ovary(2)|pancreas(1)	3	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.06e-05)|Epithelial(140;0.000551)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	134210714	134210715	+	IGR	INS	-	TTCC	TTCC	rs138146110	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134210714_134210715insTTCC								PPAPDC3 (26065 upstream) : BAT2L1 (58885 downstream)																																			---	---	---	---
BAT2L1	84726	broad.mit.edu	37	9	134328473	134328473	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134328473delT	uc004can.3	+						BAT2L1_uc010mzj.1_Intron	NM_013318	NP_037450			HLA-B associated transcript 2-like								protein binding				0																		---	---	---	---
RAPGEF1	2889	broad.mit.edu	37	9	134550474	134550474	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134550474delG	uc004cbc.2	-						RAPGEF1_uc004cbb.2_Intron|RAPGEF1_uc010mzn.2_Intron|RAPGEF1_uc004cbd.2_Intron	NM_005312	NP_005303			guanine nucleotide-releasing factor 2 isoform a						activation of MAPKK activity|nerve growth factor receptor signaling pathway|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|endosome	guanyl-nucleotide exchange factor activity|SH3 domain binding			lung(3)|ovary(2)|breast(1)|skin(1)	7		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;2.19e-05)|Epithelial(140;0.000364)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	134642520	134642520	+	IGR	DEL	C	-	-	rs869381	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134642520delC								RAPGEF1 (27303 upstream) : MED27 (92979 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	134718897	134718898	+	IGR	DEL	CT	-	-	rs2987400	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134718897_134718898delCT								RAPGEF1 (103680 upstream) : MED27 (16601 downstream)																																			---	---	---	---
MED27	9442	broad.mit.edu	37	9	134759583	134759583	+	Intron	DEL	A	-	-	rs111775468		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134759583delA	uc004cbe.1	-						MED27_uc004cbf.1_Intron|MED27_uc011mco.1_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)														---	---	---	---
GTF3C4	9329	broad.mit.edu	37	9	135546500	135546500	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135546500delA	uc010mzv.2	+						DDX31_uc004cbq.1_5'Flank|DDX31_uc010mzu.1_5'Flank|DDX31_uc004cbr.1_5'Flank|DDX31_uc004cbs.1_5'Flank|GTF3C4_uc010mzw.2_Intron	NM_012204	NP_036336			general transcription factor IIIC 4						transcription initiation from RNA polymerase III promoter	transcription factor TFIIIC complex	DNA binding|enzyme activator activity|histone acetyltransferase activity|protein binding			ovary(1)|central_nervous_system(1)	2				OV - Ovarian serous cystadenocarcinoma(145;8.15e-07)|Epithelial(140;2.6e-05)														---	---	---	---
C9orf98	158067	broad.mit.edu	37	9	135616444	135616445	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135616444_135616445insT	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	135748826	135748826	+	Intron	DEL	G	-	-	rs113549526		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135748826delG	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)														---	---	---	---
ABO	28	broad.mit.edu	37	9	136138558	136138558	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136138558delT	uc004cda.1	-						ABO_uc010naf.1_Intron|ABO_uc011mcz.1_Intron|ABO_uc010nag.1_Intron	NM_020469	NP_065202			ABO blood group (alpha						protein glycosylation	extracellular region|Golgi cisterna membrane|integral to Golgi membrane	fucosylgalactoside 3-alpha-galactosyltransferase activity|glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase activity|metal ion binding				0				OV - Ovarian serous cystadenocarcinoma(145;5.82e-06)|Epithelial(140;3.45e-05)														---	---	---	---
C9orf96	169436	broad.mit.edu	37	9	136249512	136249513	+	Intron	DEL	AT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136249512_136249513delAT	uc004cdk.2	+						C9orf96_uc004cdl.2_Intron	NM_153710	NP_714921			hypothetical protein LOC169436								ATP binding|protein kinase activity			stomach(2)|central_nervous_system(2)	4				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)														---	---	---	---
SARDH	1757	broad.mit.edu	37	9	136595584	136595585	+	Intron	INS	-	TT	TT	rs141823931	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136595584_136595585insTT	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	136761919	136761919	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136761919delA	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	136848765	136848766	+	Intron	DEL	CT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136848765_136848766delCT	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	136976836	136976837	+	IGR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136976836_136976837insA								BRD3 (43181 upstream) : WDR5 (24373 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	136977278	136977279	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136977278_136977279insT								BRD3 (43623 upstream) : WDR5 (23931 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	137165489	137165492	+	IGR	DEL	CTCC	-	-	rs141349896		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137165489_137165492delCTCC								RNU6ATAC (135803 upstream) : RXRA (43452 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	137376403	137376403	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137376403delA								RXRA (43972 upstream) : COL5A1 (157249 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	137379810	137379811	+	IGR	INS	-	TTCCTTCC	TTCCTTCC			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137379810_137379811insTTCCTTCC								RXRA (47379 upstream) : COL5A1 (153841 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	138459864	138459865	+	IGR	INS	-	A	A	rs111973902		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138459864_138459865insA								PAEP (1242 upstream) : GLT6D1 (55637 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	138509218	138509218	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138509218delG								PAEP (50596 upstream) : GLT6D1 (6284 downstream)																																			---	---	---	---
GLT6D1	360203	broad.mit.edu	37	9	138530088	138530088	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138530088delC	uc010nbd.1	-							NM_182974	NP_892019			glycosyltransferase 6 domain containing 1						carbohydrate metabolic process	integral to membrane	transferase activity, transferring hexosyl groups			ovary(1)	1		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;4.3e-07)|Epithelial(140;1.58e-06)|all cancers(34;5.36e-05)														---	---	---	---
TRAF2	7186	broad.mit.edu	37	9	139783672	139783677	+	Intron	DEL	TTTTTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139783672_139783677delTTTTTT	uc010nbu.2	+						TRAF2_uc010nbv.1_Intron|TRAF2_uc004cjv.2_Intron|TRAF2_uc011mek.1_Intron|TRAF2_uc010nbw.2_Intron	NM_021138	NP_066961			TNF receptor-associated factor 2						activation of caspase activity|activation of NF-kappaB-inducing kinase activity|activation of pro-apoptotic gene products|cellular protein complex assembly|induction of apoptosis by extracellular signals|positive regulation of interleukin-2 production|positive regulation of JUN kinase activity|positive regulation of NF-kappaB transcription factor activity|positive regulation of T cell cytokine production|protein autoubiquitination|protein homotrimerization|protein K63-linked ubiquitination|tumor necrosis factor-mediated signaling pathway	CD40 receptor complex|cytosol|internal side of plasma membrane	CD40 receptor binding|enzyme binding|protein binding|signal transducer activity|sphingolipid binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|lung(1)|breast(1)|skin(1)	4	all_cancers(76;0.11)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.229)	OV - Ovarian serous cystadenocarcinoma(145;4.48e-06)|Epithelial(140;9.55e-06)														---	---	---	---
EXD3	54932	broad.mit.edu	37	9	140234934	140234934	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140234934delA	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																		---	---	---	---
EHMT1	79813	broad.mit.edu	37	9	140682271	140682271	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140682271delC	uc011mfc.1	+						EHMT1_uc004cob.1_Intron	NM_024757	NP_079033			euchromatic histone-lysine N-methyltransferase 1						DNA methylation|embryo development|peptidyl-lysine dimethylation|peptidyl-lysine monomethylation	chromosome|nucleus	histone methyltransferase activity (H3-K27 specific)|histone methyltransferase activity (H3-K9 specific)|p53 binding|zinc ion binding			breast(2)|pancreas(1)	3	all_cancers(76;0.164)			OV - Ovarian serous cystadenocarcinoma(145;0.000183)|Epithelial(140;0.000728)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	140764177	140764177	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140764177delA	uc004cof.1	-											Homo sapiens cDNA FLJ46557 fis, clone THYMU3039846.																														---	---	---	---
FAM157B	100132403	broad.mit.edu	37	9	141115950	141115950	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:141115950delT	uc011mfe.1	+							NM_001145249	NP_001138721			family with sequence similarity 157, member B												0																		---	---	---	---
DIP2C	22982	broad.mit.edu	37	10	383222	383223	+	Intron	DEL	TC	-	-	rs71376816		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:383222_383223delTC	uc001ifp.2	-							NM_014974	NP_055789			DIP2 disco-interacting protein 2 homolog C							nucleus	catalytic activity|transcription factor binding			breast(4)|ovary(2)|large_intestine(1)	7		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)														---	---	---	---
DIP2C	22982	broad.mit.edu	37	10	685192	685193	+	Intron	INS	-	A	A	rs137912371		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:685192_685193insA	uc001ifp.2	-							NM_014974	NP_055789			DIP2 disco-interacting protein 2 homolog C							nucleus	catalytic activity|transcription factor binding			breast(4)|ovary(2)|large_intestine(1)	7		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	749711	749714	+	IGR	DEL	TCTA	-	-	rs142426285		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:749711_749714delTCTA								DIP2C (14103 upstream) : LARP4B (105770 downstream)																																			---	---	---	---
WDR37	22884	broad.mit.edu	37	10	1135643	1135668	+	Intron	DEL	GTGCTCACCCGCAATTCAACCTTCCT	-	-	rs72190929	by1000genomes;by1000genomes;by1000genomes;by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1135643_1135668delGTGCTCACCCGCAATTCAACCTTCCT	uc001igf.1	+						WDR37_uc001ige.2_Intron|WDR37_uc009xhm.1_Intron|WDR37_uc009xhn.1_Intron|WDR37_uc001igg.1_Intron|uc001igh.1_5'Flank	NM_014023	NP_054742			WD repeat domain 37												0		all_epithelial(10;0.0449)|Colorectal(49;0.142)		Epithelial(11;0.134)														---	---	---	---
ADARB2	105	broad.mit.edu	37	10	1320485	1320486	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1320485_1320486delTT	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	2052158	2052159	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:2052158_2052159delTT	uc001igo.1	-											Homo sapiens cDNA FLJ40155 fis, clone TESTI2014362.																														---	---	---	---
Unknown	0	broad.mit.edu	37	10	3012549	3012549	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3012549delT								None (None upstream) : PFKP (97203 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	3042073	3042074	+	IGR	DEL	CA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3042073_3042074delCA								None (None upstream) : PFKP (67678 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	3315761	3315761	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3315761delA								PITRM1 (100758 upstream) : KLF6 (502428 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	3451047	3451049	+	Intron	DEL	GAG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3451047_3451049delGAG	uc001igy.1	+											Homo sapiens cDNA clone IMAGE:5278070.																														---	---	---	---
Unknown	0	broad.mit.edu	37	10	3696353	3696353	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3696353delT	uc001igy.1	+											Homo sapiens cDNA clone IMAGE:5278070.																														---	---	---	---
Unknown	0	broad.mit.edu	37	10	4360798	4360798	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:4360798delA								KLF6 (533325 upstream) : LOC100216001 (260646 downstream)																																			---	---	---	---
AKR1E2	83592	broad.mit.edu	37	10	4927381	4927381	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:4927381delA	uc001ihl.1	+						tAKR_uc001ihm.3_Intron					Homo sapiens mRNA for aldo-keto reductase related protein 1, complete cds.							cytoplasm	1,5-anhydro-D-fructose reductase activity				0																		---	---	---	---
NET1	10276	broad.mit.edu	37	10	5499147	5499147	+	3'UTR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5499147delT	uc001iia.2	+	12					NET1_uc010qar.1_3'UTR|NET1_uc001iib.2_3'UTR|NET1_uc010qas.1_3'UTR	NM_001047160	NP_001040625			neuroepithelial cell transforming gene 1 isoform						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of cell growth|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|nucleus	Rho guanyl-nucleotide exchange factor activity			breast(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	5518840	5518840	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5518840delC								NET1 (18416 upstream) : CALML5 (21818 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	6048076	6048076	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:6048076delT								IL15RA (27934 upstream) : IL2RA (5430 downstream)																																			---	---	---	---
RBM17	84991	broad.mit.edu	37	10	6148740	6148740	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:6148740delT	uc001ijb.2	+						RBM17_uc010qav.1_Intron	NM_032905	NP_116294			RNA binding motif protein 17						mRNA processing|RNA splicing	spliceosomal complex	nucleotide binding|protein binding|RNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	6183773	6183773	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:6183773delT								RBM17 (24353 upstream) : PFKFB3 (3070 downstream)																																			---	---	---	---
PRKCQ	5588	broad.mit.edu	37	10	6532855	6532856	+	Intron	DEL	TT	-	-	rs73607007	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:6532855_6532856delTT	uc001ijj.1	-						PRKCQ_uc009xim.1_Intron|PRKCQ_uc001iji.1_Intron|PRKCQ_uc009xin.1_Intron|PRKCQ_uc010qax.1_Intron	NM_006257	NP_006248			protein kinase C, theta						axon guidance|cellular component disassembly involved in apoptosis|intracellular signal transduction|membrane protein ectodomain proteolysis|platelet activation|regulation of cell growth|T cell receptor signaling pathway	cytosol	ATP binding|metal ion binding|protein binding|protein kinase C activity			ovary(3)|lung(2)|large_intestine(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	6733008	6733009	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:6733008_6733009delTT								PRKCQ (110770 upstream) : SFMBT2 (471240 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	6758454	6758455	+	IGR	INS	-	GT	GT	rs145939446	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:6758454_6758455insGT								PRKCQ (136216 upstream) : SFMBT2 (445794 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	6820659	6820659	+	5'Flank	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:6820659delG	uc001ijm.2	+											Homo sapiens cDNA FLJ36835 fis, clone ASTRO2010996.																														---	---	---	---
SFMBT2	57713	broad.mit.edu	37	10	7245679	7245680	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7245679_7245680insT	uc009xio.1	-						SFMBT2_uc001ijn.1_Intron|SFMBT2_uc010qay.1_Intron	NM_001029880	NP_001025051			Scm-like with four mbt domains 2						regulation of transcription, DNA-dependent	nucleus				ovary(4)|upper_aerodigestive_tract(2)|large_intestine(1)|central_nervous_system(1)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	7563485	7563485	+	IGR	DEL	T	-	-	rs112917564		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7563485delT								SFMBT2 (110035 upstream) : ITIH5 (38151 downstream)																																			---	---	---	---
ITIH5	80760	broad.mit.edu	37	10	7697413	7697413	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7697413delA	uc001ijq.2	-						ITIH5_uc001ijr.1_Intron	NM_030569	NP_085046			inter-alpha trypsin inhibitor heavy chain						hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			ovary(2)|central_nervous_system(2)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	7720976	7720981	+	IGR	DEL	CGCGCG	-	-	rs141829074	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7720976_7720981delCGCGCG								ITIH5 (12042 upstream) : ITIH2 (24255 downstream)																																			---	---	---	---
KIN	22944	broad.mit.edu	37	10	7816627	7816629	+	Intron	DEL	AAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7816627_7816629delAAA	uc001ijt.2	-						KIN_uc010qaz.1_Intron|KIN_uc009xip.2_Intron|KIN_uc010qba.1_Intron	NM_012311	NP_036443			HsKin17 protein						DNA recombination|DNA repair|DNA replication|interspecies interaction between organisms|mRNA processing	cytoplasm|nuclear matrix	double-stranded DNA binding|RNA binding|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
TAF3	83860	broad.mit.edu	37	10	7989450	7989450	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7989450delC	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	8193886	8193889	+	IGR	DEL	CACT	-	-	rs71800068	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:8193886_8193889delCACT								GATA3 (76724 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	8244922	8244922	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:8244922delT								GATA3 (127760 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	9059073	9059075	+	IGR	DEL	TTG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:9059073_9059075delTTG								GATA3 (941911 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	9333817	9333817	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:9333817delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	9738981	9738981	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:9738981delC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	10437562	10437562	+	IGR	DEL	T	-	-	rs113960082		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:10437562delT								None (None upstream) : SFTA1P (388840 downstream)																																			---	---	---	---
CELF2	10659	broad.mit.edu	37	10	11150312	11150312	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11150312delT	uc001iki.3	+						CELF2_uc010qbi.1_Intron|CELF2_uc010qbj.1_Intron|CELF2_uc001ikk.2_Intron|CELF2_uc001ikl.3_Intron|uc001ikn.1_5'Flank	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	11947908	11947908	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11947908delA								C10orf47 (33634 upstream) : UPF2 (14114 downstream)																																			---	---	---	---
UPF2	26019	broad.mit.edu	37	10	12072883	12072883	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12072883delA	uc001ila.2	-						UPF2_uc001ilb.2_Intron|UPF2_uc001ilc.2_Intron|UPF2_uc009xiz.1_Intron	NM_080599	NP_542166			UPF2 regulator of nonsense transcripts homolog						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)																---	---	---	---
CDC123	8872	broad.mit.edu	37	10	12285129	12285129	+	Intron	DEL	G	-	-	rs75196259		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12285129delG	uc001ill.2	+						CDC123_uc001ilm.2_Intron	NM_006023	NP_006014			cell division cycle 123						cell cycle arrest|cell division|positive regulation of cell proliferation|regulation of mitotic cell cycle	cytoplasm				central_nervous_system(1)	1																		---	---	---	---
MCM10	55388	broad.mit.edu	37	10	13233564	13233567	+	Intron	DEL	AAGC	-	-	rs112703555		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13233564_13233567delAAGC	uc001ima.2	+						MCM10_uc001imb.2_Intron|MCM10_uc001imc.2_Intron	NM_182751	NP_877428			minichromosome maintenance complex component 10						cell cycle checkpoint|DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle	nucleoplasm	metal ion binding|protein binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	13417680	13417680	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13417680delT								SEPHS1 (27400 upstream) : BEND7 (62804 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	13623986	13623987	+	IGR	DEL	TT	-	-	rs78194971		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13623986_13623987delTT								BEND7 (79010 upstream) : PRPF18 (4952 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	14856070	14856071	+	IGR	DEL	AA	-	-	rs76564968		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14856070_14856071delAA								FAM107B (39174 upstream) : CDNF (5180 downstream)																																			---	---	---	---
DCLRE1C	64421	broad.mit.edu	37	10	14970265	14970265	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14970265delA	uc001inn.2	-						DCLRE1C_uc010qbx.1_Intron|DCLRE1C_uc001inl.2_Intron|DCLRE1C_uc009xji.2_Intron|DCLRE1C_uc001inm.2_Intron|DCLRE1C_uc001ino.2_Intron|DCLRE1C_uc009xjh.2_Intron|DCLRE1C_uc001inp.2_Intron|DCLRE1C_uc001inq.2_Intron|DCLRE1C_uc001inr.2_Intron|DCLRE1C_uc009xjj.1_Intron	NM_001033855	NP_001029027			artemis protein isoform a						DNA recombination	nucleus	5'-3' exonuclease activity|single-stranded DNA specific endodeoxyribonuclease activity			ovary(1)	1													Involved_in_tolerance_or_repair_of_DNA_crosslinks|NHEJ					---	---	---	---
Unknown	0	broad.mit.edu	37	10	15016316	15016316	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15016316delC								MEIG1 (1466 upstream) : ACBD7 (40755 downstream)																																			---	---	---	---
ITGA8	8516	broad.mit.edu	37	10	15719443	15719443	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15719443delA	uc001ioc.1	-						ITGA8_uc010qcb.1_Intron	NM_003638	NP_003629			integrin, alpha 8 precursor						cell differentiation|cell-cell adhesion|cell-matrix adhesion|integrin-mediated signaling pathway|nervous system development	integrin complex	receptor activity			ovary(3)|lung(3)	6																		---	---	---	---
PTER	9317	broad.mit.edu	37	10	16531549	16531549	+	Intron	DEL	T	-	-	rs113895158		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:16531549delT	uc001iog.1	+						PTER_uc001ioh.1_Intron|PTER_uc001ioi.1_Intron|PTER_uc009xjp.1_Intron	NM_030664	NP_109589			phosphotriesterase related						catabolic process		hydrolase activity, acting on ester bonds|zinc ion binding			ovary(2)	2																		---	---	---	---
C1QL3	389941	broad.mit.edu	37	10	16558045	16558045	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:16558045delA	uc001ioj.1	-							NM_001010908	NP_001010908			complement component 1, q subcomponent-like 3							collagen				ovary(1)	1																		---	---	---	---
ST8SIA6	338596	broad.mit.edu	37	10	17453172	17453175	+	Intron	DEL	TGTG	-	-	rs72283269		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17453172_17453175delTGTG	uc001ipd.2	-						ST8SIA6_uc010qce.1_Intron	NM_001004470	NP_001004470			ST8 alpha-N-acetyl-neuraminide						post-translational protein modification|protein N-linked glycosylation via asparagine	integral to Golgi membrane	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity			ovary(1)	1																		---	---	---	---
CACNB2	783	broad.mit.edu	37	10	18514066	18514066	+	Intron	DEL	T	-	-	rs74754039		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:18514066delT	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	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)													---	---	---	---
CACNB2	783	broad.mit.edu	37	10	18799243	18799243	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:18799243delT	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|CACNB2_uc010qcn.1_Intron|CACNB2_uc010qco.1_Intron|CACNB2_uc001iqa.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)													---	---	---	---
CACNB2	783	broad.mit.edu	37	10	18805156	18805156	+	Intron	DEL	A	-	-	rs66536954		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:18805156delA	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|CACNB2_uc010qcn.1_Intron|CACNB2_uc010qco.1_Intron|CACNB2_uc001iqa.2_Intron|NSUN6_uc001iqb.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)													---	---	---	---
Unknown	0	broad.mit.edu	37	10	19196463	19196463	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:19196463delA								ARL5B (229523 upstream) : PLXDC2 (908909 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	19526277	19526277	+	IGR	DEL	T	-	-	rs76022484		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:19526277delT								ARL5B (559337 upstream) : PLXDC2 (579095 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	19620286	19620286	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:19620286delT								ARL5B (653346 upstream) : PLXDC2 (485086 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	19637092	19637092	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:19637092delA								ARL5B (670152 upstream) : PLXDC2 (468280 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	20698573	20698574	+	IGR	INS	-	TCTT	TCTT	rs148099452	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:20698573_20698574insTCTT								PLXDC2 (129458 upstream) : NEBL (370331 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	20943926	20943926	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:20943926delG								PLXDC2 (374811 upstream) : NEBL (124979 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	21051794	21051809	+	IGR	DEL	GAGAAAAAGAAAACAT	-	-	rs72226421		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21051794_21051809delGAGAAAAAGAAAACAT								PLXDC2 (482679 upstream) : NEBL (17096 downstream)																																			---	---	---	---
NEBL	10529	broad.mit.edu	37	10	21215335	21215335	+	Intron	DEL	T	-	-	rs66810000		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21215335delT	uc001iqk.2	-							NM_213569	NP_998734			nebulette non-muscle isoform						regulation of actin filament length		actin binding|structural constituent of muscle			ovary(2)	2																		---	---	---	---
NEBL	10529	broad.mit.edu	37	10	21283814	21283814	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21283814delG	uc001iqk.2	-							NM_213569	NP_998734			nebulette non-muscle isoform						regulation of actin filament length		actin binding|structural constituent of muscle			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	21651012	21651012	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21651012delA								NEBL (187896 upstream) : C10orf114 (132410 downstream)																																			---	---	---	---
MLLT10	8028	broad.mit.edu	37	10	22007389	22007389	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22007389delT	uc001iqs.2	+						MLLT10_uc001iqt.2_Intron|MLLT10_uc001iqv.2_Intron|MLLT10_uc001iqy.2_Intron|MLLT10_uc001ira.2_Intron|MLLT10_uc001irb.2_Intron	NM_004641	NP_004632			myeloid/lymphoid or mixed-lineage leukemia						positive regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(1)|skin(1)	2								T	MLL|PICALM|CDK6	AL								---	---	---	---
Unknown	0	broad.mit.edu	37	10	23378439	23378440	+	IGR	DEL	GT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:23378439_23378440delGT								ARMC3 (51927 upstream) : MSRB2 (5987 downstream)																																			---	---	---	---
KIAA1217	56243	broad.mit.edu	37	10	24039936	24039936	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:24039936delT	uc001irs.2	+							NM_001098500	NP_001091970			sickle tail isoform 2						embryonic skeletal system development	cytoplasm				ovary(5)|skin(2)	7																		---	---	---	---
KIAA1217	56243	broad.mit.edu	37	10	24133637	24133637	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:24133637delT	uc001irs.2	+							NM_001098500	NP_001091970			sickle tail isoform 2						embryonic skeletal system development	cytoplasm				ovary(5)|skin(2)	7																		---	---	---	---
KIAA1217	56243	broad.mit.edu	37	10	24165673	24165674	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:24165673_24165674insT	uc001irs.2	+							NM_001098500	NP_001091970			sickle tail isoform 2						embryonic skeletal system development	cytoplasm				ovary(5)|skin(2)	7																		---	---	---	---
KIAA1217	56243	broad.mit.edu	37	10	24435618	24435618	+	Intron	DEL	A	-	-	rs78262492		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:24435618delA	uc001irs.2	+							NM_001098500	NP_001091970			sickle tail isoform 2						embryonic skeletal system development	cytoplasm				ovary(5)|skin(2)	7																		---	---	---	---
GPR158	57512	broad.mit.edu	37	10	25595946	25595947	+	Intron	DEL	AG	-	-	rs67926384		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:25595946_25595947delAG	uc001isj.2	+							NM_020752	NP_065803			G protein-coupled receptor 158 precursor							integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(4)|large_intestine(2)|pancreas(1)|skin(1)	8																		---	---	---	---
GPR158	57512	broad.mit.edu	37	10	25667335	25667335	+	Intron	DEL	T	-	-	rs10712934		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:25667335delT	uc001isj.2	+							NM_020752	NP_065803			G protein-coupled receptor 158 precursor							integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(4)|large_intestine(2)|pancreas(1)|skin(1)	8																		---	---	---	---
MYO3A	53904	broad.mit.edu	37	10	26418441	26418441	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:26418441delA	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																		---	---	---	---
APBB1IP	54518	broad.mit.edu	37	10	26841564	26841565	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:26841564_26841565delAA	uc001iss.2	+							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																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	26859987	26859988	+	IGR	DEL	CA	-	-	rs74624409		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:26859987_26859988delCA								APBB1IP (3257 upstream) : C10orf50 (18806 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	26946043	26946044	+	IGR	DEL	AC	-	-	rs34769345		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:26946043_26946044delAC								LOC731789 (3661 upstream) : PDSS1 (40551 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	26946297	26946298	+	IGR	INS	-	CTT	CTT	rs140510650	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:26946297_26946298insCTT								LOC731789 (3915 upstream) : PDSS1 (40297 downstream)																																			---	---	---	---
ABI1	10006	broad.mit.edu	37	10	27054256	27054256	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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																		---	---	---	---
ARMC4	55130	broad.mit.edu	37	10	28270269	28270269	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28270269delA	uc009xky.2	-						ARMC4_uc010qds.1_Intron|ARMC4_uc010qdt.1_Intron|ARMC4_uc001itz.2_Intron|ARMC4_uc010qdu.1_Intron	NM_018076	NP_060546			armadillo repeat containing 4								binding			ovary(4)|skin(2)	6																		---	---	---	---
MPP7	143098	broad.mit.edu	37	10	28517689	28517690	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28517689_28517690insA	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	28671177	28671178	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28671177_28671178delTT								MPP7 (79182 upstream) : WAC (150249 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	29644377	29644377	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:29644377delC								LYZL1 (44220 upstream) : LOC387647 (54106 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	30193766	30193775	+	IGR	DEL	CTTCCCTTCT	-	-	rs147512483		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30193766_30193775delCTTCCCTTCT								SVIL (167902 upstream) : KIAA1462 (107954 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	30752027	30752028	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30752027_30752028insT								MAP3K8 (1266 upstream) : LYZL2 (148681 downstream)																																			---	---	---	---
ZNF438	220929	broad.mit.edu	37	10	31172825	31172825	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:31172825delA	uc010qdz.1	-						ZNF438_uc001ivn.2_Intron|ZNF438_uc010qdy.1_Intron|ZNF438_uc001ivo.3_Intron|ZNF438_uc009xlg.2_Intron|ZNF438_uc001ivp.3_Intron|ZNF438_uc010qea.1_Intron|ZNF438_uc010qeb.1_Intron|ZNF438_uc010qec.1_Intron	NM_182755	NP_877432			zinc finger protein 438 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|breast(1)	2		Prostate(175;0.0587)																---	---	---	---
Unknown	0	broad.mit.edu	37	10	31834619	31834619	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:31834619delA								ZEB1 (16492 upstream) : ARHGAP12 (260606 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	31917200	31917205	+	IGR	DEL	AGATGG	-	-	rs138079479		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:31917200_31917205delAGATGG								ZEB1 (99073 upstream) : ARHGAP12 (178020 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	32064621	32064622	+	IGR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:32064621_32064622insA								ZEB1 (246494 upstream) : ARHGAP12 (30603 downstream)																																			---	---	---	---
EPC1	80314	broad.mit.edu	37	10	32572253	32572253	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:32572253delT	uc001iwg.1	-						EPC1_uc001iwi.3_Intron|EPC1_uc009xlt.2_Intron|EPC1_uc001iwh.1_Intron	NM_025209	NP_079485			enhancer of polycomb 1						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)																---	---	---	---
Unknown	0	broad.mit.edu	37	10	33179797	33179797	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:33179797delA								C10orf68 (8006 upstream) : ITGB1 (9451 downstream)																																			---	---	---	---
ITGB1	3688	broad.mit.edu	37	10	33225462	33225462	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:33225462delA	uc001iws.3	-						ITGB1_uc001iwp.3_5'Flank|ITGB1_uc001iwq.3_5'Flank|ITGB1_uc001iwr.3_5'Flank|ITGB1_uc001iwt.3_Intron|ITGB1_uc001iwu.1_5'Flank	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	33273766	33273767	+	IGR	INS	-	A	A	rs151309680	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:33273766_33273767insA								ITGB1 (26473 upstream) : NRP1 (192653 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	33420893	33420893	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:33420893delA								ITGB1 (173600 upstream) : NRP1 (45527 downstream)																																			---	---	---	---
NRP1	8829	broad.mit.edu	37	10	33510802	33510802	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:33510802delA	uc001iwx.3	-						NRP1_uc001iwv.3_Intron|NRP1_uc009xlz.2_Intron|NRP1_uc001iww.3_Intron|NRP1_uc001iwy.3_Intron|NRP1_uc001iwz.2_Intron|NRP1_uc001ixa.2_Intron|NRP1_uc001ixb.1_Intron|NRP1_uc001ixc.1_Intron	NM_003873	NP_003864			neuropilin 1 isoform a						axon guidance|cell adhesion|cell-cell signaling|organ morphogenesis|positive regulation of cell proliferation	extracellular region|integral to membrane|plasma membrane	growth factor binding|heparin binding|metal ion binding|vascular endothelial growth factor receptor activity			central_nervous_system(2)|ovary(1)|skin(1)	4					Palifermin(DB00039)|Pegaptanib(DB04895)													---	---	---	---
Unknown	0	broad.mit.edu	37	10	33790785	33790785	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:33790785delA								NRP1 (166779 upstream) : PARD3 (609313 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	33863513	33863513	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:33863513delA								NRP1 (239507 upstream) : PARD3 (536585 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	33884840	33884840	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:33884840delA								NRP1 (260834 upstream) : PARD3 (515258 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	34041230	34041231	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:34041230_34041231delAA								NRP1 (417224 upstream) : PARD3 (358867 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	34233732	34233733	+	IGR	INS	-	A	A	rs60968419		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:34233732_34233733insA								NRP1 (609726 upstream) : PARD3 (166365 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	34389353	34389353	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:34389353delT								NRP1 (765347 upstream) : PARD3 (10745 downstream)																																			---	---	---	---
PARD3	56288	broad.mit.edu	37	10	34875475	34875475	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:34875475delA	uc010qej.1	-						PARD3_uc010qek.1_Intron|PARD3_uc010qel.1_Intron|PARD3_uc010qem.1_Intron|PARD3_uc010qen.1_Intron|PARD3_uc010qeo.1_Intron|PARD3_uc010qep.1_Intron|PARD3_uc010qeq.1_Intron|PARD3_uc001ixq.1_Intron|PARD3_uc001ixr.1_Intron|PARD3_uc001ixt.1_Intron|PARD3_uc001ixu.1_Intron	NM_019619	NP_062565			partitioning-defective protein 3 homolog						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|asymmetric cell division|axonogenesis|cell cycle|establishment of epithelial cell polarity|protein complex assembly|protein targeting to membrane|tight junction assembly	cell cortex|cytoskeleton|cytosol|endomembrane system|tight junction	phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-4,5-bisphosphate binding|protein binding			ovary(1)	1		Breast(68;0.0707)																---	---	---	---
Unknown	0	broad.mit.edu	37	10	36452798	36452798	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:36452798delA								FZD8 (522436 upstream) : ANKRD30A (961987 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	36859137	36859137	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:36859137delA								FZD8 (928775 upstream) : ANKRD30A (555648 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	37030723	37030723	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:37030723delA								None (None upstream) : ANKRD30A (384062 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	37151478	37151478	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:37151478delT								None (None upstream) : ANKRD30A (263307 downstream)																																			---	---	---	---
ANKRD30A	91074	broad.mit.edu	37	10	37520152	37520152	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:37520152delA	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	37599380	37599380	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:37599380delA								ANKRD30A (77885 upstream) : ZNF248 (491067 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	37794749	37794750	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:37794749_37794750delTT								ANKRD30A (273254 upstream) : ZNF248 (295697 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	38203812	38203812	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38203812delT								ZNF248 (56800 upstream) : ZNF25 (34983 downstream)																																			---	---	---	---
HSD17B7P2	158160	broad.mit.edu	37	10	38666843	38666843	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38666843delT	uc001izq.2	+							NR_003086				Homo sapiens 17-beta-hydroxysteroid dehydrogenase type VII isoform mRNA, complete cds.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	42418454	42418454	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42418454delA								None (None upstream) : LOC441666 (408861 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	42619620	42619620	+	IGR	DEL	A	-	-	rs35875633		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42619620delA								None (None upstream) : LOC441666 (207695 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	42626332	42626334	+	IGR	DEL	ATT	-	-	rs78701857		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42626332_42626334delATT								None (None upstream) : LOC441666 (200981 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	42659018	42659019	+	IGR	INS	-	GAA	GAA	rs147530473		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42659018_42659019insGAA								None (None upstream) : LOC441666 (168296 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	42759121	42759122	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42759121_42759122insT								None (None upstream) : LOC441666 (68193 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	44624111	44624111	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:44624111delT								HNRNPA3P1 (338246 upstream) : CXCL12 (241496 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	45300220	45300220	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45300220delA								CXCL12 (419678 upstream) : TMEM72 (106544 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	45357617	45357618	+	Intron	DEL	CT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45357617_45357618delCT	uc001jbk.1	-						uc001jbl.2_Intron					Homo sapiens cDNA FLJ31956 fis, clone NT2RP7007359.																														---	---	---	---
RASSF4	83937	broad.mit.edu	37	10	45464449	45464450	+	Intron	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45464449_45464450delTG	uc001jbo.2	+						RASSF4_uc001jbp.2_Intron|RASSF4_uc009xmn.2_Intron|RASSF4_uc001jbq.2_Intron	NM_032023	NP_114412			Ras association domain family 4						cell cycle|signal transduction		protein binding			large_intestine(1)	1																		---	---	---	---
ALOX5	240	broad.mit.edu	37	10	45927636	45927639	+	Intron	DEL	AAAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45927636_45927639delAAAA	uc001jce.2	+						ALOX5_uc009xmt.2_Intron|ALOX5_uc010qfg.1_Intron	NM_000698	NP_000689			arachidonate 5-lipoxygenase						hormone biosynthetic process|leukotriene biosynthetic process|prostanoid metabolic process	cytosol|nuclear envelope lumen|nuclear matrix|nuclear membrane	arachidonate 5-lipoxygenase activity|iron ion binding|lipoxygenase activity|protein binding			ovary(1)|pancreas(1)	2		Lung SC(717;0.0257)			Diethylcarbamazine(DB00711)|Hydrocortisone(DB00741)|Leflunomide(DB01097)|Masoprocol(DB00179)|Meclofenamic acid(DB00939)|Minocycline(DB01017)|Montelukast(DB00471)|Quinacrine(DB01103)|Vitamin E(DB00163)|Zileuton(DB00744)													---	---	---	---
MARCH8	220972	broad.mit.edu	37	10	45986072	45986072	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45986072delA	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	45987746	45987746	+	Intron	DEL	T	-	-	rs74663458		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	46094205	46094205	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:46094205delT								MARCH8 (3851 upstream) : ANUBL1 (16835 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	46098340	46098341	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:46098340_46098341delAA								MARCH8 (7986 upstream) : ANUBL1 (12699 downstream)																																			---	---	---	---
ANXA8	653145	broad.mit.edu	37	10	47030122	47030122	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47030122delA	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	47155015	47155016	+	Intron	INS	-	TCCT	TCCT	rs147112054	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47155015_47155016insTCCT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	47370000	47370000	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47370000delT								LOC642826 (126498 upstream) : FAM35B2 (9720 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	47617821	47617822	+	IGR	INS	-	T	T	rs150450015	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47617821_47617822insT								FAM35B2 (196585 upstream) : ANTXRL (40412 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	47621349	47621349	+	IGR	DEL	T	-	-	rs71696628		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47621349delT								FAM35B2 (200113 upstream) : ANTXRL (36885 downstream)																																			---	---	---	---
ANTXRL	195977	broad.mit.edu	37	10	47664623	47664624	+	Intron	INS	-	GC	GC			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47664623_47664624insGC	uc001jel.2	+							NR_003601				Homo sapiens cDNA FLJ32754 fis, clone TESTI2001671.												0																		---	---	---	---
ANTXRL	195977	broad.mit.edu	37	10	47666072	47666073	+	Intron	INS	-	G	G	rs151070050		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47666072_47666073insG	uc001jel.2	+							NR_003601				Homo sapiens cDNA FLJ32754 fis, clone TESTI2001671.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	48484742	48484743	+	IGR	DEL	GT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:48484742_48484743delGT								GDF10 (45576 upstream) : FRMPD2L1 (359300 downstream)																																			---	---	---	---
WDFY4	57705	broad.mit.edu	37	10	50111154	50111154	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50111154delA	uc001jha.3	+							NM_020945	NP_065996			WDFY family member 4							integral to membrane	binding				0																		---	---	---	---
WDFY4	57705	broad.mit.edu	37	10	50142632	50142632	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50142632delC	uc001jha.3	+						LRRC18_uc001jhe.1_Intron	NM_020945	NP_065996			WDFY family member 4							integral to membrane	binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	50760717	50760718	+	IGR	DEL	TT	-	-	rs71879873		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50760717_50760718delTT								PGBD3 (13133 upstream) : CHAT (56423 downstream)																																			---	---	---	---
OGDHL	55753	broad.mit.edu	37	10	50972223	50972223	+	5'Flank	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50972223delT	uc001jie.2	-						OGDHL_uc010qgt.1_5'Flank|OGDHL_uc010qgu.1_5'Flank|OGDHL_uc009xoh.2_5'Flank	NM_018245	NP_060715			oxoglutarate dehydrogenase-like isoform a						glycolysis	mitochondrial matrix	oxoglutarate dehydrogenase (succinyl-transferring) activity|thiamine pyrophosphate binding			pancreas(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	50998220	50998220	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50998220delT								OGDHL (27795 upstream) : PARG (28107 downstream)																																			---	---	---	---
PARG	8505	broad.mit.edu	37	10	51574358	51574358	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:51574358delG	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_5'Flank	NM_003631	NP_003622			poly (ADP-ribose) glycohydrolase						carbohydrate metabolic process	nucleus	poly(ADP-ribose) glycohydrolase activity			ovary(2)	2				Epithelial(53;0.213)														---	---	---	---
PRKG1	5592	broad.mit.edu	37	10	53254862	53254862	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:53254862delT	uc001jjm.2	+						PRKG1_uc001jjn.2_Intron|PRKG1_uc001jjo.2_Intron	NM_001098512	NP_001091982			protein kinase, cGMP-dependent, type I isoform						actin cytoskeleton organization|platelet activation|signal transduction	cytosol	ATP binding|cGMP binding|cGMP-dependent protein kinase activity			lung(2)|stomach(1)|ovary(1)|central_nervous_system(1)|skin(1)	6		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)														---	---	---	---
PRKG1	5592	broad.mit.edu	37	10	53600935	53600936	+	Intron	DEL	TC	-	-	rs35188534		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:53600935_53600936delTC	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	54949533	54949533	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:54949533delT								MBL2 (418073 upstream) : PCDH15 (613002 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	55116409	55116409	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:55116409delT								MBL2 (584949 upstream) : PCDH15 (446126 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	55160470	55160470	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:55160470delA								MBL2 (629010 upstream) : PCDH15 (402065 downstream)																																			---	---	---	---
PCDH15	65217	broad.mit.edu	37	10	55910194	55910194	+	Intron	DEL	T	-	-	rs75127870		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:55910194delT	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	56515849	56515850	+	Intron	INS	-	CACT	CACT	rs143374986	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:56515849_56515850insCACT	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	56595457	56595458	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:56595457_56595458insA	uc001jjv.1	-							NM_001142770	NP_001136242			protocadherin 15 isoform CD2-2 precursor						equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound	extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse	calcium ion binding			pancreas(5)|ovary(4)|upper_aerodigestive_tract(2)|skin(2)	13		Melanoma(3;0.117)|Lung SC(717;0.238)													HNSCC(58;0.16)			---	---	---	---
PCDH15	65217	broad.mit.edu	37	10	57177525	57177525	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:57177525delA	uc001jjv.1	-							NM_001142770	NP_001136242			protocadherin 15 isoform CD2-2 precursor						equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound	extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse	calcium ion binding			pancreas(5)|ovary(4)|upper_aerodigestive_tract(2)|skin(2)	13		Melanoma(3;0.117)|Lung SC(717;0.238)													HNSCC(58;0.16)			---	---	---	---
Unknown	0	broad.mit.edu	37	10	58129167	58129167	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:58129167delA								ZWINT (8133 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	58759539	58759539	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:58759539delA								ZWINT (638505 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	59248846	59248846	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:59248846delA								None (None upstream) : IPMK (706772 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	60052776	60052777	+	IGR	INS	-	TC	TC	rs150650806	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:60052776_60052777insTC								CISD1 (3758 upstream) : UBE2D1 (41962 downstream)																																			---	---	---	---
BICC1	80114	broad.mit.edu	37	10	60548865	60548865	+	Intron	DEL	A	-	-	rs75442527		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:60548865delA	uc001jki.1	+							NM_001080512	NP_001073981			bicaudal C homolog 1						multicellular organismal development		RNA binding			ovary(2)|lung(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	60631346	60631346	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:60631346delA								BICC1 (42501 upstream) : PHYHIPL (305002 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	61225793	61225793	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61225793delA								FAM13C (103132 upstream) : SLC16A9 (184729 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	61745129	61745129	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61745129delT								C10orf40 (24458 upstream) : ANK3 (43031 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	61769325	61769326	+	IGR	INS	-	AAC	AAC			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61769325_61769326insAAC								C10orf40 (48654 upstream) : ANK3 (18834 downstream)																																			---	---	---	---
ANK3	288	broad.mit.edu	37	10	61824265	61824265	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61824265delT	uc001jky.2	-						ANK3_uc001jkw.2_Intron|ANK3_uc009xpa.2_Intron|ANK3_uc001jkx.2_Intron|ANK3_uc010qih.1_Intron|ANK3_uc001jkz.3_Intron|ANK3_uc001jkv.2_Intron	NM_020987	NP_066267			ankyrin 3 isoform 1						establishment of protein localization|signal transduction	basolateral plasma membrane|cytoplasm|cytoskeleton	protein binding			skin(9)|ovary(6)|pancreas(2)|central_nervous_system(2)	19																		---	---	---	---
ANK3	288	broad.mit.edu	37	10	61918737	61918737	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61918737delA	uc001jky.2	-						ANK3_uc001jkx.2_Intron|ANK3_uc010qih.1_Intron|ANK3_uc001jkz.3_Intron|ANK3_uc001jlb.1_Intron|ANK3_uc001jlc.1_Intron	NM_020987	NP_066267			ankyrin 3 isoform 1						establishment of protein localization|signal transduction	basolateral plasma membrane|cytoplasm|cytoskeleton	protein binding			skin(9)|ovary(6)|pancreas(2)|central_nervous_system(2)	19																		---	---	---	---
ANK3	288	broad.mit.edu	37	10	62086458	62086458	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:62086458delG	uc001jky.2	-						ANK3_uc010qih.1_Intron|ANK3_uc001jkz.3_Intron|ANK3_uc001jlb.1_Intron	NM_020987	NP_066267			ankyrin 3 isoform 1						establishment of protein localization|signal transduction	basolateral plasma membrane|cytoplasm|cytoskeleton	protein binding			skin(9)|ovary(6)|pancreas(2)|central_nervous_system(2)	19																		---	---	---	---
ANK3	288	broad.mit.edu	37	10	62295689	62295689	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:62295689delA	uc010qih.1	-						ANK3_uc001jkz.3_Intron|ANK3_uc001jlb.1_Intron	NM_001149	NP_001140			ankyrin 3 isoform 2						establishment of protein localization|signal transduction	basolateral plasma membrane|cytoplasm|cytoskeleton	protein binding			skin(9)|ovary(6)|pancreas(2)|central_nervous_system(2)	19																		---	---	---	---
RHOBTB1	9886	broad.mit.edu	37	10	62665333	62665333	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:62665333delA	uc001jli.2	-						RHOBTB1_uc001jlh.2_Intron|RHOBTB1_uc001jlj.2_Intron|RHOBTB1_uc001jlk.2_Intron|RHOBTB1_uc009xpe.1_Intron	NM_014836	NP_055651			Rho-related BTB domain containing 1						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|plasma membrane	GTP binding			upper_aerodigestive_tract(1)	1	Prostate(12;0.0112)																	---	---	---	---
Unknown	0	broad.mit.edu	37	10	62935332	62935332	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:62935332delA								RHOBTB1 (174134 upstream) : TMEM26 (231069 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	62940520	62940520	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:62940520delT								RHOBTB1 (179322 upstream) : TMEM26 (225881 downstream)																																			---	---	---	---
ZNF365	22891	broad.mit.edu	37	10	64425757	64425757	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64425757delA	uc001jmd.1	+						ZNF365_uc001jmc.2_Intron|ZNF365_uc001jme.1_Intron|ZNF365_uc001jmf.1_Intron|ZNF365_uc009xpg.1_Intron	NM_199452	NP_955524			zinc finger protein 365 isoform D											ovary(1)|skin(1)	2	Prostate(12;0.0297)|all_hematologic(501;0.228)																	---	---	---	---
Unknown	0	broad.mit.edu	37	10	64665654	64665657	+	IGR	DEL	GAAA	-	-	rs10569806		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64665654_64665657delGAAA								EGR2 (86727 upstream) : NRBF2 (227350 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	66919858	66919858	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:66919858delA								ANXA2P3 (333224 upstream) : CTNNA3 (759867 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	67184349	67184349	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:67184349delA								ANXA2P3 (597715 upstream) : CTNNA3 (495376 downstream)																																			---	---	---	---
CTNNA3	29119	broad.mit.edu	37	10	67714660	67714660	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:67714660delT	uc009xpn.1	-						CTNNA3_uc001jmw.2_Intron	NM_001127384	NP_001120856			catenin, alpha 3						cell-cell adhesion	actin cytoskeleton|cytoplasm|fascia adherens	cadherin binding|structural molecule activity			skin(3)|ovary(2)|pancreas(1)|lung(1)|central_nervous_system(1)	8																		---	---	---	---
CTNNA3	29119	broad.mit.edu	37	10	67742090	67742090	+	Intron	DEL	G	-	-	rs142435526	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:67742090delG	uc009xpn.1	-						CTNNA3_uc001jmw.2_Intron	NM_001127384	NP_001120856			catenin, alpha 3						cell-cell adhesion	actin cytoskeleton|cytoplasm|fascia adherens	cadherin binding|structural molecule activity			skin(3)|ovary(2)|pancreas(1)|lung(1)|central_nervous_system(1)	8																		---	---	---	---
CTNNA3	29119	broad.mit.edu	37	10	67861735	67861736	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:67861735_67861736insT	uc009xpn.1	-						CTNNA3_uc001jmw.2_Intron	NM_001127384	NP_001120856			catenin, alpha 3						cell-cell adhesion	actin cytoskeleton|cytoplasm|fascia adherens	cadherin binding|structural molecule activity			skin(3)|ovary(2)|pancreas(1)|lung(1)|central_nervous_system(1)	8																		---	---	---	---
CTNNA3	29119	broad.mit.edu	37	10	68422537	68422538	+	Intron	DEL	GA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:68422537_68422538delGA	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	68959102	68959103	+	Intron	INS	-	T	T	rs149486795	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:68959102_68959103insT	uc009xpn.1	-						CTNNA3_uc001jmw.2_Intron|CTNNA3_uc001jmx.3_Intron|CTNNA3_uc009xpo.1_Intron|CTNNA3_uc001jna.2_Intron	NM_001127384	NP_001120856			catenin, alpha 3						cell-cell adhesion	actin cytoskeleton|cytoplasm|fascia adherens	cadherin binding|structural molecule activity			skin(3)|ovary(2)|pancreas(1)|lung(1)|central_nervous_system(1)	8																		---	---	---	---
CTNNA3	29119	broad.mit.edu	37	10	69049727	69049728	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:69049727_69049728delAA	uc009xpn.1	-						CTNNA3_uc001jmw.2_Intron|CTNNA3_uc001jmx.3_Intron|CTNNA3_uc009xpo.1_Intron|CTNNA3_uc001jna.2_Intron	NM_001127384	NP_001120856			catenin, alpha 3						cell-cell adhesion	actin cytoskeleton|cytoplasm|fascia adherens	cadherin binding|structural molecule activity			skin(3)|ovary(2)|pancreas(1)|lung(1)|central_nervous_system(1)	8																		---	---	---	---
SIRT1	23411	broad.mit.edu	37	10	69662847	69662847	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:69662847delA	uc001jnd.2	+						SIRT1_uc010qis.1_Intron|SIRT1_uc009xpp.2_Intron|SIRT1_uc001jne.2_Intron	NM_012238	NP_036370			sirtuin 1 isoform a						apoptosis|cell aging|cellular response to hydrogen peroxide|cellular response to starvation|chromatin silencing at rDNA|DNA repair|DNA replication|establishment of chromatin silencing|histone H3 deacetylation|interspecies interaction between organisms|maintenance of chromatin silencing|muscle organ development|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of DNA damage response, signal transduction by p53 class mediator|negative regulation of fat cell differentiation|negative regulation of helicase activity|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|peptidyl-lysine acetylation|peptidyl-lysine deacetylation|positive regulation of anti-apoptosis|positive regulation of chromatin silencing|positive regulation of DNA repair|regulation of apoptosis|regulation of cell proliferation|regulation of endodeoxyribonuclease activity|regulation of protein import into nucleus, translocation|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|rRNA processing|transcription, DNA-dependent|triglyceride mobilization|white fat cell differentiation	chromatin silencing complex|cytoplasm|nuclear euchromatin|nuclear heterochromatin|nuclear inner membrane|nucleolus|PML body|rDNA heterochromatin	bHLH transcription factor binding|histone binding|HLH domain binding|identical protein binding|mitogen-activated protein kinase binding|NAD+ binding|NAD-dependent histone deacetylase activity (H3-K9 specific)|p53 binding|protein C-terminus binding|transcription corepressor activity|zinc ion binding				0																		---	---	---	---
SIRT1	23411	broad.mit.edu	37	10	69668900	69668900	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:69668900delT	uc001jnd.2	+						SIRT1_uc010qis.1_Intron|SIRT1_uc009xpp.2_Intron|SIRT1_uc001jne.2_Intron	NM_012238	NP_036370			sirtuin 1 isoform a						apoptosis|cell aging|cellular response to hydrogen peroxide|cellular response to starvation|chromatin silencing at rDNA|DNA repair|DNA replication|establishment of chromatin silencing|histone H3 deacetylation|interspecies interaction between organisms|maintenance of chromatin silencing|muscle organ development|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of DNA damage response, signal transduction by p53 class mediator|negative regulation of fat cell differentiation|negative regulation of helicase activity|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|peptidyl-lysine acetylation|peptidyl-lysine deacetylation|positive regulation of anti-apoptosis|positive regulation of chromatin silencing|positive regulation of DNA repair|regulation of apoptosis|regulation of cell proliferation|regulation of endodeoxyribonuclease activity|regulation of protein import into nucleus, translocation|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|rRNA processing|transcription, DNA-dependent|triglyceride mobilization|white fat cell differentiation	chromatin silencing complex|cytoplasm|nuclear euchromatin|nuclear heterochromatin|nuclear inner membrane|nucleolus|PML body|rDNA heterochromatin	bHLH transcription factor binding|histone binding|HLH domain binding|identical protein binding|mitogen-activated protein kinase binding|NAD+ binding|NAD-dependent histone deacetylase activity (H3-K9 specific)|p53 binding|protein C-terminus binding|transcription corepressor activity|zinc ion binding				0																		---	---	---	---
HERC4	26091	broad.mit.edu	37	10	69700185	69700185	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:69700185delT	uc001jng.3	-						HERC4_uc009xpq.2_Intron|HERC4_uc001jnf.3_Intron|HERC4_uc001jnh.3_Intron|HERC4_uc009xpr.2_Intron|HERC4_uc001jni.3_Intron	NM_022079	NP_071362			hect domain and RLD 4 isoform a						cell differentiation|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|spermatogenesis	cytosol	ubiquitin-protein ligase activity			ovary(1)|breast(1)|skin(1)	3																		---	---	---	---
SLC25A16	8034	broad.mit.edu	37	10	70261254	70261254	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70261254delA	uc001joi.2	-						SLC25A16_uc010qix.1_Intron|SLC25A16_uc010qiy.1_Intron|SLC25A16_uc001joj.2_Intron	NM_152707	NP_689920			solute carrier family 25, member 16						coenzyme biosynthetic process|pantothenate metabolic process	integral to membrane|mitochondrial inner membrane	binding|solute:solute antiporter activity				0																		---	---	---	---
CCAR1	55749	broad.mit.edu	37	10	70484381	70484381	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70484381delA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	70581403	70581404	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70581403_70581404delTT								CCAR1 (30096 upstream) : STOX1 (5890 downstream)																																			---	---	---	---
DDX21	9188	broad.mit.edu	37	10	70714171	70714171	+	5'Flank	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70714171delA	uc001jov.1	+						DDX21_uc001jow.1_5'Flank	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	70840637	70840638	+	IGR	INS	-	T	T	rs147888815	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70840637_70840638insT								KIAA1279 (63903 upstream) : SRGN (7190 downstream)																																			---	---	---	---
VPS26A	9559	broad.mit.edu	37	10	70892911	70892911	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70892911delT	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																		---	---	---	---
SUPV3L1	6832	broad.mit.edu	37	10	70960397	70960397	+	Intron	DEL	A	-	-	rs35423280		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70960397delA	uc001jpe.1	+						SUPV3L1_uc010qjd.1_Intron	NM_003171	NP_003162			suppressor of var1, 3-like 1 precursor						DNA duplex unwinding	mitochondrial nucleoid|nucleus	ATP binding|DNA binding|DNA helicase activity|RNA binding			urinary_tract(1)|ovary(1)	2																		---	---	---	---
HK1	3098	broad.mit.edu	37	10	71096887	71096887	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71096887delA	uc001jpl.3	+						HK1_uc009xqc.1_Intron|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																		---	---	---	---
TSPAN15	23555	broad.mit.edu	37	10	71224421	71224422	+	Intron	INS	-	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71224421_71224422insG	uc001jpo.1	+							NM_012339	NP_036471			transmembrane 4 superfamily member 15							integral to plasma membrane|membrane fraction					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	71331252	71331252	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71331252delT								TSPAN15 (63829 upstream) : NEUROG3 (540 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	71416454	71416457	+	IGR	DEL	GAGA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71416454_71416457delGAGA								C10orf35 (23107 upstream) : COL13A1 (145187 downstream)																																			---	---	---	---
AIFM2	84883	broad.mit.edu	37	10	71873764	71873765	+	Intron	INS	-	CT	CT			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71873764_71873765insCT	uc010qjg.1	-						AIFM2_uc001jqp.1_3'UTR	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	72060044	72060044	+	3'UTR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72060044delT	uc001jqx.1	-	5					LRRC20_uc001jqy.1_3'UTR|LRRC20_uc001jqz.1_3'UTR	NM_207119	NP_997002			leucine rich repeat containing 20 isoform 1												0																		---	---	---	---
SGPL1	8879	broad.mit.edu	37	10	72589331	72589331	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72589331delT	uc001jrm.2	+							NM_003901	NP_003892			sphingosine-1-phosphate lyase 1						apoptosis|carboxylic acid metabolic process|ceramide metabolic process|sphingolipid catabolic process	integral to endoplasmic reticulum membrane	carboxy-lyase activity|pyridoxal phosphate binding|sphinganine-1-phosphate aldolase activity				0					Pyridoxal Phosphate(DB00114)													---	---	---	---
Unknown	0	broad.mit.edu	37	10	72800810	72800811	+	IGR	DEL	GT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72800810_72800811delGT								PCBD1 (152269 upstream) : UNC5B (171487 downstream)																																			---	---	---	---
CDH23	64072	broad.mit.edu	37	10	73154699	73154700	+	5'Flank	DEL	TC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73154699_73154700delTC	uc001jrx.3	+						CDH23_uc001jrw.3_5'Flank|CDH23_uc001jrv.2_5'Flank|CDH23_uc009xql.2_5'Flank	NM_022124	NP_071407			cadherin-like 23 isoform 1 precursor						calcium ion transport|calcium-dependent cell-cell adhesion|cytosolic calcium ion homeostasis|equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	cytosol|integral to membrane|plasma membrane|stereocilium	calcium ion binding|protein binding			central_nervous_system(5)|large_intestine(4)|ovary(2)	11																		---	---	---	---
CDH23	64072	broad.mit.edu	37	10	73416552	73416553	+	Intron	INS	-	AG	AG			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73416552_73416553insAG	uc001jrx.3	+						CDH23_uc001jry.2_Intron|CDH23_uc001jrz.2_Intron	NM_022124	NP_071407			cadherin-like 23 isoform 1 precursor						calcium ion transport|calcium-dependent cell-cell adhesion|cytosolic calcium ion homeostasis|equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	cytosol|integral to membrane|plasma membrane|stereocilium	calcium ion binding|protein binding			central_nervous_system(5)|large_intestine(4)|ovary(2)	11																		---	---	---	---
ASCC1	51008	broad.mit.edu	37	10	73940733	73940733	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73940733delT	uc001jst.1	-						ASCC1_uc001jsr.1_Intron|ASCC1_uc001jss.1_Intron|ASCC1_uc001jsu.1_Intron|ASCC1_uc010qju.1_Intron					RecName: Full=Activating signal cointegrator 1 complex subunit 1; AltName: Full=ASC-1 complex subunit p50; AltName: Full=Trip4 complex subunit p50;						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|transcription factor complex	RNA binding				0																		---	---	---	---
ASCC1	51008	broad.mit.edu	37	10	73949561	73949562	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73949561_73949562delAA	uc001jst.1	-						ASCC1_uc001jsr.1_Intron|ASCC1_uc001jss.1_Intron|ASCC1_uc001jsu.1_Intron|ASCC1_uc010qju.1_Intron					RecName: Full=Activating signal cointegrator 1 complex subunit 1; AltName: Full=ASC-1 complex subunit p50; AltName: Full=Trip4 complex subunit p50;						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|transcription factor complex	RNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	74038562	74038562	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74038562delT								DDIT4 (2765 upstream) : DNAJB12 (54026 downstream)																																			---	---	---	---
CBARA1	10367	broad.mit.edu	37	10	74136032	74136032	+	Intron	DEL	A	-	-	rs35947688		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74136032delA	uc001jtb.1	-						CBARA1_uc010qjw.1_Intron|CBARA1_uc010qjx.1_Intron|CBARA1_uc009xqo.1_Intron	NM_006077	NP_006068			calcium binding atopy-related autoantigen 1						calcium ion import|defense response|elevation of mitochondrial calcium ion concentration	integral to membrane|mitochondrial inner membrane	calcium ion binding|protein binding			ovary(1)	1																		---	---	---	---
CCDC109A	90550	broad.mit.edu	37	10	74467365	74467366	+	Intron	DEL	GT	-	-	rs72099506		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74467365_74467366delGT	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)																	---	---	---	---
FAM149B1	317662	broad.mit.edu	37	10	74948492	74948492	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74948492delA	uc009xqz.2	+						FAM149B1_uc010qkf.1_Intron|FAM149B1_uc001jtq.2_Intron	NM_173348	NP_775483			hypothetical protein LOC317662												0																		---	---	---	---
MRPS16	51021	broad.mit.edu	37	10	75011301	75011301	+	Intron	DEL	T	-	-	rs113802791		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75011301delT	uc001jts.1	-						DNAJC9_uc010qkg.1_5'Flank|MRPS16_uc010qkh.1_Intron|MRPS16_uc001jtt.1_Intron|uc001jtu.1_5'Flank	NM_016065	NP_057149			mitochondrial ribosomal protein S16 precursor						translation	mitochondrial small ribosomal subunit	protein binding|structural constituent of ribosome				0	Prostate(51;0.0119)																	---	---	---	---
MYST4	23522	broad.mit.edu	37	10	76657071	76657071	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76657071delC	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	77097376	77097377	+	Intron	INS	-	A	A	rs144953760	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:77097376_77097377insA	uc001jxd.1	+											Homo sapiens cDNA FLJ13383 fis, clone PLACE1001024.																														---	---	---	---
Unknown	0	broad.mit.edu	37	10	77148155	77148156	+	IGR	INS	-	G	G	rs146817433	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:77148155_77148156insG								COMTD1 (152385 upstream) : ZNF503 (9449 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	77236754	77236755	+	IGR	DEL	TT	-	-	rs146172157	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:77236754_77236755delTT								C10orf41 (68015 upstream) : MIR606 (75461 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	77274074	77274076	+	IGR	DEL	TTT	-	-	rs111654453		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:77274074_77274076delTTT								C10orf41 (105335 upstream) : MIR606 (38140 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	77398682	77398682	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:77398682delC								MIR606 (86371 upstream) : C10orf11 (143837 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	77531040	77531040	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:77531040delT								MIR606 (218729 upstream) : C10orf11 (11479 downstream)																																			---	---	---	---
C10orf11	83938	broad.mit.edu	37	10	77728939	77728940	+	Intron	INS	-	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:77728939_77728940insG	uc001jxi.2	+							NM_032024	NP_114413			chromosome 10 open reading frame 11												0	Prostate(51;0.0095)|all_epithelial(25;0.0221)																	---	---	---	---
KCNMA1	3778	broad.mit.edu	37	10	78756367	78756368	+	Intron	DEL	AG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:78756367_78756368delAG	uc001jxn.2	-						KCNMA1_uc001jxj.2_Intron|KCNMA1_uc001jxk.1_Intron|KCNMA1_uc009xrt.1_Intron|KCNMA1_uc001jxl.1_Intron|KCNMA1_uc001jxo.2_Intron|KCNMA1_uc001jxm.2_Intron|KCNMA1_uc001jxq.2_Intron	NM_001161352	NP_001154824			large conductance calcium-activated potassium						cellular potassium ion homeostasis|negative regulation of cell volume|platelet activation|positive regulation of apoptosis|regulation of membrane potential|response to calcium ion|response to carbon monoxide|response to hypoxia|response to osmotic stress|smooth muscle contraction involved in micturition	apical plasma membrane|caveola|integral to membrane|voltage-gated potassium channel complex	actin binding|calcium-activated potassium channel activity|large conductance calcium-activated potassium channel activity|metal ion binding|voltage-gated potassium channel activity			pancreas(2)|ovary(1)	3	all_cancers(46;0.203)|all_epithelial(25;0.00604)|Prostate(51;0.0198)		OV - Ovarian serous cystadenocarcinoma(4;0.0586)|Epithelial(14;0.081)|all cancers(16;0.183)		Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Chlorzoxazone(DB00356)|Cromoglicate(DB01003)|Cyclothiazide(DB00606)|Diazoxide(DB01119)|Enflurane(DB00228)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Quinethazone(DB01325)|Trichlormethiazide(DB01021)													---	---	---	---
KCNMA1	3778	broad.mit.edu	37	10	79090892	79090895	+	Intron	DEL	AGAG	-	-	rs141579288		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:79090892_79090895delAGAG	uc001jxn.2	-						KCNMA1_uc001jxj.2_Intron|KCNMA1_uc009xrt.1_Intron|KCNMA1_uc001jxo.2_Intron|KCNMA1_uc001jxm.2_Intron|KCNMA1_uc001jxq.2_Intron	NM_001161352	NP_001154824			large conductance calcium-activated potassium						cellular potassium ion homeostasis|negative regulation of cell volume|platelet activation|positive regulation of apoptosis|regulation of membrane potential|response to calcium ion|response to carbon monoxide|response to hypoxia|response to osmotic stress|smooth muscle contraction involved in micturition	apical plasma membrane|caveola|integral to membrane|voltage-gated potassium channel complex	actin binding|calcium-activated potassium channel activity|large conductance calcium-activated potassium channel activity|metal ion binding|voltage-gated potassium channel activity			pancreas(2)|ovary(1)	3	all_cancers(46;0.203)|all_epithelial(25;0.00604)|Prostate(51;0.0198)		OV - Ovarian serous cystadenocarcinoma(4;0.0586)|Epithelial(14;0.081)|all cancers(16;0.183)		Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Chlorzoxazone(DB00356)|Cromoglicate(DB01003)|Cyclothiazide(DB00606)|Diazoxide(DB01119)|Enflurane(DB00228)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Quinethazone(DB01325)|Trichlormethiazide(DB01021)													---	---	---	---
KCNMA1	3778	broad.mit.edu	37	10	79121599	79121599	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:79121599delA	uc001jxn.2	-						KCNMA1_uc001jxj.2_Intron|KCNMA1_uc001jxo.2_Intron|KCNMA1_uc001jxm.2_Intron|KCNMA1_uc001jxq.2_Intron	NM_001161352	NP_001154824			large conductance calcium-activated potassium						cellular potassium ion homeostasis|negative regulation of cell volume|platelet activation|positive regulation of apoptosis|regulation of membrane potential|response to calcium ion|response to carbon monoxide|response to hypoxia|response to osmotic stress|smooth muscle contraction involved in micturition	apical plasma membrane|caveola|integral to membrane|voltage-gated potassium channel complex	actin binding|calcium-activated potassium channel activity|large conductance calcium-activated potassium channel activity|metal ion binding|voltage-gated potassium channel activity			pancreas(2)|ovary(1)	3	all_cancers(46;0.203)|all_epithelial(25;0.00604)|Prostate(51;0.0198)		OV - Ovarian serous cystadenocarcinoma(4;0.0586)|Epithelial(14;0.081)|all cancers(16;0.183)		Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Chlorzoxazone(DB00356)|Cromoglicate(DB01003)|Cyclothiazide(DB00606)|Diazoxide(DB01119)|Enflurane(DB00228)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Quinethazone(DB01325)|Trichlormethiazide(DB01021)													---	---	---	---
Unknown	0	broad.mit.edu	37	10	79693053	79693054	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:79693053_79693054insT								LOC100128292 (3471 upstream) : POLR3A (42852 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	79817444	79817444	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:79817444delT								RPS24 (874 upstream) : LOC283050 (885640 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	79830635	79830635	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:79830635delT								RPS24 (14065 upstream) : LOC283050 (872449 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	80357742	80357742	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:80357742delC								RPS24 (541172 upstream) : LOC283050 (345342 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	80544791	80544791	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:80544791delA								RPS24 (728221 upstream) : LOC283050 (158293 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	81076921	81076921	+	IGR	DEL	T	-	-	rs11306322		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81076921delT								ZMIZ1 (636 upstream) : PPIF (30299 downstream)																																	OREG0020308	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	10	81269169	81269171	+	Intron	DEL	AAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81269169_81269171delAAA	uc010qls.1	-											SubName: Full=cDNA FLJ60964, weakly similar to Homo sapiens dentin sialophosphoprotein (DSPP), mRNA;																														---	---	---	---
TSPAN14	81619	broad.mit.edu	37	10	82217995	82218004	+	Intron	DEL	AGGTGACTGA	-	-	rs5786458		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:82217995_82218004delAGGTGACTGA	uc001kcj.3	+						TSPAN14_uc009xss.2_Intron|TSPAN14_uc001kci.3_Intron	NM_030927	NP_112189			tetraspanin 14 isoform 1							integral to membrane				ovary(1)|central_nervous_system(1)	2			Colorectal(32;0.229)															---	---	---	---
Unknown	0	broad.mit.edu	37	10	82432413	82432413	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:82432413delA								SH2D4B (26097 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	82713217	82713217	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:82713217delA								SH2D4B (306901 upstream) : NRG3 (921853 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	82938527	82938527	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:82938527delA								SH2D4B (532211 upstream) : NRG3 (696543 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	83284560	83284560	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:83284560delG								SH2D4B (878244 upstream) : NRG3 (350510 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	83408156	83408157	+	IGR	INS	-	T	T	rs150310775	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:83408156_83408157insT								None (None upstream) : NRG3 (226913 downstream)																																			---	---	---	---
NRG3	10718	broad.mit.edu	37	10	84260393	84260395	+	Intron	DEL	AAG	-	-	rs149599561		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:84260393_84260395delAAG	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	84438510	84438510	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:84438510delT	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	84457942	84457944	+	Intron	DEL	TTC	-	-	rs5786563		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:84457942_84457944delTTC	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)														---	---	---	---
GHITM	27069	broad.mit.edu	37	10	85912464	85912464	+	3'UTR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85912464delT	uc001kcs.1	+	9					GHITM_uc010qma.1_3'UTR|GHITM_uc010qmb.1_3'UTR	NM_014394	NP_055209			growth hormone inducible transmembrane protein						apoptosis	integral to membrane|mitochondrial inner membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	86377210	86377210	+	IGR	DEL	G	-	-	rs113226623		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:86377210delG								FAM190B (98934 upstream) : GRID1 (982102 downstream)																																			---	---	---	---
WAPAL	23063	broad.mit.edu	37	10	88212863	88212864	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88212863_88212864insA	uc001kdo.2	-						WAPAL_uc009xsv.2_Intron|WAPAL_uc001kdn.2_Intron|WAPAL_uc009xsw.2_Intron	NM_015045	NP_055860			wings apart-like homolog						cell division|interspecies interaction between organisms|mitosis|negative regulation of chromatin binding|negative regulation of DNA replication|negative regulation of sister chromatid cohesion|protein localization to chromatin|regulation of cohesin localization to chromatin	chromatin|cohesin complex|cytoplasm	protein binding			ovary(1)	1																		---	---	---	---
GLUD1	2746	broad.mit.edu	37	10	88842977	88842979	+	Intron	DEL	AAA	-	-	rs140873695		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88842977_88842979delAAA	uc001keh.2	-						GLUD1_uc001keg.2_Intron|GLUD1_uc010qmp.1_Intron	NM_005271	NP_005262			glutamate dehydrogenase 1 precursor						glutamate biosynthetic process|glutamate catabolic process|positive regulation of insulin secretion	mitochondrial matrix	ADP binding|ATP binding|glutamate dehydrogenase|glutamate dehydrogenase activity|GTP binding|identical protein binding|leucine binding|NAD+ binding				0					L-Glutamic Acid(DB00142)|NADH(DB00157)													---	---	---	---
RNLS	55328	broad.mit.edu	37	10	90026530	90026530	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90026530delA	uc010qms.1	-											SubName: Full=cDNA FLJ55083, highly similar to Renalase (EC 1.4.-.-);							extracellular region	oxidoreductase activity			ovary(1)	1																		---	---	---	---
STAMBPL1	57559	broad.mit.edu	37	10	90682641	90682641	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90682641delT	uc001kfk.2	+						STAMBPL1_uc010qmx.1_Intron|STAMBPL1_uc009xto.2_Intron|STAMBPL1_uc001kfl.2_Intron|STAMBPL1_uc001kfn.2_Intron	NM_020799	NP_065850			STAM binding protein-like 1								metal ion binding|metallopeptidase activity|protein binding			ovary(1)	1		Colorectal(252;0.0381)		Colorectal(12;6.38e-05)|COAD - Colon adenocarcinoma(12;7.75e-05)														---	---	---	---
STAMBPL1	57559	broad.mit.edu	37	10	90693651	90693651	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90693651delT	uc010qmx.1	+						uc001kfo.1_Intron	NM_020799	NP_065850			STAM binding protein-like 1								metal ion binding|metallopeptidase activity|protein binding			ovary(1)	1		Colorectal(252;0.0381)		Colorectal(12;6.38e-05)|COAD - Colon adenocarcinoma(12;7.75e-05)														---	---	---	---
SLC16A12	387700	broad.mit.edu	37	10	91253659	91253659	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91253659delA	uc001kgm.2	-							NM_213606	NP_998771			solute carrier family 16 (monocarboxylic acid							integral to membrane|plasma membrane	symporter activity			skin(1)	1																		---	---	---	---
SLC16A12	387700	broad.mit.edu	37	10	91279141	91279141	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91279141delA	uc001kgm.2	-							NM_213606	NP_998771			solute carrier family 16 (monocarboxylic acid							integral to membrane|plasma membrane	symporter activity			skin(1)	1																		---	---	---	---
HTR7	3363	broad.mit.edu	37	10	92533872	92533873	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:92533872_92533873delAA	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)													---	---	---	---
RPP30	10556	broad.mit.edu	37	10	92633569	92633570	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:92633569_92633570insT	uc009xtx.2	+						RPP30_uc001khd.2_Intron|RPP30_uc010qnj.1_Intron	NM_006413	NP_006404			ribonuclease P/MRP 30kDa subunit isoform b						tRNA processing	nucleolar ribonuclease P complex	protein binding|ribonuclease P activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	92776136	92776136	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:92776136delA								ANKRD1 (95104 upstream) : NUDT9P1 (135625 downstream)																																			---	---	---	---
PCGF5	84333	broad.mit.edu	37	10	92957874	92957874	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:92957874delC	uc001khh.2	+						PCGF5_uc001khg.2_Intron	NM_032373	NP_115749			polycomb group ring finger 5						regulation of transcription, DNA-dependent|transcription, DNA-dependent	centrosome|PcG protein complex	zinc ion binding			lung(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	93377173	93377173	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93377173delC								LOC100188947 (5956 upstream) : PPP1R3C (11028 downstream)																																			---	---	---	---
BTAF1	9044	broad.mit.edu	37	10	93722539	93722539	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93722539delT	uc001khr.2	+						BTAF1_uc001khs.1_Intron	NM_003972	NP_003963			BTAF1 RNA polymerase II, B-TFIID transcription						negative regulation of transcription, DNA-dependent	nucleus	ATP binding|DNA binding|helicase activity|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Colorectal(252;0.0846)																---	---	---	---
CPEB3	22849	broad.mit.edu	37	10	93961841	93961841	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93961841delA	uc001khw.1	-						CPEB3_uc001khu.1_Intron|CPEB3_uc001khv.1_Intron|CPEB3_uc010qnn.1_Intron	NM_014912	NP_055727			cytoplasmic polyadenylation element binding								nucleotide binding|RNA binding				0		Colorectal(252;0.0869)																---	---	---	---
MARCH5	54708	broad.mit.edu	37	10	94079055	94079055	+	Intron	DEL	T	-	-	rs142807049		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94079055delT	uc001khx.1	+						MARCH5_uc010qno.1_Intron	NM_017824	NP_060294			membrane-associated ring finger (C3HC4) 5						cell aging|protein autoubiquitination|protein localization in mitochondrion|protein polyubiquitination|regulation of mitochondrial fission	endoplasmic reticulum membrane|integral to membrane|mitochondrial outer membrane	GTPase binding|ubiquitin-protein ligase activity|zinc ion binding			skin(1)	1																		---	---	---	---
IDE	3416	broad.mit.edu	37	10	94226082	94226082	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94226082delT	uc001kia.2	-						IDE_uc010qnp.1_Intron|IDE_uc001khz.2_Intron	NM_004969	NP_004960			insulin-degrading enzyme isoform 1 precursor						beta-amyloid metabolic process|bradykinin catabolic process|interspecies interaction between organisms|sex differentiation	cell surface|extracellular space|soluble fraction	ATP binding|metalloendopeptidase activity|protein homodimerization activity|signal transducer activity|zinc ion binding			ovary(2)|central_nervous_system(1)	3					Bacitracin(DB00626)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)													---	---	---	---
IDE	3416	broad.mit.edu	37	10	94258949	94258950	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94258949_94258950delTT	uc001kia.2	-						IDE_uc010qnp.1_5'Flank|IDE_uc001khz.2_5'Flank	NM_004969	NP_004960			insulin-degrading enzyme isoform 1 precursor						beta-amyloid metabolic process|bradykinin catabolic process|interspecies interaction between organisms|sex differentiation	cell surface|extracellular space|soluble fraction	ATP binding|metalloendopeptidase activity|protein homodimerization activity|signal transducer activity|zinc ion binding			ovary(2)|central_nervous_system(1)	3					Bacitracin(DB00626)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)													---	---	---	---
KIF11	3832	broad.mit.edu	37	10	94399351	94399351	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94399351delA	uc001kic.2	+						KIF11_uc010qnq.1_Intron	NM_004523	NP_004514			kinesin family member 11						blood coagulation|cell division|microtubule-based movement|spindle assembly involved in mitosis	chromatin remodeling complex|cytosol|kinesin complex|microtubule|spindle pole	ATP binding|microtubule motor activity|protein kinase binding			skin(1)	1																		---	---	---	---
EXOC6	54536	broad.mit.edu	37	10	94693774	94693775	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94693774_94693775insA	uc001kig.2	+						EXOC6_uc010qnr.1_Intron|EXOC6_uc001kie.2_Intron|EXOC6_uc009xub.2_Intron|EXOC6_uc009xuc.2_Intron|EXOC6_uc001kih.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)																---	---	---	---
TCTN3	26123	broad.mit.edu	37	10	97431524	97431524	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97431524delT	uc001klb.3	-						TCTN3_uc001kla.3_Intron|TCTN3_uc010qoi.1_Intron	NM_015631	NP_056446			tectonic 3 isoform a precursor						apoptosis	integral to membrane					0		Colorectal(252;0.0815)		Epithelial(162;1.69e-07)|all cancers(201;5.63e-06)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	97707512	97707513	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97707512_97707513delAA	uc001klg.1	-						uc001klj.1_Intron					Homo sapiens cDNA FLJ34077 fis, clone FCBBF3003481, weakly similar to ZINC FINGER PROTEIN 195.																														---	---	---	---
Unknown	0	broad.mit.edu	37	10	98043208	98043208	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98043208delC								BLNK (11875 upstream) : DNTT (20877 downstream)																																			---	---	---	---
TM9SF3	56889	broad.mit.edu	37	10	98299115	98299115	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98299115delA	uc001kmm.3	-						TM9SF3_uc010qot.1_Intron	NM_020123	NP_064508			transmembrane 9 superfamily member 3 precursor							integral to membrane	binding				0		Colorectal(252;0.158)		Epithelial(162;1.84e-09)|all cancers(201;2.84e-08)														---	---	---	---
PIK3AP1	118788	broad.mit.edu	37	10	98398229	98398236	+	Intron	DEL	ACACACAC	-	-	rs67101495		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98398229_98398236delACACACAC	uc001kmq.2	-						PIK3AP1_uc001kmp.2_Intron	NM_152309	NP_689522			phosphoinositide-3-kinase adaptor protein 1							cytoplasm|plasma membrane				upper_aerodigestive_tract(3)|ovary(1)|skin(1)	5		Colorectal(252;0.0442)		Epithelial(162;6.29e-08)|all cancers(201;3.18e-06)														---	---	---	---
C10orf12	26148	broad.mit.edu	37	10	98714563	98714563	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98714563delT	uc009xvg.1	+						LCOR_uc001kmr.2_Intron|LCOR_uc001kms.1_Intron|LCOR_uc001kmt.1_Intron|LCOR_uc001kmu.1_Intron	NM_015652	NP_056467			hypothetical protein LOC26148											skin(2)	2		Colorectal(252;0.172)		Epithelial(162;6.35e-09)|all cancers(201;3.21e-07)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	98749616	98749616	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98749616delT								C10orf12 (4032 upstream) : SLIT1 (8179 downstream)																																			---	---	---	---
SLIT1	6585	broad.mit.edu	37	10	98845144	98845144	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98845144delT	uc001kmw.2	-						SLIT1_uc009xvh.1_Intron	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)														---	---	---	---
RRP12	23223	broad.mit.edu	37	10	99163847	99163847	+	5'Flank	DEL	A	-	-	rs75824188		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99163847delA	uc001knf.2	-						RRP12_uc010qou.1_5'Flank|RRP12_uc009xvn.2_5'Flank	NM_015179	NP_055994			ribosomal RNA processing 12 homolog isoform 1							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)														---	---	---	---
MMS19	64210	broad.mit.edu	37	10	99228377	99228377	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99228377delT	uc001kns.3	-						MMS19_uc009xvs.2_5'Flank|MMS19_uc009xvt.2_Intron|MMS19_uc001knr.2_Intron|MMS19_uc010qox.1_Intron|MMS19_uc001knt.2_Intron|MMS19_uc001knu.1_Intron	NM_022362	NP_071757			MMS19 nucleotide excision repair homolog						chromosome segregation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|response to hormone stimulus|transcription, DNA-dependent|two-component signal transduction system (phosphorelay)	cytoplasm|holo TFIIH complex|MMXD complex	estrogen receptor binding|protein binding, bridging|receptor signaling complex scaffold activity|transcription coactivator activity				0		Colorectal(252;0.0846)		Epithelial(162;3.33e-10)|all cancers(201;2.74e-08)									Direct_reversal_of_damage|NER					---	---	---	---
PI4K2A	55361	broad.mit.edu	37	10	99356865	99356866	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99356865_99356866delTT	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)														---	---	---	---
C10orf28	27291	broad.mit.edu	37	10	99944488	99944489	+	Intron	INS	-	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99944488_99944489insC	uc001kow.3	+						C10orf28_uc001kox.3_Intron|C10orf28_uc001koy.3_Intron|C10orf28_uc009xvx.2_Intron|C10orf28_uc009xvy.2_Intron|C10orf28_uc001koz.3_Intron	NM_014472	NP_055287			growth inhibition and differentiation related								nucleotide binding			large_intestine(1)|skin(1)	2		Colorectal(252;0.234)		Epithelial(162;7.18e-11)|all cancers(201;8.75e-09)														---	---	---	---
HPSE2	60495	broad.mit.edu	37	10	100319613	100319613	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:100319613delT	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	100554001	100554001	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:100554001delT	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	100877890	100877891	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:100877890_100877891delAA	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)														---	---	---	---
COX15	1355	broad.mit.edu	37	10	101487560	101487560	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101487560delT	uc001kqb.3	-						COX15_uc001kqc.3_Intron|COX15_uc010qpj.1_Intron	NM_078470	NP_510870			COX15 homolog isoform 1						heme a biosynthetic process|respiratory chain complex IV assembly|respiratory gaseous exchange	integral to membrane|mitochondrial respiratory chain	cytochrome-c oxidase activity			ovary(1)	1		Colorectal(252;0.234)		Epithelial(162;3.08e-10)|all cancers(201;2.43e-08)														---	---	---	---
DNMBP	23268	broad.mit.edu	37	10	101661660	101661660	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101661660delT	uc001kqj.2	-						DNMBP_uc001kqg.2_Intron|DNMBP_uc001kqh.2_Intron	NM_015221	NP_056036			dynamin binding protein						intracellular signal transduction|regulation of Rho protein signal transduction	cell junction|cytoskeleton|Golgi stack|synapse	protein binding|Rho guanyl-nucleotide exchange factor activity			ovary(5)|skin(1)	6		Colorectal(252;0.234)		Epithelial(162;2.94e-10)|all cancers(201;3.15e-08)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	101787027	101787027	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101787027delA								DNMBP (17351 upstream) : CPN1 (15038 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	101868347	101868348	+	IGR	DEL	TA	-	-	rs7076325	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101868347_101868348delTA								CPN1 (26705 upstream) : ERLIN1 (41500 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	101868348	101868349	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101868348_101868349delAA								CPN1 (26706 upstream) : ERLIN1 (41499 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	102660262	102660262	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102660262delT								PAX2 (70565 upstream) : FAM178A (12064 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	102835356	102835357	+	IGR	DEL	CT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102835356_102835357delCT								KAZALD1 (7470 upstream) : TLX1NB (13722 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	102930256	102930256	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102930256delT								TLX1 (32711 upstream) : LBX1 (56478 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	102931205	102931205	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102931205delA								TLX1 (33660 upstream) : LBX1 (55529 downstream)																																			---	---	---	---
BTRC	8945	broad.mit.edu	37	10	103131589	103131589	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103131589delT	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)														---	---	---	---
LDB1	8861	broad.mit.edu	37	10	103876290	103876291	+	Intron	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103876290_103876291delAC	uc009xwz.2	-						LDB1_uc001kuk.3_5'Flank|LDB1_uc001kul.3_5'Flank	NM_001113407	NP_001106878			LIM domain binding 1 isoform 1						histone H3-K4 acetylation|negative regulation of erythrocyte differentiation|negative regulation of transcription, DNA-dependent|positive regulation of hemoglobin biosynthetic process|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription elongation, DNA-dependent|transcription, DNA-dependent|transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery	nuclear chromatin|protein complex	LIM domain binding|protein homodimerization activity|transcription corepressor activity			large_intestine(1)	1		Colorectal(252;0.122)		Epithelial(162;1.11e-07)|all cancers(201;1.82e-06)														---	---	---	---
GBF1	8729	broad.mit.edu	37	10	104141579	104141580	+	Intron	INS	-	GA	GA	rs141680642	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104141579_104141580insGA	uc001kux.1	+						GBF1_uc001kuy.1_Intron|GBF1_uc001kuz.1_Intron	NM_004193	NP_004184			golgi-specific brefeldin A resistant guanine						COPI coating of Golgi vesicle|post-Golgi vesicle-mediated transport|regulation of ARF protein signal transduction|retrograde vesicle-mediated transport, Golgi to ER	Golgi membrane	ARF guanyl-nucleotide exchange factor activity|protein binding			ovary(1)|central_nervous_system(1)	2		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)														---	---	---	---
PSD	5662	broad.mit.edu	37	10	104177927	104177928	+	Intron	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104177927_104177928delAC	uc001kvg.1	-						PSD_uc001kvh.1_Intron|PSD_uc009xxd.1_Intron|PSD_uc001kvi.1_Intron|FBXL15_uc001kvj.1_5'Flank|FBXL15_uc001kvk.2_5'Flank|FBXL15_uc001kvl.1_5'Flank	NM_002779	NP_002770			pleckstrin and Sec7 domain containing						regulation of ARF protein signal transduction	cytoplasm|plasma membrane|ruffle	ARF guanyl-nucleotide exchange factor activity|signal transducer activity			breast(2)|urinary_tract(1)	3				Epithelial(162;1.27e-08)|all cancers(201;2.85e-07)														---	---	---	---
CNNM2	54805	broad.mit.edu	37	10	104814054	104814054	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104814054delT	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)												OREG0020489	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
PCGF6	84108	broad.mit.edu	37	10	105089842	105089842	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105089842delT	uc001kwt.2	-						PCGF6_uc001kwu.2_Intron|PCGF6_uc009xxk.2_Intron|PCGF6_uc009xxl.2_Intron|PCGF6_uc009xxm.2_Intron	NM_001011663	NP_001011663			polycomb group ring finger 6 isoform a						negative regulation of transcription, DNA-dependent	PcG protein complex	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			kidney(1)	1		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;2.57e-09)|all cancers(201;7.21e-08)|BRCA - Breast invasive adenocarcinoma(275;0.205)														---	---	---	---
SH3PXD2A	9644	broad.mit.edu	37	10	105487096	105487096	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105487096delA	uc001kxj.1	-						SH3PXD2A_uc010qqu.1_Intron	NM_014631	NP_055446			SH3 multiple domains 1						cell communication|superoxide metabolic process	cell junction|cell projection|cytoplasm|podosome	phosphatidylinositol binding|protein binding				0		Colorectal(252;0.0815)|Breast(234;0.131)		Epithelial(162;4.09e-10)|all cancers(201;2.73e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0119)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	106244853	106244854	+	IGR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:106244853_106244854insA								CCDC147 (30014 upstream) : SORCS3 (156005 downstream)																																			---	---	---	---
SORCS3	22986	broad.mit.edu	37	10	106783300	106783300	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:106783300delT	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	107025727	107025727	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:107025727delT								SORCS3 (734 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	107333692	107333692	+	IGR	DEL	G	-	-	rs143700282		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:107333692delG								SORCS3 (308699 upstream) : SORCS1 (999730 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	108293776	108293776	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:108293776delT								None (None upstream) : SORCS1 (39646 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	108312653	108312653	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:108312653delA								None (None upstream) : SORCS1 (20769 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	109624670	109624670	+	IGR	DEL	C	-	-	rs112305029		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:109624670delC								SORCS1 (700378 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	109947106	109947106	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:109947106delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	111080596	111080596	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:111080596delT								None (None upstream) : XPNPEP1 (543928 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	111698601	111698602	+	IGR	INS	-	G	G	rs59043744	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:111698601_111698602insG								XPNPEP1 (15399 upstream) : ADD3 (57506 downstream)																																			---	---	---	---
ADD3	120	broad.mit.edu	37	10	111845166	111845169	+	Intron	DEL	CAGT	-	-	rs71990234		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:111845166_111845169delCAGT	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)														---	---	---	---
MXI1	4601	broad.mit.edu	37	10	112043720	112043721	+	Intron	INS	-	T	T	rs145540678	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112043720_112043721insT	uc001kza.2	+						MXI1_uc001kyy.2_Intron|MXI1_uc001kyz.2_Intron|MXI1_uc010qrc.1_Intron|MXI1_uc009xxu.2_Intron|MXI1_uc009xxv.2_Intron	NM_005962	NP_005953			MAX interactor 1 isoform a						cytoplasmic sequestering of transcription factor|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|transcription corepressor activity				0		Breast(234;0.052)|Lung NSC(174;0.223)		Epithelial(162;1.33e-05)|all cancers(201;0.000277)|BRCA - Breast invasive adenocarcinoma(275;0.127)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	112090059	112090059	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112090059delA								SMNDC1 (25352 upstream) : DUSP5 (167566 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	112163768	112163768	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112163768delA								SMNDC1 (99061 upstream) : DUSP5 (93857 downstream)																																			---	---	---	---
VTI1A	143187	broad.mit.edu	37	10	114223387	114223389	+	Intron	DEL	AAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114223387_114223389delAAA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	114688251	114688252	+	IGR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114688251_114688252insA								LOC143188 (73124 upstream) : TCF7L2 (21757 downstream)																																			---	---	---	---
TCF7L2	6934	broad.mit.edu	37	10	114753273	114753273	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114753273delA	uc001lae.3	+						TCF7L2_uc001lac.3_Intron|TCF7L2_uc010qrk.1_Intron|TCF7L2_uc010qrl.1_Intron|TCF7L2_uc010qrm.1_Intron|TCF7L2_uc010qrn.1_Intron|TCF7L2_uc001lad.3_Intron|TCF7L2_uc001lag.3_Intron|TCF7L2_uc001laf.3_Intron|TCF7L2_uc010qro.1_Intron|TCF7L2_uc001lah.2_Intron|TCF7L2_uc010qrp.1_Intron|TCF7L2_uc010qrq.1_Intron|TCF7L2_uc010qrr.1_Intron|TCF7L2_uc010qrs.1_Intron|TCF7L2_uc010qrt.1_Intron	NM_001146274	NP_001139746			transcription factor 7-like 2 isoform 1						anti-apoptosis|blood vessel development|canonical Wnt receptor signaling pathway involved in positive regulation of epithelial to mesenchymal transition|cell cycle arrest|cell proliferation|fat cell differentiation|glucose homeostasis|maintenance of DNA repeat elements|myoblast cell fate commitment|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|pancreas development|positive regulation of heparan sulfate proteoglycan biosynthetic process|positive regulation of insulin secretion|positive regulation of protein binding|positive regulation of protein export from nucleus|positive regulation of protein kinase B signaling cascade|positive regulation of transcription from RNA polymerase II promoter|regulation of hormone metabolic process|regulation of smooth muscle cell proliferation|response to glucose stimulus	beta-catenin-TCF7L2 complex|PML body|protein-DNA complex	armadillo repeat domain binding|beta-catenin binding|gamma-catenin binding|nuclear hormone receptor binding|protein kinase binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding			large_intestine(3)|ovary(1)	4		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)														---	---	---	---
TCF7L2	6934	broad.mit.edu	37	10	114885141	114885141	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114885141delT	uc001lae.3	+						TCF7L2_uc001lac.3_Intron|TCF7L2_uc010qrk.1_Intron|TCF7L2_uc010qrl.1_Intron|TCF7L2_uc010qrm.1_Intron|TCF7L2_uc010qrn.1_Intron|TCF7L2_uc001lad.3_Intron|TCF7L2_uc001lag.3_Intron|TCF7L2_uc001laf.3_Intron|TCF7L2_uc010qro.1_Intron|TCF7L2_uc001lah.2_Intron|TCF7L2_uc010qrp.1_Intron|TCF7L2_uc010qrq.1_Intron|TCF7L2_uc010qrr.1_Intron|TCF7L2_uc010qrs.1_Intron|TCF7L2_uc010qrt.1_Intron|TCF7L2_uc010qru.1_Intron|TCF7L2_uc010qrv.1_5'Flank	NM_001146274	NP_001139746			transcription factor 7-like 2 isoform 1						anti-apoptosis|blood vessel development|canonical Wnt receptor signaling pathway involved in positive regulation of epithelial to mesenchymal transition|cell cycle arrest|cell proliferation|fat cell differentiation|glucose homeostasis|maintenance of DNA repeat elements|myoblast cell fate commitment|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|pancreas development|positive regulation of heparan sulfate proteoglycan biosynthetic process|positive regulation of insulin secretion|positive regulation of protein binding|positive regulation of protein export from nucleus|positive regulation of protein kinase B signaling cascade|positive regulation of transcription from RNA polymerase II promoter|regulation of hormone metabolic process|regulation of smooth muscle cell proliferation|response to glucose stimulus	beta-catenin-TCF7L2 complex|PML body|protein-DNA complex	armadillo repeat domain binding|beta-catenin binding|gamma-catenin binding|nuclear hormone receptor binding|protein kinase binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding			large_intestine(3)|ovary(1)	4		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)														---	---	---	---
HABP2	3026	broad.mit.edu	37	10	115338240	115338240	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115338240delT	uc001lai.3	+						HABP2_uc010qrz.1_Intron|HABP2_uc010qry.1_Intron	NM_004132	NP_004123			hyaluronan binding protein 2 preproprotein						cell adhesion|proteolysis	extracellular space	glycosaminoglycan binding|serine-type endopeptidase activity			ovary(2)|skin(1)	3		Colorectal(252;0.0233)|Breast(234;0.0672)		Epithelial(162;0.00319)|all cancers(201;0.0112)														---	---	---	---
NRAP	4892	broad.mit.edu	37	10	115377063	115377063	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115377063delC	uc001laj.2	-						NRAP_uc009xyb.2_Intron|NRAP_uc001lak.2_Intron|NRAP_uc001lal.3_Intron	NM_198060	NP_932326			nebulin-related anchoring protein isoform S							fascia adherens|muscle tendon junction	actin binding|muscle alpha-actinin binding|zinc ion binding			ovary(6)|central_nervous_system(3)|upper_aerodigestive_tract(1)	10		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)														---	---	---	---
CASP7	840	broad.mit.edu	37	10	115458426	115458426	+	Intron	DEL	T	-	-	rs68033243		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115458426delT	uc001lan.2	+						CASP7_uc001lam.2_Intron|CASP7_uc001lao.2_Intron|CASP7_uc001lap.2_Intron|CASP7_uc001laq.2_Intron|CASP7_uc010qsa.1_Intron	NM_033339	NP_203125			caspase 7 isoform alpha						activation of caspase activity by cytochrome c|cellular component disassembly involved in apoptosis|induction of apoptosis by intracellular signals|proteolysis	cytosol|endoplasmic reticulum membrane|mitochondrial membrane|nucleoplasm	cysteine-type endopeptidase activity|protein binding			ovary(1)	1		Colorectal(252;0.0946)|Breast(234;0.188)		Epithelial(162;0.012)|all cancers(201;0.014)														---	---	---	---
VWA2	340706	broad.mit.edu	37	10	116026655	116026655	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116026655delT	uc001lbl.1	+						VWA2_uc001lbk.1_Intron|VWA2_uc009xyf.1_Intron	NM_198496	NP_940898			von Willebrand factor A domain containing 2							extracellular region				ovary(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	5				Epithelial(162;0.036)|all cancers(201;0.0793)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	116571258	116571258	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116571258delA								ABLIM1 (43239 upstream) : FAM160B1 (10245 downstream)																																			---	---	---	---
ATRNL1	26033	broad.mit.edu	37	10	117079153	117079153	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:117079153delT	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	117685101	117685101	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:117685101delA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	118987955	118987957	+	IGR	DEL	CCT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118987955_118987957delCCT								KCNK18 (18146 upstream) : SLC18A2 (12759 downstream)																																			---	---	---	---
PDZD8	118987	broad.mit.edu	37	10	119066757	119066757	+	Intron	DEL	T	-	-	rs138996448		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:119066757delT	uc001lde.1	-							NM_173791	NP_776152			PDZ domain containing 8						intracellular signal transduction		metal ion binding				0		Colorectal(252;0.19)		all cancers(201;0.0121)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	119204196	119204196	+	IGR	DEL	T	-	-	rs72205850		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:119204196delT								PDZD8 (69259 upstream) : EMX2OS (39609 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	120016741	120016741	+	IGR	DEL	T	-	-	rs113813736	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120016741delT								CASC2 (47082 upstream) : C10orf84 (51831 downstream)																																			---	---	---	---
C10orf84	63877	broad.mit.edu	37	10	120095476	120095477	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120095476_120095477delTT	uc001ldo.2	-						C10orf84_uc010qss.1_Intron	NM_022063	NP_071346			hypothetical protein LOC63877												0		Colorectal(252;0.101)		all cancers(201;0.0244)														---	---	---	---
GRK5	2869	broad.mit.edu	37	10	121022528	121022528	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121022528delT	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)														---	---	---	---
GRK5	2869	broad.mit.edu	37	10	121157275	121157286	+	Intron	DEL	AGTTGGTAGTGG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121157275_121157286delAGTTGGTAGTGG	uc001led.2	+						GRK5_uc009xzh.2_Intron|GRK5_uc010qta.1_Intron	NM_005308	NP_005299			G protein-coupled receptor kinase 5						G-protein signaling, coupled to cAMP nucleotide second messenger|regulation of G-protein coupled receptor protein signaling pathway|tachykinin receptor signaling pathway	cytoplasm|plasma membrane|soluble fraction	ATP binding|G-protein coupled receptor kinase activity|phospholipid binding|protein kinase C binding|signal transducer activity			lung(2)|stomach(1)	3		Lung NSC(174;0.0971)|all_lung(145;0.127)|Ovarian(717;0.249)		all cancers(201;0.0227)														---	---	---	---
RGS10	6001	broad.mit.edu	37	10	121281081	121281082	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121281081_121281082delAA	uc001lee.2	-						RGS10_uc001lef.2_Intron|RGS10_uc001leg.2_Intron	NM_002925	NP_002916			regulator of G-protein signaling 10 isoform b						negative regulation of signal transduction	cytoplasm|plasma membrane	GTPase activator activity|protein binding|signal transducer activity				0		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.00105)|GBM - Glioblastoma multiforme(135;0.195)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	122511471	122511475	+	IGR	DEL	TTTTG	-	-	rs138983704		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:122511471_122511475delTTTTG								PPAPDC1A (162104 upstream) : WDR11 (99220 downstream)																																			---	---	---	---
FGFR2	2263	broad.mit.edu	37	10	123271536	123271537	+	Intron	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123271536_123271537delTG	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	123360432	123360433	+	5'Flank	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123360432_123360433delTT	uc010qtk.1	-						FGFR2_uc010qtj.1_5'Flank|FGFR2_uc010qtl.1_5'Flank|FGFR2_uc010qtm.1_5'Flank|FGFR2_uc001lfm.2_5'Flank|FGFR2_uc001lfn.3_5'Flank|FGFR2_uc001lfo.1_5'Flank	NM_000141	NP_000132			fibroblast growth factor receptor 2 isoform 1						angiogenesis|axonogenesis|bone mineralization|bone morphogenesis|branch elongation involved in salivary gland morphogenesis|branching involved in embryonic placenta morphogenesis|branching morphogenesis of a nerve|bud elongation involved in lung branching|cell fate commitment|cell growth|cell-cell signaling|cellular response to protein stimulus|embryonic digestive tract morphogenesis|embryonic pattern specification|epithelial cell proliferation involved in salivary gland morphogenesis|fibroblast growth factor receptor signaling pathway involved in hemopoiesis|fibroblast growth factor receptor signaling pathway involved in mammary gland specification|fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptosis in bone marrow|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development|fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow|hair follicle morphogenesis|insulin receptor signaling pathway|lacrimal gland development|lateral sprouting from an epithelium|limb bud formation|lung alveolus development|lung lobe morphogenesis|lung-associated mesenchyme development|mammary gland bud formation|membranous septum morphogenesis|mesenchymal cell differentiation involved in lung development|mesenchymal cell proliferation involved in lung development|midbrain development|multicellular organism growth|negative regulation of transcription from RNA polymerase II promoter|odontogenesis|organ growth|otic vesicle formation|outflow tract septum morphogenesis|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of cell cycle|positive regulation of cell division|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of ERK1 and ERK2 cascade|positive regulation of mesenchymal cell proliferation|positive regulation of transcription from RNA polymerase II promoter|post-embryonic development|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis|prostate epithelial cord elongation|pyramidal neuron development|regulation of branching involved in prostate gland morphogenesis|regulation of cell fate commitment|regulation of fibroblast growth factor receptor signaling pathway|regulation of multicellular organism growth|regulation of smooth muscle cell differentiation|regulation of smoothened signaling pathway|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development|ureteric bud development|ventricular cardiac muscle tissue morphogenesis|ventricular zone neuroblast division	cell cortex|cell surface|excitatory synapse|extracellular region|integral to membrane|nucleus|plasma membrane	ATP binding|fibroblast growth factor binding|fibroblast growth factor binding|fibroblast growth factor receptor activity|heparin binding|protein binding			endometrium(44)|skin(28)|lung(11)|ovary(4)|cervix(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|soft_tissue(1)|central_nervous_system(1)	96		Lung NSC(174;0.0841)|all_lung(145;0.106)|all_neural(114;0.107)	STAD - Stomach adenocarcinoma(1;7.52e-05)|all cancers(1;0.0722)	all cancers(201;9.73e-05)|GBM - Glioblastoma multiforme(135;0.0845)	Palifermin(DB00039)		5	Mis		gastric. NSCLC|endometrial		Crouzon|Pfeiffer|and Apert syndromes		Apert_syndrome|Saethre-Chotzen_syndrome				---	---	---	---
ATE1	11101	broad.mit.edu	37	10	123593159	123593159	+	Intron	DEL	A	-	-	rs115127406	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123593159delA	uc001lfp.2	-						ATE1_uc001lfq.2_Intron|ATE1_uc010qtr.1_Intron|ATE1_uc010qts.1_Intron|ATE1_uc010qtt.1_Intron|ATE1_uc001lfr.2_Intron|ATE1_uc009xzu.2_Intron	NM_007041	NP_008972			arginyltransferase 1 isoform 2						protein arginylation	cytoplasm|nucleus	acyltransferase activity|arginyltransferase activity				0		all_neural(114;0.061)|Lung NSC(174;0.095)|all_lung(145;0.124)|Breast(234;0.212)																---	---	---	---
ATE1	11101	broad.mit.edu	37	10	123611091	123611095	+	Intron	DEL	TTTTG	-	-	rs144563129		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123611091_123611095delTTTTG	uc001lfp.2	-						ATE1_uc001lfq.2_Intron|ATE1_uc010qtr.1_Intron|ATE1_uc010qts.1_Intron|ATE1_uc010qtt.1_Intron|ATE1_uc001lfr.2_Intron|ATE1_uc009xzu.2_Intron	NM_007041	NP_008972			arginyltransferase 1 isoform 2						protein arginylation	cytoplasm|nucleus	acyltransferase activity|arginyltransferase activity				0		all_neural(114;0.061)|Lung NSC(174;0.095)|all_lung(145;0.124)|Breast(234;0.212)																---	---	---	---
ATE1	11101	broad.mit.edu	37	10	123676354	123676355	+	Intron	DEL	AA	-	-	rs113526423		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123676354_123676355delAA	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)																---	---	---	---
TACC2	10579	broad.mit.edu	37	10	123834369	123834369	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123834369delT	uc001lfv.2	+						TACC2_uc001lfw.2_Intron|TACC2_uc009xzx.2_Intron|TACC2_uc010qtv.1_Intron	NM_206862	NP_996744			transforming, acidic coiled-coil containing							microtubule organizing center|nucleus	nuclear hormone receptor binding			ovary(4)|breast(3)|skin(2)|central_nervous_system(1)	10		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)																---	---	---	---
Unknown	0	broad.mit.edu	37	10	124022637	124022637	+	IGR	DEL	T	-	-	rs141851342		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124022637delT								TACC2 (8582 upstream) : BTBD16 (8184 downstream)																																			---	---	---	---
DMBT1	1755	broad.mit.edu	37	10	124317340	124317340	+	5'Flank	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124317340delA	uc001lgk.1	+						DMBT1_uc001lgl.1_5'Flank|DMBT1_uc001lgm.1_5'Flank|DMBT1_uc009xzz.1_5'Flank|DMBT1_uc010qtx.1_5'Flank	NM_007329	NP_015568			deleted in malignant brain tumors 1 isoform b						epithelial cell differentiation|induction of bacterial agglutination|innate immune response|interspecies interaction between organisms|protein transport|response to virus	extrinsic to membrane|phagocytic vesicle membrane|zymogen granule membrane	calcium-dependent protein binding|Gram-negative bacterial cell surface binding|Gram-positive bacterial cell surface binding|pattern recognition receptor activity|scavenger receptor activity|zymogen binding			central_nervous_system(7)	7		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)																---	---	---	---
ACADSB	36	broad.mit.edu	37	10	124788862	124788862	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124788862delA	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	10	125014092	125014093	+	IGR	INS	-	CAC	CAC			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:125014092_125014093insCAC								BUB3 (89206 upstream) : GPR26 (411778 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	125206327	125206327	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:125206327delC	uc001lhg.1	+											full-length cDNA clone CS0DD008YJ14 of Neuroblastoma Cot 50-normalized of Homo sapiens (human).																														---	---	---	---
GPR26	2849	broad.mit.edu	37	10	125422954	125422955	+	5'Flank	DEL	GA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:125422954_125422955delGA	uc001lhh.2	+							NM_153442	NP_703143			G protein-coupled receptor 26						activation of adenylate cyclase activity by G-protein signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			skin(1)	1		Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)																---	---	---	---
Unknown	0	broad.mit.edu	37	10	126069060	126069060	+	IGR	DEL	C	-	-	rs59709781		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126069060delC								CHST15 (215854 upstream) : OAT (16812 downstream)																																			---	---	---	---
CTBP2	1488	broad.mit.edu	37	10	126714531	126714532	+	Intron	DEL	GT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126714531_126714532delGT	uc009yak.2	-						CTBP2_uc009yal.2_Intron|CTBP2_uc001lif.3_Intron|CTBP2_uc001lih.3_Intron|CTBP2_uc001lie.3_Intron	NM_001329	NP_001320			C-terminal binding protein 2 isoform 1						negative regulation of cell proliferation|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent|viral genome replication|white fat cell differentiation	cell junction|synapse|transcriptional repressor complex	NAD binding|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor|protein binding				0		all_lung(145;0.0132)|Lung NSC(174;0.0193)|all_neural(114;0.116)|Colorectal(57;0.173)		Colorectal(40;0.00572)|COAD - Colon adenocarcinoma(40;0.0127)|GBM - Glioblastoma multiforme(135;0.147)														---	---	---	---
CTBP2	1488	broad.mit.edu	37	10	126753113	126753113	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126753113delA	uc009yak.2	-						CTBP2_uc009yal.2_Intron|CTBP2_uc001lif.3_Intron|CTBP2_uc001lih.3_Intron	NM_001329	NP_001320			C-terminal binding protein 2 isoform 1						negative regulation of cell proliferation|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent|viral genome replication|white fat cell differentiation	cell junction|synapse|transcriptional repressor complex	NAD binding|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor|protein binding				0		all_lung(145;0.0132)|Lung NSC(174;0.0193)|all_neural(114;0.116)|Colorectal(57;0.173)		Colorectal(40;0.00572)|COAD - Colon adenocarcinoma(40;0.0127)|GBM - Glioblastoma multiforme(135;0.147)														---	---	---	---
C10orf122	387718	broad.mit.edu	37	10	127360745	127360745	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127360745delG	uc001lik.3	-						C10orf122_uc001lij.2_Intron	NM_001128202	NP_001121674			hypothetical protein LOC387718												0																		---	---	---	---
FANK1	92565	broad.mit.edu	37	10	127589533	127589533	+	Intron	DEL	T	-	-	rs113742142		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127589533delT	uc001ljh.3	+						FANK1_uc010quk.1_Intron|FANK1_uc009yan.2_Intron	NM_145235	NP_660278			fibronectin type III and ankyrin repeat domains							cytoplasm|nucleus				ovary(1)	1		all_lung(145;0.00752)|Lung NSC(174;0.0115)|Colorectal(57;0.0847)|all_neural(114;0.0936)																---	---	---	---
ADAM12	8038	broad.mit.edu	37	10	127940175	127940182	+	Intron	DEL	ATGGATGC	-	-	rs4962534	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127940175_127940182delATGGATGC	uc001ljk.2	-						ADAM12_uc010qul.1_Intron|ADAM12_uc001ljm.2_Intron|ADAM12_uc001ljn.2_Intron|ADAM12_uc001ljl.3_Intron	NM_003474	NP_003465			ADAM metallopeptidase domain 12 isoform 1						cell adhesion|epidermal growth factor receptor signaling pathway|myoblast fusion|proteolysis	extracellular region|integral to membrane|plasma membrane	metalloendopeptidase activity|protein binding|SH3 domain binding|zinc ion binding			breast(4)|ovary(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	9		all_epithelial(44;7.06e-05)|all_lung(145;0.00563)|Lung NSC(174;0.00834)|Colorectal(57;0.102)|all_neural(114;0.107)|Breast(234;0.22)		COAD - Colon adenocarcinoma(40;0.141)|Colorectal(40;0.216)														---	---	---	---
DOCK1	1793	broad.mit.edu	37	10	128863283	128863284	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:128863283_128863284insT	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	128994990	128994991	+	Intron	INS	-	GAG	GAG	rs111836841		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:128994990_128994991insGAG	uc001ljt.2	+						DOCK1_uc010qun.1_Intron|FAM196A_uc001ljv.1_5'Flank	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	129084444	129084444	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129084444delT	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	129178160	129178160	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129178160delA	uc001ljt.2	+						DOCK1_uc010qun.1_Intron|DOCK1_uc009yaq.2_Intron	NM_001380	NP_001371			dedicator of cytokinesis 1						apoptosis|axon guidance|blood coagulation|integrin-mediated signaling pathway|phagocytosis, engulfment|small GTPase mediated signal transduction	cytosol|membrane	GTP binding|GTPase activator activity|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding			central_nervous_system(4)|ovary(2)|lung(1)|breast(1)|kidney(1)	9		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	129625952	129625952	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129625952delC								FOXI2 (86502 upstream) : CLRN3 (50162 downstream)																																			---	---	---	---
PTPRE	5791	broad.mit.edu	37	10	129776501	129776501	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129776501delA	uc001lkb.2	+						PTPRE_uc009yat.2_Intron	NM_006504	NP_006495			protein tyrosine phosphatase, receptor type, E						negative regulation of insulin receptor signaling pathway|protein phosphorylation	cytoplasm|integral to membrane|intermediate filament cytoskeleton|nucleus|plasma membrane	transmembrane receptor protein tyrosine phosphatase activity			ovary(1)	1		all_epithelial(44;1.66e-05)|all_lung(145;0.00456)|Lung NSC(174;0.0066)|all_neural(114;0.0936)|Colorectal(57;0.141)|Breast(234;0.166)|Melanoma(40;0.203)																---	---	---	---
Unknown	0	broad.mit.edu	37	10	130217031	130217031	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:130217031delA								MKI67 (292563 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	130254920	130254920	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:130254920delA								MKI67 (330452 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	130831170	130831170	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:130831170delA								MKI67 (906702 upstream) : MGMT (434284 downstream)																																			---	---	---	---
MGMT	4255	broad.mit.edu	37	10	131424674	131424677	+	Intron	DEL	CTTG	-	-	rs138703293		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:131424674_131424677delCTTG	uc001lkh.2	+							NM_002412	NP_002403			O-6-methylguanine-DNA methyltransferase											ovary(1)|breast(1)	2		all_cancers(35;9.44e-09)|all_epithelial(44;6.98e-08)|Lung NSC(174;0.0157)|all_lung(145;0.0201)|all_neural(114;0.0732)|Colorectal(57;0.0792)|Breast(234;0.167)		OV - Ovarian serous cystadenocarcinoma(35;0.00291)									Direct_reversal_of_damage					---	---	---	---
MGMT	4255	broad.mit.edu	37	10	131546775	131546775	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:131546775delA	uc001lkh.2	+							NM_002412	NP_002403			O-6-methylguanine-DNA methyltransferase											ovary(1)|breast(1)	2		all_cancers(35;9.44e-09)|all_epithelial(44;6.98e-08)|Lung NSC(174;0.0157)|all_lung(145;0.0201)|all_neural(114;0.0732)|Colorectal(57;0.0792)|Breast(234;0.167)		OV - Ovarian serous cystadenocarcinoma(35;0.00291)									Direct_reversal_of_damage					---	---	---	---
Unknown	0	broad.mit.edu	37	10	132492617	132492617	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132492617delT								GLRX3 (509833 upstream) : TCERG1L (398039 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	132854389	132854389	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132854389delA								GLRX3 (871605 upstream) : TCERG1L (36267 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	132879310	132879311	+	IGR	DEL	CA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132879310_132879311delCA								GLRX3 (896526 upstream) : TCERG1L (11345 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	133611455	133611460	+	IGR	DEL	CCCACA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133611455_133611460delCCCACA								TCERG1L (501471 upstream) : PPP2R2D (136500 downstream)																																			---	---	---	---
STK32C	282974	broad.mit.edu	37	10	134081575	134081576	+	Intron	DEL	GT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134081575_134081576delGT	uc001lle.1	-						STK32C_uc001lld.1_Intron|STK32C_uc010quu.1_Intron|STK32C_uc009ybc.1_Intron|STK32C_uc009ybd.1_Intron	NM_173575	NP_775846			serine/threonine kinase 32C								ATP binding|metal ion binding|protein serine/threonine kinase activity			large_intestine(2)|lung(2)|breast(1)	5		all_cancers(35;2.72e-11)|all_epithelial(44;2.33e-08)|Lung NSC(174;0.000855)|all_lung(145;0.00146)|all_neural(114;0.0299)|Breast(234;0.106)|Colorectal(31;0.112)|Melanoma(40;0.124)|Glioma(114;0.203)		Epithelial(32;3.99e-05)|all cancers(32;5.58e-05)|OV - Ovarian serous cystadenocarcinoma(35;9.96e-05)|BRCA - Breast invasive adenocarcinoma(275;0.222)														---	---	---	---
TUBGCP2	10844	broad.mit.edu	37	10	135127882	135127883	+	5'Flank	INS	-	CT	CT			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135127882_135127883insCT	uc001lmh.1	-											Homo sapiens spindle pole body protein spc97 homolog GCP2 mRNA, complete cds.						G2/M transition of mitotic cell cycle|microtubule nucleation|protein complex assembly	centrosome|cytoplasmic microtubule|cytosol|spindle pole	protein binding				0		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.87e-06)|all cancers(32;8.98e-06)|Epithelial(32;1.15e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	341780	341780	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:341780delT								IFITM3 (20866 upstream) : B4GALNT4 (28015 downstream)																																			---	---	---	---
ANO9	338440	broad.mit.edu	37	11	442950	442950	+	5'Flank	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:442950delC	uc001lpi.2	-						ANO9_uc010qvv.1_5'Flank	NM_001012302	NP_001012302			tumor protein p53 inducible protein 5							chloride channel complex	chloride channel activity			central_nervous_system(2)|ovary(1)|skin(1)	4																		---	---	---	---
CDHR5	53841	broad.mit.edu	37	11	617603	617603	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:617603delG	uc001lqj.2	-	15	2391	c.2286delC	c.(2284-2286)CCCfs	p.P762fs	IRF7_uc009ycb.2_5'Flank|IRF7_uc010qwf.1_5'Flank|IRF7_uc001lqf.2_5'Flank|IRF7_uc010qwg.1_5'Flank|IRF7_uc001lqg.2_5'Flank|IRF7_uc001lqh.2_5'Flank|IRF7_uc001lqi.2_5'Flank|IRF7_uc010qwh.1_5'Flank|CDHR5_uc001lqk.2_Frame_Shift_Del_p.P568fs|CDHR5_uc009ycc.2_Frame_Shift_Del_p.P596fs|CDHR5_uc009ycd.2_Frame_Shift_Del_p.P756fs|CDHR5_uc001lql.2_Frame_Shift_Del_p.P762fs	NM_021924	NP_068743	Q9HBB8	CDHR5_HUMAN	mucin and cadherin-like isoform 1	762	Cytoplasmic (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	1572848	1572851	+	IGR	DEL	CCAC	-	-	rs143072940	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1572848_1572851delCCAC								MOB2 (64872 upstream) : DUSP8 (2430 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	1740024	1740024	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1740024delA								KRTAP5-6 (21040 upstream) : CTSD (33961 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	2885052	2885052	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2885052delA								KCNQ1 (14713 upstream) : KCNQ1DN (6211 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	2960026	2960027	+	IGR	DEL	TT	-	-	rs145129510		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2960026_2960027delTT								PHLDA2 (9376 upstream) : NAP1L4 (5634 downstream)																																			---	---	---	---
NUP98	4928	broad.mit.edu	37	11	3717748	3717748	+	Intron	DEL	A	-	-	rs147702438		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3717748delA	uc001lyh.2	-						NUP98_uc001lyi.2_Intron|NUP98_uc001lyg.2_Intron	NM_016320	NP_057404			nucleoporin 98kD isoform 1						carbohydrate metabolic process|DNA replication|glucose transport|interspecies interaction between organisms|mitotic prometaphase|mRNA transport|nuclear pore organization|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear membrane|nucleoplasm|Nup107-160 complex	protein binding|structural constituent of nuclear pore|transporter activity			breast(4)|skin(3)|ovary(2)|central_nervous_system(1)|lung(1)|kidney(1)	12		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199)				T	HOXA9|NSD1|WHSC1L1|DDX10|TOP1|HOXD13|PMX1|HOXA13|HOXD11|HOXA11|RAP1GDS1|HOXC11	AML								---	---	---	---
STIM1	6786	broad.mit.edu	37	11	3944023	3944023	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3944023delA	uc001lyv.2	+						STIM1_uc009yef.2_Intron	NM_003156	NP_003147			stromal interaction molecule 1 precursor						activation of store-operated calcium channel activity|calcium ion transport|detection of calcium ion|platelet activation	integral to endoplasmic reticulum membrane|integral to plasma membrane|microtubule	calcium ion binding|microtubule plus-end binding			pancreas(1)	1		Breast(177;0.00159)|Medulloblastoma(188;0.00258)|all_neural(188;0.0233)		BRCA - Breast invasive adenocarcinoma(625;0.114)|LUSC - Lung squamous cell carcinoma(625;0.141)														---	---	---	---
RRM1	6240	broad.mit.edu	37	11	4135384	4135384	+	Intron	DEL	A	-	-	rs78379041		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4135384delA	uc001lyw.3	+						RRM1_uc009yej.2_5'Flank|RRM1_uc009yeh.1_Intron|RRM1_uc009yei.2_Intron|RRM1_uc010qyc.1_Intron|RRM1_uc010qyd.1_5'Flank	NM_001033	NP_001024			ribonucleoside-diphosphate reductase M1 chain						deoxyribonucleotide biosynthetic process|DNA replication|nucleobase, nucleoside and nucleotide interconversion	cytosol|nucleoplasm|ribonucleoside-diphosphate reductase complex	ATP binding|ribonucleoside-diphosphate reductase activity			skin(1)	1		Medulloblastoma(188;0.0025)|Breast(177;0.00502)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0848)|LUSC - Lung squamous cell carcinoma(625;0.205)	Clofarabine(DB00631)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Hydroxyurea(DB01005)													---	---	---	---
OR51T1	401665	broad.mit.edu	37	11	4901846	4901846	+	5'Flank	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4901846delT	uc010qyp.1	+							NM_001004759	NP_001004759			olfactory receptor, family 51, subfamily T,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|large_intestine(1)	3		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;4.77e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|LUSC - Lung squamous cell carcinoma(625;0.19)														---	---	---	---
HBG2	3048	broad.mit.edu	37	11	5559122	5559123	+	Intron	INS	-	GG	GG	rs150877031	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5559122_5559123insGG	uc001mak.1	-											Homo sapiens hemoglobin gamma-G (HBG2) mRNA, partial cds.						blood coagulation	hemoglobin complex	heme binding|oxygen binding|oxygen transporter activity			skin(1)	1		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.76e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)														---	---	---	---
APBB1	322	broad.mit.edu	37	11	6427624	6427625	+	Intron	DEL	TT	-	-	rs78743239		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6427624_6427625delTT	uc001mdb.1	-						APBB1_uc001mdd.3_5'Flank|APBB1_uc001mda.2_5'Flank|APBB1_uc001mdc.1_Intron|APBB1_uc010rae.1_5'Flank|APBB1_uc010raf.1_5'Flank|APBB1_uc009yfa.2_5'Flank|APBB1_uc009yey.2_5'Flank|APBB1_uc010rag.1_5'Flank|APBB1_uc009yfb.2_5'Flank|APBB1_uc001mde.2_5'Flank|APBB1_uc010rah.1_Intron	NM_001164	NP_001155			amyloid beta A4 precursor protein-binding,						apoptosis|axonogenesis|cell cycle arrest|histone H4 acetylation|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of thymidylate synthase biosynthetic process|positive regulation of apoptosis|positive regulation of transcription, DNA-dependent|response to DNA damage stimulus|signal transduction|transcription, DNA-dependent	cytoplasm|growth cone|lamellipodium|nucleus|plasma membrane|synapse	beta-amyloid binding|chromatin binding|histone binding|proline-rich region binding|transcription factor binding			breast(2)	2		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;6.49e-08)|BRCA - Breast invasive adenocarcinoma(625;0.194)														---	---	---	---
DNHD1	144132	broad.mit.edu	37	11	6557699	6557699	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6557699delA	uc001mdw.3	+							NM_144666	NP_653267			dynein heavy chain domain 1 isoform 1						microtubule-based movement	dynein complex	microtubule motor activity			ovary(2)	2		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)														---	---	---	---
DCHS1	8642	broad.mit.edu	37	11	6678167	6678167	+	5'Flank	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6678167delT	uc001mem.1	-							NM_003737	NP_003728			dachsous 1 precursor						calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|large_intestine(1)|pancreas(1)	5		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	6680147	6680152	+	IGR	DEL	TTGGAT	-	-	rs77043645		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6680147_6680152delTTGGAT								DCHS1 (3073 upstream) : MRPL17 (21464 downstream)																																			---	---	---	---
OR2D3	120775	broad.mit.edu	37	11	6942227	6942227	+	5'Flank	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6942227delA	uc010rav.1	+							NM_001004684	NP_001004684			olfactory receptor, family 2, subfamily D,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.78e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	7127093	7127096	+	IGR	DEL	ATAC	-	-	rs71470461		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7127093_7127096delATAC								RBMXL2 (14714 upstream) : MIR302E (128901 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	7141883	7141884	+	IGR	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7141883_7141884delTG								RBMXL2 (29504 upstream) : MIR302E (114113 downstream)																																			---	---	---	---
SYT9	143425	broad.mit.edu	37	11	7404896	7404897	+	Intron	INS	-	T	T	rs142516528	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7404896_7404897insT	uc001mfe.2	+						SYT9_uc001mfd.2_Intron|SYT9_uc009yfi.2_Intron	NM_175733	NP_783860			synaptotagmin IX							cell junction|integral to membrane|synaptic vesicle membrane	metal ion binding|transporter activity			ovary(2)|large_intestine(1)	3				Epithelial(150;1.34e-07)|LUSC - Lung squamous cell carcinoma(625;0.0949)														---	---	---	---
PPFIBP2	8495	broad.mit.edu	37	11	7655602	7655602	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7655602delT	uc001mfj.3	+						PPFIBP2_uc010rbb.1_Intron|PPFIBP2_uc001mfk.1_Intron|PPFIBP2_uc010rbc.1_Intron|PPFIBP2_uc010rbd.1_Intron|PPFIBP2_uc010rbe.1_Intron|PPFIBP2_uc001mfl.3_Intron|PPFIBP2_uc009yfj.1_Intron	NM_003621	NP_003612			PTPRF interacting protein, binding protein 2						cell communication|DNA integration	intracellular	DNA binding|integrase activity|protein binding			ovary(2)|breast(2)	4				Epithelial(150;2.01e-07)|BRCA - Breast invasive adenocarcinoma(625;0.236)														---	---	---	---
STK33	65975	broad.mit.edu	37	11	8574365	8574365	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8574365delT	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)														---	---	---	---
SCUBE2	57758	broad.mit.edu	37	11	9091710	9091711	+	Intron	DEL	AG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9091710_9091711delAG	uc001mhh.1	-						SCUBE2_uc001mhi.1_Intron|SCUBE2_uc001mhj.1_Intron	NM_020974	NP_066025			CEGP1 protein precursor							extracellular region	calcium ion binding			ovary(1)|skin(1)	2				all cancers(16;8.57e-09)|Epithelial(150;4.42e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0116)														---	---	---	---
ZNF143	7702	broad.mit.edu	37	11	9493100	9493100	+	Intron	DEL	G	-	-	rs7119680	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9493100delG	uc001mhr.2	+						ZNF143_uc009yfu.2_Intron|ZNF143_uc010rby.1_Intron	NM_003442	NP_003433			zinc finger protein 143						regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase III promoter|transcription from RNA polymerase II promoter|transcription from RNA polymerase III promoter	nucleoplasm	DNA binding|zinc ion binding				0				all cancers(16;4.12e-09)|Epithelial(150;2.29e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0212)														---	---	---	---
ZNF143	7702	broad.mit.edu	37	11	9538741	9538741	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9538741delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	10334418	10334419	+	IGR	INS	-	GT	GT	rs150981819	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10334418_10334419insGT								ADM (5495 upstream) : AMPD3 (137449 downstream)																																			---	---	---	---
TEAD1	7003	broad.mit.edu	37	11	12753628	12753629	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:12753628_12753629delTT	uc001mkj.3	+							NM_021961	NP_068780			TEA domain family member 1						hippo signaling cascade		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0				Epithelial(150;0.00223)|BRCA - Breast invasive adenocarcinoma(625;0.236)														---	---	---	---
TEAD1	7003	broad.mit.edu	37	11	12958637	12958637	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:12958637delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	13612784	13612784	+	IGR	DEL	A	-	-	rs113532355		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:13612784delA								PTH (95217 upstream) : FAR1 (77422 downstream)																																			---	---	---	---
COPB1	1315	broad.mit.edu	37	11	14493468	14493468	+	Intron	DEL	A	-	-	rs78677969		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:14493468delA	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																		---	---	---	---
PSMA1	5682	broad.mit.edu	37	11	14528721	14528722	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:14528721_14528722delTT	uc001mlk.2	-						PSMA1_uc001mll.2_Intron|PSMA1_uc010rcp.1_Intron|PSMA1_uc001mlj.2_Intron	NM_002786	NP_002777			proteasome alpha 1 subunit isoform 2						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|polysome|proteasome core complex, alpha-subunit complex	protein binding|RNA binding|threonine-type endopeptidase activity			upper_aerodigestive_tract(1)|skin(1)	2																		---	---	---	---
PSMA1	5682	broad.mit.edu	37	11	14635944	14635944	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:14635944delA	uc001mll.2	-							NM_148976	NP_683877			proteasome alpha 1 subunit isoform 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|polysome|proteasome core complex, alpha-subunit complex	protein binding|RNA binding|threonine-type endopeptidase activity			upper_aerodigestive_tract(1)|skin(1)	2																		---	---	---	---
PDE3B	5140	broad.mit.edu	37	11	14690423	14690424	+	Intron	INS	-	C	C	rs139085249	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:14690423_14690424insC	uc001mln.2	+						PDE3B_uc001mlm.2_Intron|PDE3B_uc010rcr.1_Intron	NM_000922	NP_000913			phosphodiesterase 3B						cAMP catabolic process|insulin receptor signaling pathway|negative regulation of lipid catabolic process|platelet activation	cytosol|endoplasmic reticulum|Golgi apparatus|guanyl-nucleotide exchange factor complex|integral to membrane|microsome	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity|metal ion binding|protein kinase B binding				0																		---	---	---	---
INSC	387755	broad.mit.edu	37	11	15170175	15170176	+	Intron	INS	-	ATGCC	ATGCC	rs138073791	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:15170175_15170176insATGCC	uc001mly.2	+						INSC_uc001mlz.2_Intron|INSC_uc001mma.2_5'Flank|INSC_uc010rcs.1_5'Flank|INSC_uc001mmb.2_5'Flank|INSC_uc001mmc.2_5'Flank	NM_001031853	NP_001027024			inscuteable isoform a						cell differentiation|nervous system development	cytoplasm	binding			upper_aerodigestive_tract(2)|ovary(2)|central_nervous_system(1)	5																		---	---	---	---
INSC	387755	broad.mit.edu	37	11	15215482	15215483	+	Intron	INS	-	ACC	ACC	rs144945461	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:15215482_15215483insACC	uc001mly.2	+						INSC_uc001mlz.2_Intron|INSC_uc001mma.2_Intron|INSC_uc010rcs.1_Intron|INSC_uc001mmb.2_Intron|INSC_uc001mmc.2_Intron	NM_001031853	NP_001027024			inscuteable isoform a						cell differentiation|nervous system development	cytoplasm	binding			upper_aerodigestive_tract(2)|ovary(2)|central_nervous_system(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	15836345	15836347	+	IGR	DEL	TGT	-	-	rs141807521		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:15836345_15836347delTGT								INSC (567593 upstream) : SOX6 (151649 downstream)																																			---	---	---	---
SOX6	55553	broad.mit.edu	37	11	15991786	15991786	+	3'UTR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:15991786delT	uc001mme.2	-	16					SOX6_uc001mmd.2_3'UTR|SOX6_uc001mmf.2_3'UTR|SOX6_uc001mmg.2_3'UTR	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																		---	---	---	---
PLEKHA7	144100	broad.mit.edu	37	11	16888740	16888740	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:16888740delC	uc001mmo.2	-						PLEKHA7_uc010rcu.1_Intron	NM_175058	NP_778228			pleckstrin homology domain containing, family A						epithelial cell-cell adhesion|zonula adherens maintenance	centrosome|zonula adherens	delta-catenin binding			skin(2)|central_nervous_system(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	17248124	17248124	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17248124delT								PIK3C2A (18594 upstream) : NUCB2 (33763 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	17268646	17268646	+	IGR	DEL	T	-	-	rs112031549		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17268646delT								PIK3C2A (39116 upstream) : NUCB2 (13241 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	17273539	17273539	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17273539delA								PIK3C2A (44009 upstream) : NUCB2 (8348 downstream)																																			---	---	---	---
ABCC8	6833	broad.mit.edu	37	11	17439295	17439296	+	Intron	DEL	TC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17439295_17439296delTC	uc001mnc.2	-							NM_000352	NP_000343			ATP-binding cassette, sub-family C, member 8						carbohydrate metabolic process|energy reserve metabolic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances|potassium ion transmembrane transporter activity|sulfonylurea receptor activity			ovary(1)	1				READ - Rectum adenocarcinoma(2;0.0325)|Colorectal(2;0.1)	Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)|Gliclazide(DB01120)|Mitiglinide(DB01252)|Nateglinide(DB00731)|Repaglinide(DB00912)													---	---	---	---
Unknown	0	broad.mit.edu	37	11	17574067	17574078	+	IGR	DEL	GTTCCTACCTCC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17574067_17574078delGTTCCTACCTCC								USH1C (8104 upstream) : MYOD1 (167032 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	17732673	17732708	+	IGR	DEL	CTGTGAGAAGCGTGCAGGGAGTTTGTGGCGTGCGTT	-	-	rs66854071	by1000genomes;by1000genomes;by1000genomes;by1000genomes;by1000genomes;by1000genomes;by1000genomes;by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17732673_17732708delCTGTGAGAAGCGTGCAGGGAGTTTGTGGCGTGCGTT								USH1C (166710 upstream) : MYOD1 (8402 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	18409068	18409069	+	5'Flank	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18409068_18409069insA	hsa-mir-3159|MI0014188	+																																									---	---	---	---
Unknown	0	broad.mit.edu	37	11	18857076	18857079	+	IGR	DEL	TTTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18857076_18857079delTTTT								PTPN5 (43687 upstream) : MRGPRX1 (98282 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	19101791	19101791	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:19101791delC								MRGPRX2 (19563 upstream) : ZDHHC13 (36901 downstream)																																			---	---	---	---
CSRP3	8048	broad.mit.edu	37	11	19214121	19214121	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:19214121delT	uc001mpk.2	-							NM_003476	NP_003467			cysteine and glycine-rich protein 3						cell differentiation|skeletal muscle tissue development	cytoskeleton|nucleus	protein binding|zinc ion binding				0																		---	---	---	---
NAV2	89797	broad.mit.edu	37	11	19653037	19653037	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:19653037delT	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	20053281	20053282	+	Intron	DEL	TG	-	-	rs138973325		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20053281_20053282delTG	uc010rdm.1	+						NAV2_uc001mpp.2_Intron|NAV2_uc001mpr.3_Intron|NAV2_uc001mpt.2_Intron|NAV2_uc009yhx.2_Intron|NAV2_uc009yhy.1_Intron	NM_145117	NP_660093			neuron navigator 2 isoform 2							nucleus	ATP binding|helicase activity			skin(4)|ovary(1)|pancreas(1)	6																		---	---	---	---
NELL1	4745	broad.mit.edu	37	11	21088906	21088907	+	Intron	INS	-	T	T	rs149289019	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:21088906_21088907insT	uc001mqe.2	+						NELL1_uc001mqf.2_Intron|NELL1_uc009yid.2_Intron|NELL1_uc010rdo.1_Intron|NELL1_uc010rdp.1_Intron	NM_006157	NP_006148			nel-like 1 isoform 1 precursor						cell adhesion|nervous system development	extracellular region	calcium ion binding|structural molecule activity			ovary(2)|large_intestine(1)	3																		---	---	---	---
NELL1	4745	broad.mit.edu	37	11	21443639	21443640	+	Intron	DEL	AT	-	-	rs143636433	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:21443639_21443640delAT	uc001mqe.2	+						NELL1_uc001mqf.2_Intron|NELL1_uc009yid.2_Intron|NELL1_uc010rdo.1_Intron|NELL1_uc010rdp.1_Intron|NELL1_uc001mqg.2_Intron|NELL1_uc001mqh.2_Intron	NM_006157	NP_006148			nel-like 1 isoform 1 precursor						cell adhesion|nervous system development	extracellular region	calcium ion binding|structural molecule activity			ovary(2)|large_intestine(1)	3																		---	---	---	---
NELL1	4745	broad.mit.edu	37	11	21550017	21550018	+	Intron	DEL	TT	-	-	rs113113444		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:21550017_21550018delTT	uc001mqe.2	+						NELL1_uc001mqf.2_Intron|NELL1_uc009yid.2_Intron|NELL1_uc010rdo.1_Intron|NELL1_uc010rdp.1_Intron|NELL1_uc001mqh.2_Intron	NM_006157	NP_006148			nel-like 1 isoform 1 precursor						cell adhesion|nervous system development	extracellular region	calcium ion binding|structural molecule activity			ovary(2)|large_intestine(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	23131499	23131499	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:23131499delA								SVIP (280117 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	25630476	25630477	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:25630476_25630477insT								LUZP2 (526294 upstream) : ANO3 (580352 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	25755067	25755067	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:25755067delA								LUZP2 (650885 upstream) : ANO3 (455762 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	26069758	26069759	+	IGR	DEL	CT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:26069758_26069759delCT								LUZP2 (965576 upstream) : ANO3 (141070 downstream)																																			---	---	---	---
ANO3	63982	broad.mit.edu	37	11	26252945	26252945	+	Intron	DEL	T	-	-	rs5790565		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:26252945delT	uc010rdr.1	+							NM_031418	NP_113606			transmembrane protein 16C							chloride channel complex	chloride channel activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4																		---	---	---	---
SLC5A12	159963	broad.mit.edu	37	11	26692193	26692193	+	3'UTR	DEL	A	-	-	rs6484242	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:26692193delA	uc001mra.2	-	15					SLC5A12_uc001mrb.2_RNA	NM_178498	NP_848593			solute carrier family 5 (sodium/glucose						sodium ion transport	apical plasma membrane|integral to membrane	symporter activity			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	27330978	27330987	+	IGR	DEL	GTGTGTGTGT	-	-	rs5790644		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:27330978_27330987delGTGTGTGTGT								BBOX1 (181624 upstream) : CCDC34 (29074 downstream)																																			---	---	---	---
LGR4	55366	broad.mit.edu	37	11	27455348	27455348	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:27455348delA	uc001mrj.3	-						LGR4_uc001mrk.3_Intron	NM_018490	NP_060960			leucine-rich repeat-containing G protein-coupled							integral to membrane|plasma membrane	protein-hormone receptor activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	28695928	28695928	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:28695928delA								METT5D1 (340874 upstream) : None (None downstream)																																	OREG0020852	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	28930945	28930945	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:28930945delT								METT5D1 (575891 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	29379438	29379438	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:29379438delT								None (None upstream) : KCNA4 (652328 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	30008239	30008239	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:30008239delT								None (None upstream) : KCNA4 (23527 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	30992565	30992566	+	Intron	DEL	CA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:30992565_30992566delCA	uc009yjk.1	-						uc009yjl.1_Intron|DCDC1_uc001msu.1_Intron					RecName: Full=Doublecortin domain-containing protein 5;																														---	---	---	---
Unknown	0	broad.mit.edu	37	11	31029210	31029210	+	Intron	DEL	T	-	-	rs71955537		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:31029210delT	uc009yjk.1	-						uc009yjl.1_Intron|DCDC1_uc001msu.1_Intron					RecName: Full=Doublecortin domain-containing protein 5;																														---	---	---	---
DCDC1	341019	broad.mit.edu	37	11	31272306	31272306	+	Intron	DEL	T	-	-	rs67217675		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:31272306delT	uc001msu.1	-											SubName: Full=Putative uncharacterized protein ENSP00000343496;						intracellular signal transduction					skin(1)	1	Lung SC(675;0.225)																	---	---	---	---
RCN1	5954	broad.mit.edu	37	11	31960906	31960908	+	Intron	DEL	AAC	-	-	rs77455012		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:31960906_31960908delAAC	uc010rea.1	+							NM_002901	NP_002892			reticulocalbin 1 precursor							endoplasmic reticulum lumen	calcium ion binding			large_intestine(1)	1	Lung SC(675;0.225)																	---	---	---	---
Unknown	0	broad.mit.edu	37	11	32338840	32338841	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32338840_32338841delAA								RCN1 (211569 upstream) : WT1 (70484 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	32359110	32359110	+	IGR	DEL	T	-	-	rs35841878		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32359110delT								RCN1 (231839 upstream) : WT1 (50215 downstream)																																			---	---	---	---
WT1	7490	broad.mit.edu	37	11	32431441	32431441	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32431441delT	uc001mtn.1	-						WT1_uc001mtl.1_Intron|WT1_uc001mtm.1_Intron|WT1_uc001mto.1_Intron|WT1_uc001mtp.1_Intron|WT1_uc001mtq.1_Intron|WT1_uc009yjs.1_Intron	NM_024426	NP_077744			Wilms tumor 1 isoform D						adrenal cortex formation|branching involved in ureteric bud morphogenesis|camera-type eye development|cardiac muscle cell fate commitment|cellular response to cAMP|cellular response to gonadotropin stimulus|germ cell development|glomerular basement membrane development|glomerular visceral epithelial cell differentiation|induction of apoptosis|male genitalia development|male gonad development|mesenchymal to epithelial transition|metanephric epithelium development|metanephric S-shaped body morphogenesis|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of female gonad development|negative regulation of metanephric glomerular mesangial cell proliferation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|negative regulation of translation|positive regulation of male gonad development|positive regulation of transcription, DNA-dependent|posterior mesonephric tubule development|regulation of organ formation|RNA splicing|sex determination|vasculogenesis|visceral serous pericardium development	cytoplasm|nuclear speck|nucleoplasm	C2H2 zinc finger domain binding|RNA binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|zinc ion binding		EWSR1/WT1(231)	haematopoietic_and_lymphoid_tissue(318)|soft_tissue(231)|kidney(132)|pleura(2)|lung(2)|upper_aerodigestive_tract(1)|peritoneum(1)	687	Breast(20;0.247)		OV - Ovarian serous cystadenocarcinoma(30;0.128)					D|Mis|N|F|S	EWSR1	Wilms|desmoplastic small round cell tumor	Wilms			Denys-Drash_syndrome|Frasier_syndrome|Familial_Wilms_tumor|Wilms_tumor-Aniridia-ambiguous_Genitals-mental_Retardation				---	---	---	---
CCDC73	493860	broad.mit.edu	37	11	32629366	32629369	+	Intron	DEL	AGAT	-	-	rs57759315		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32629366_32629369delAGAT	uc001mtv.2	-							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	33215031	33215032	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33215031_33215032delTT								CSTF3 (31994 upstream) : HIPK3 (64136 downstream)																																			---	---	---	---
NAT10	55226	broad.mit.edu	37	11	34162954	34162955	+	Intron	INS	-	TC	TC	rs141705432		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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)																---	---	---	---
Unknown	0	broad.mit.edu	37	11	34718170	34718170	+	IGR	DEL	T	-	-	rs11330192		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34718170delT								EHF (35089 upstream) : APIP (178544 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	34765467	34765468	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34765467_34765468delTT								EHF (82386 upstream) : APIP (131246 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	35108333	35108333	+	IGR	DEL	A	-	-	rs72429276		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35108333delA								PDHX (90659 upstream) : CD44 (52084 downstream)																																			---	---	---	---
LDLRAD3	143458	broad.mit.edu	37	11	36155521	36155522	+	Intron	DEL	TA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:36155521_36155522delTA	uc001mwk.1	+						LDLRAD3_uc010rey.1_Intron|LDLRAD3_uc010rez.1_Intron|LDLRAD3_uc010rfa.1_Intron	NM_174902	NP_777562			low density lipoprotein receptor class A domain							integral to membrane	receptor activity			central_nervous_system(1)	1	all_lung(20;0.089)|Lung NSC(22;0.175)|all_epithelial(35;0.177)	all_hematologic(20;0.124)																---	---	---	---
PRR5L	79899	broad.mit.edu	37	11	36406387	36406387	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:36406387delT	uc001mwo.3	+						PRR5L_uc001mwp.2_Intron|PRR5L_uc009ykk.2_Intron	NM_001160167	NP_001153639			protor-2 isoform a											ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	36738906	36738906	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:36738906delT								C11orf74 (42516 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	37143266	37143266	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:37143266delT								C11orf74 (446876 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	37576681	37576681	+	IGR	DEL	A	-	-	rs72387607		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:37576681delA								C11orf74 (880291 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	37948840	37948840	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:37948840delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	38221237	38221238	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:38221237_38221238insT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	38385309	38385309	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:38385309delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	38766914	38766915	+	IGR	DEL	AT	-	-	rs35435933		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:38766914_38766915delAT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	39971023	39971023	+	IGR	DEL	A	-	-	rs6485164	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:39971023delA								None (None upstream) : LRRC4C (164730 downstream)																																			---	---	---	---
LRRC4C	57689	broad.mit.edu	37	11	40161900	40161900	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:40161900delG	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	40345883	40345883	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:40345883delT	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	41946430	41946430	+	IGR	DEL	A	-	-	rs67327667		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:41946430delA								LRRC4C (465107 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	42010406	42010407	+	IGR	INS	-	AAAG	AAAG	rs71868073		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:42010406_42010407insAAAG								LRRC4C (529083 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	42719912	42719912	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:42719912delT								None (None upstream) : API5 (613593 downstream)																																			---	---	---	---
TTC17	55761	broad.mit.edu	37	11	43418508	43418511	+	Intron	DEL	AAAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43418508_43418511delAAAA	uc001mxi.2	+						TTC17_uc001mxh.2_Intron|TTC17_uc010rfj.1_Intron|TTC17_uc001mxj.2_Intron	NM_018259	NP_060729			tetratricopeptide repeat domain 17								binding			ovary(5)	5																		---	---	---	---
HSD17B12	51144	broad.mit.edu	37	11	43710368	43710369	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43710368_43710369insT	uc001mxq.3	+						HSD17B12_uc001mxp.2_Intron	NM_016142	NP_057226			hydroxysteroid (17-beta) dehydrogenase 12						long-chain fatty-acyl-CoA biosynthetic process|steroid biosynthetic process|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane	estradiol 17-beta-dehydrogenase activity|long-chain-3-hydroxyacyl-CoA dehydrogenase activity				0																		---	---	---	---
ALKBH3	221120	broad.mit.edu	37	11	43926993	43926993	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43926993delT	uc001mxs.2	+						ALKBH3_uc009ykp.2_Intron|ALKBH3_uc001mxt.2_Intron|ALKBH3_uc009ykq.2_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	45029597	45029598	+	IGR	DEL	CT	-	-	rs61288662		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45029597_45029598delCT								LOC221122 (30021 upstream) : PRDM11 (85966 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	45836009	45836009	+	IGR	DEL	T	-	-	rs141754680		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45836009delT								SLC35C1 (1443 upstream) : CRY2 (32660 downstream)																																			---	---	---	---
MAPK8IP1	9479	broad.mit.edu	37	11	45924884	45924884	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45924884delC	uc001nbr.2	+							NM_005456	NP_005447			mitogen-activated protein kinase 8 interacting						vesicle-mediated transport	nucleus|perinuclear region of cytoplasm	kinesin binding|MAP-kinase scaffold activity|protein kinase inhibitor activity			ovary(2)|breast(1)|skin(1)	4				GBM - Glioblastoma multiforme(35;0.231)														---	---	---	---
PHF21A	51317	broad.mit.edu	37	11	46127167	46127167	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46127167delA	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																		---	---	---	---
KIAA0652	9776	broad.mit.edu	37	11	46658328	46658328	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46658328delT	uc009yld.2	+						KIAA0652_uc001nda.2_Intron|KIAA0652_uc001ndb.2_Intron|KIAA0652_uc001ncz.2_Intron|KIAA0652_uc001ndc.2_Intron|KIAA0652_uc010rgv.1_Intron	NM_001142673	NP_001136145			autophagy-related protein 13 isoform 1						autophagic vacuole assembly	cytosol|pre-autophagosomal structure|ULK1-ATG13-FIP200 complex	protein binding				0				GBM - Glioblastoma multiforme(35;0.226)														---	---	---	---
KIAA0652	9776	broad.mit.edu	37	11	46666873	46666873	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46666873delT	uc009yld.2	+						KIAA0652_uc001nda.2_Intron|KIAA0652_uc001ndb.2_Intron|KIAA0652_uc001ncz.2_Intron|KIAA0652_uc001ndc.2_Intron|KIAA0652_uc010rgv.1_Intron	NM_001142673	NP_001136145			autophagy-related protein 13 isoform 1						autophagic vacuole assembly	cytosol|pre-autophagosomal structure|ULK1-ATG13-FIP200 complex	protein binding				0				GBM - Glioblastoma multiforme(35;0.226)														---	---	---	---
ARFGAP2	84364	broad.mit.edu	37	11	47187430	47187430	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47187430delT	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	47240294	47240298	+	Intron	DEL	AAAAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47240294_47240298delAAAAA	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				---	---	---	---
DDB2	1643	broad.mit.edu	37	11	47247828	47247829	+	Intron	DEL	TC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47247828_47247829delTC	uc001neb.2	+						DDB2_uc001nec.2_Intron|DDB2_uc009yli.1_Intron|DDB2_uc001ned.2_Intron|DDB2_uc001nee.2_Intron|DDB2_uc001nef.2_Intron|DDB2_uc001neg.2_Intron|DDB2_uc001neh.2_Intron	NM_000107	NP_000098			damage-specific DNA binding protein 2						nucleotide-excision repair, DNA damage removal|protein autoubiquitination|protein polyubiquitination|response to UV	nucleoplasm|protein complex	damaged DNA binding|protein binding			kidney(2)|ovary(1)	3								Mis|N			skin basal cell|skin squamous cell|melanoma		Direct_reversal_of_damage|NER	Xeroderma_Pigmentosum				---	---	---	---
CELF1	10658	broad.mit.edu	37	11	47490570	47490570	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47490570delG	uc001nfl.2	-						CELF1_uc001nfk.1_RNA|CELF1_uc001nfm.2_Intron|CELF1_uc001nfn.2_Intron	NM_001025596	NP_001020767			CUG triplet repeat, RNA-binding protein 1						embryo development|mRNA splice site selection|regulation of RNA splicing|RNA interference	cytoplasm|nucleus|ribonucleoprotein complex	BRE binding|mRNA binding|nucleotide binding|translation repressor activity, nucleic acid binding			central_nervous_system(2)|ovary(1)	3																		---	---	---	---
AGBL2	79841	broad.mit.edu	37	11	47699526	47699526	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47699526delT	uc001ngg.2	-						AGBL2_uc001ngf.2_Intron|AGBL2_uc010rhq.1_Intron|AGBL2_uc001ngh.1_Intron	NM_024783	NP_079059			carboxypeptidase 2, cytosolic						proteolysis	cytosol	metallocarboxypeptidase activity|zinc ion binding			ovary(2)	2																		---	---	---	---
FNBP4	23360	broad.mit.edu	37	11	47739767	47739767	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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																		---	---	---	---
FNBP4	23360	broad.mit.edu	37	11	47744543	47744543	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47744543delT	uc009ylv.2	-	15	2943	c.2790delA	c.(2788-2790)AAAfs	p.K930fs	FNBP4_uc001ngi.2_Frame_Shift_Del_p.K244fs|FNBP4_uc001ngj.2_Frame_Shift_Del_p.K837fs	NM_015308	NP_056123	Q8N3X1	FNBP4_HUMAN	formin binding protein 4	930										ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	47899219	47899222	+	IGR	DEL	TCTA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47899219_47899222delTCTA								NUP160 (29162 upstream) : PTPRJ (102888 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	47944297	47944297	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47944297delT								NUP160 (74240 upstream) : PTPRJ (57813 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	48377974	48377979	+	IGR	DEL	GGGGTA	-	-	rs113652187		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48377974_48377979delGGGGTA								OR4C45 (3975 upstream) : OR4A47 (132366 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	48804651	48804651	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48804651delC								OR4A47 (293379 upstream) : FOLH1 (363537 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	48849535	48849536	+	IGR	INS	-	CA	CA	rs147911541		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48849535_48849536insCA								OR4A47 (338263 upstream) : FOLH1 (318652 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	48864295	48864295	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48864295delT								OR4A47 (353023 upstream) : FOLH1 (303893 downstream)																																			---	---	---	---
FOLH1	2346	broad.mit.edu	37	11	49193295	49193295	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:49193295delA	uc001ngy.2	-						FOLH1_uc001ngz.2_Intron|FOLH1_uc009yly.2_Intron|FOLH1_uc009ylz.2_Intron|FOLH1_uc009yma.2_Intron	NM_004476	NP_004467			folate hydrolase 1 isoform 1						proteolysis	cytoplasm|integral to plasma membrane|membrane fraction|nucleus	carboxypeptidase activity|dipeptidase activity|metal ion binding|metallopeptidase activity			large_intestine(1)|ovary(1)|skin(1)	3					Capromab(DB00089)|L-Glutamic Acid(DB00142)													---	---	---	---
Unknown	0	broad.mit.edu	37	11	50779833	50779833	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:50779833delG								LOC646813 (400030 upstream) : OR4A5 (631615 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	51241844	51241845	+	IGR	INS	-	T	T	rs74660220	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:51241844_51241845insT								LOC646813 (862041 upstream) : OR4A5 (169603 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	54920046	54920047	+	IGR	INS	-	A	A	rs145555928	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:54920046_54920047insA								None (None upstream) : TRIM48 (109611 downstream)																																			---	---	---	---
TRIM48	79097	broad.mit.edu	37	11	55035952	55035952	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55035952delT	uc010rid.1	+							NM_024114	NP_077019			tripartite motif-containing 48							intracellular	zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	56103413	56103413	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56103413delT								OR8K3 (16694 upstream) : OR8K1 (10102 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	56140346	56140346	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56140346delC								OR8J1 (11675 upstream) : OR5R1 (44390 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	56454101	56454101	+	IGR	DEL	A	-	-	rs34350613		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56454101delA								OR5AR1 (22009 upstream) : OR9G9 (13763 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	56489558	56489558	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56489558delA								OR9G9 (20779 upstream) : OR9G4 (20747 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	56539795	56539795	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56539795delG								OR9G4 (28508 upstream) : OR5AK2 (216594 downstream)																																			---	---	---	---
RTN4RL2	349667	broad.mit.edu	37	11	57228625	57228625	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57228625delG	uc010rjt.1	+							NM_178570	NP_848665			reticulon 4 receptor-like 2 precursor						axon regeneration	anchored to plasma membrane	receptor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	57635399	57635400	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57635399_57635400delTT								CTNND1 (48748 upstream) : OR9Q1 (155953 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	58225263	58225263	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58225263delA								OR5B12 (17639 upstream) : OR5B21 (49388 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	58503055	58503055	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58503055delC								GLYAT (3608 upstream) : GLYATL2 (98487 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	59003426	59003426	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59003426delA								MPEG1 (22932 upstream) : OR5AN1 (128506 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	59303937	59303937	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59303937delA								OR4D9 (20609 upstream) : OSBP (37934 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	59304262	59304262	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59304262delT								OR4D9 (20934 upstream) : OSBP (37609 downstream)																																			---	---	---	---
OSBP	5007	broad.mit.edu	37	11	59368589	59368596	+	Intron	DEL	AAAAAAAA	-	-	rs34934607		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59368589_59368596delAAAAAAAA	uc001noc.1	-						OSBP_uc009ymr.1_5'Flank	NM_002556	NP_002547			oxysterol binding protein						lipid transport	Golgi membrane	oxysterol binding			large_intestine(1)	1		all_epithelial(135;0.000236)		BRCA - Breast invasive adenocarcinoma(625;0.00607)|LUSC - Lung squamous cell carcinoma(625;0.207)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	59681131	59681131	+	IGR	DEL	T	-	-	rs71831362		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59681131delT								TCN1 (47090 upstream) : PLAC1L (126617 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	59897934	59897934	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59897934delT								MS4A2 (31920 upstream) : MS4A6A (41147 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	60787934	60787935	+	IGR	DEL	TG	-	-	rs35234891		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60787934_60787935delTG								CD6 (88 upstream) : CD5 (81995 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	61377268	61377268	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61377268delA								SYT7 (28970 upstream) : RPLP0P2 (5240 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	61963100	61963100	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61963100delA								SCGB1D1 (2091 upstream) : SCGB2A1 (13040 downstream)																																			---	---	---	---
SLC22A9	114571	broad.mit.edu	37	11	63165376	63165376	+	Intron	DEL	A	-	-	rs142308371		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63165376delA	uc001nww.2	+						SLC22A9_uc001nwx.2_Intron	NM_080866	NP_543142			solute carrier family 22 (organic anion/cation						transmembrane transport	integral to membrane				breast(2)|large_intestine(1)	3																		---	---	---	---
HRASLS5	117245	broad.mit.edu	37	11	63251806	63251806	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63251806delA	uc001nwy.2	-						HRASLS5_uc001nwz.2_Intron|HRASLS5_uc010rmq.1_Intron|HRASLS5_uc009yos.2_Intron	NM_054108	NP_473449			HRAS-like suppressor family, member 5 isoform 1											ovary(1)	1																		---	---	---	---
HRASLS5	117245	broad.mit.edu	37	11	63256148	63256151	+	Intron	DEL	TTTT	-	-	rs35614311		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63256148_63256151delTTTT	uc001nwy.2	-						HRASLS5_uc001nwz.2_Intron|HRASLS5_uc010rmq.1_Intron|HRASLS5_uc009yos.2_Intron	NM_054108	NP_473449			HRAS-like suppressor family, member 5 isoform 1											ovary(1)	1																		---	---	---	---
RTN3	10313	broad.mit.edu	37	11	63451602	63451610	+	Intron	DEL	TTTTTTTTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63451602_63451610delTTTTTTTTT	uc001nxq.2	+						RTN3_uc001nxo.2_Intron|RTN3_uc001nxm.2_Intron|RTN3_uc001nxn.2_Intron|RTN3_uc001nxp.2_Intron|RTN3_uc009yov.2_Intron|RTN3_uc010rmt.1_Intron|RTN3_uc010rmu.1_Intron	NM_201428	NP_958831			reticulon 3 isoform b						apoptosis|endoplasmic reticulum tubular network organization|interspecies interaction between organisms|response to stress|vesicle-mediated transport	endoplasmic reticulum membrane|extracellular space|Golgi membrane|integral to membrane				ovary(1)	1																		---	---	---	---
MARK2	2011	broad.mit.edu	37	11	63669164	63669165	+	Intron	INS	-	TG	TG			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63669164_63669165insTG	uc001nxw.2	+						MARK2_uc001nxx.2_Intron|MARK2_uc001nxy.2_Intron|MARK2_uc001nxv.3_Intron|MARK2_uc001nxz.3_Intron|MARK2_uc009yoy.2_Intron	NM_001039469	NP_001034558			MAP/microtubule affinity-regulating kinase 2						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																OREG0021038	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
MARK2	2011	broad.mit.edu	37	11	63672817	63672817	+	Intron	DEL	C	-	-	rs34826752		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63672817delC	uc001nxw.2	+						MARK2_uc001nxx.2_Intron|MARK2_uc001nxy.2_Intron|MARK2_uc001nxv.3_Intron|MARK2_uc001nxz.3_Intron|MARK2_uc009yoy.2_Intron	NM_001039469	NP_001034558			MAP/microtubule affinity-regulating kinase 2						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																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	64276947	64276947	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64276947delA								RPS6KA4 (137261 upstream) : SLC22A11 (46151 downstream)																																			---	---	---	---
MAP4K2	5871	broad.mit.edu	37	11	64565076	64565076	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64565076delC	uc001obh.2	-						MAP4K2_uc001obg.2_5'Flank|MAP4K2_uc001obi.2_Intron	NM_004579	NP_004570			mitogen-activated protein kinase kinase kinase						activation of JUN kinase activity|immune response|positive regulation of JNK cascade|vesicle targeting	basolateral plasma membrane|Golgi membrane|soluble fraction	ATP binding|mitogen-activated protein kinase kinase kinase binding|protein serine/threonine kinase activity|small GTPase regulator activity			ovary(1)|pancreas(1)	2																		---	---	---	---
GPHA2	170589	broad.mit.edu	37	11	64705823	64705823	+	5'Flank	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64705823delA	uc001oca.2	-							NM_130769	NP_570125			glycoprotein hormone alpha 2 precursor							extracellular region	hormone activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	65273963	65273963	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65273963delA								MALAT1 (26 upstream) : SCYL1 (18585 downstream)																																			---	---	---	---
MAP3K11	4296	broad.mit.edu	37	11	65376091	65376092	+	Intron	DEL	TT	-	-	rs112101273		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65376091_65376092delTT	uc001oew.2	-						MAP3K11_uc001oev.2_5'Flank|MAP3K11_uc010rol.1_Intron|MAP3K11_uc001oex.1_5'Flank	NM_002419	NP_002410			mitogen-activated protein kinase kinase kinase						activation of JUN kinase activity|cell proliferation|G1 phase of mitotic cell cycle|microtubule-based process|positive regulation of JNK cascade|protein autophosphorylation	centrosome|microtubule	ATP binding|JUN kinase kinase kinase activity|mitogen-activated protein kinase kinase kinase binding|protein homodimerization activity			breast(3)|lung(1)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
CTSW	1521	broad.mit.edu	37	11	65647105	65647105	+	5'Flank	DEL	A	-	-	rs12225345	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65647105delA	uc001ogc.1	+						CTSW_uc001ogb.1_5'Flank	NM_001335	NP_001326			cathepsin W preproprotein						immune response|proteolysis		cysteine-type endopeptidase activity			central_nervous_system(1)	1				READ - Rectum adenocarcinoma(159;0.168)														---	---	---	---
BANF1	8815	broad.mit.edu	37	11	65770687	65770687	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65770687delT	uc001ogo.2	+						EIF1AD_uc001ogm.1_5'Flank|EIF1AD_uc001ogn.1_5'Flank|BANF1_uc001ogp.2_Intron	NM_003860	NP_003851			barrier to autointegration factor 1						initiation of viral infection|interspecies interaction between organisms|provirus integration|response to virus	chromosome|cytosol|nucleoplasm	DNA binding				0																		---	---	---	---
C11orf80	79703	broad.mit.edu	37	11	66523809	66523809	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66523809delT	uc001ojf.2	+						C11orf80_uc001ojg.2_Intron|C11orf80_uc001ojh.2_Intron|C11orf80_uc001oji.2_5'Flank|C11orf80_uc010rpk.1_Intron	NM_024650	NP_078926			hypothetical protein LOC79703												0																		---	---	---	---
C11orf80	79703	broad.mit.edu	37	11	66575995	66575996	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66575995_66575996delAA	uc001ojf.2	+						C11orf80_uc001ojg.2_Intron|C11orf80_uc001ojh.2_Intron|C11orf80_uc001oji.2_Intron	NM_024650	NP_078926			hypothetical protein LOC79703												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	66863765	66863765	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66863765delA								RHOD (24278 upstream) : KDM2A (22975 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	66874951	66874952	+	IGR	DEL	CA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66874951_66874952delCA								RHOD (35464 upstream) : KDM2A (11788 downstream)																																			---	---	---	---
KDM2A	22992	broad.mit.edu	37	11	67001962	67001962	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67001962delT	uc001ojw.2	+						KDM2A_uc001ojx.2_Intron|KDM2A_uc001ojy.2_Intron	NM_012308	NP_036440			F-box and leucine-rich repeat protein 11						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	DNA binding|histone demethylase activity (H3-K36 specific)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|zinc ion binding			ovary(4)|lung(3)|breast(1)|skin(1)	9																		---	---	---	---
CLCF1	23529	broad.mit.edu	37	11	67139219	67139219	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67139219delG	uc001okq.2	-						LOC100130987_uc010rpo.1_Intron|CLCF1_uc010rpp.1_Intron	NM_013246	NP_037378			cardiotrophin-like cytokine factor 1 precursor						B cell differentiation|cytokine-mediated signaling pathway|JAK-STAT cascade|negative regulation of neuron apoptosis|positive regulation of astrocyte differentiation|positive regulation of B cell proliferation|positive regulation of immunoglobulin production|positive regulation of isotype switching to IgE isotypes|positive regulation of tyrosine phosphorylation of Stat3 protein	extracellular space	ciliary neurotrophic factor receptor binding|cytokine activity|growth factor activity|protein heterodimerization activity				0			BRCA - Breast invasive adenocarcinoma(15;2.39e-06)													OREG0021129	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
CORO1B	57175	broad.mit.edu	37	11	67209168	67209169	+	Intron	DEL	GG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67209168_67209169delGG	uc001olj.1	-						CORO1B_uc009yrs.1_Intron|CORO1B_uc001olk.1_Intron|CORO1B_uc009yrt.1_Intron|CORO1B_uc009yru.1_Intron|CORO1B_uc001oll.1_Intron|CORO1B_uc010rps.1_Intron|CORO1B_uc009yrv.1_Frame_Shift_Del_p.P163fs	NM_020441	NP_065174			coronin, actin binding protein, 1B						actin cytoskeleton organization	actin cytoskeleton|cytoplasm	actin filament binding			large_intestine(1)|ovary(1)	2			BRCA - Breast invasive adenocarcinoma(15;3.26e-06)															---	---	---	---
AIP	9049	broad.mit.edu	37	11	67258150	67258151	+	Intron	DEL	CT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67258150_67258151delCT	uc001olv.2	+							NM_003977	NP_003968			aryl hydrocarbon receptor interacting protein						protein maturation by protein folding|protein targeting to mitochondrion	nucleus	signal transducer activity|transcription coactivator activity|transcription factor binding|unfolded protein binding				0														Familial_Isolated_Pituitary_Adenoma_				---	---	---	---
Unknown	0	broad.mit.edu	37	11	67328832	67328832	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67328832delA								CABP2 (37933 upstream) : GSTP1 (22234 downstream)																																			---	---	---	---
SUV420H1	51111	broad.mit.edu	37	11	67928127	67928128	+	Intron	DEL	GA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67928127_67928128delGA	uc001onm.1	-						SUV420H1_uc009yse.1_Intron|SUV420H1_uc001onn.1_Intron|SUV420H1_uc009ysf.2_Intron	NM_017635	NP_060105			suppressor of variegation 4-20 homolog 1 isoform						regulation of transcription, DNA-dependent|transcription, DNA-dependent		protein binding			ovary(2)|kidney(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	68411119	68411119	+	IGR	DEL	A	-	-	rs78217649		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68411119delA								SAPS3 (28320 upstream) : GAL (40864 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	68434016	68434016	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68434016delG								SAPS3 (51217 upstream) : GAL (17967 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	68625317	68625318	+	IGR	INS	-	AA	AA	rs144171546	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68625317_68625318insAA								CPT1A (15918 upstream) : MRPL21 (33429 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	68632550	68632550	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68632550delA								CPT1A (23151 upstream) : MRPL21 (26197 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	68939917	68939917	+	IGR	DEL	T	-	-	rs72313933		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68939917delT								TPCN2 (10010 upstream) : MYEOV (121705 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	68965050	68965051	+	IGR	INS	-	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68965050_68965051insC								TPCN2 (35143 upstream) : MYEOV (96571 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	69580465	69580466	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69580465_69580466delTT								FGF19 (61359 upstream) : FGF4 (7331 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	69663292	69663293	+	IGR	INS	-	TTTCT	TTTCT	rs146449202	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69663292_69663293insTTTCT								FGF3 (29100 upstream) : ANO1 (261115 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	69852643	69852646	+	IGR	DEL	TCTT	-	-	rs35710685		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69852643_69852646delTCTT								FGF3 (218451 upstream) : ANO1 (71762 downstream)																																			---	---	---	---
FADD	8772	broad.mit.edu	37	11	70053123	70053124	+	3'UTR	INS	-	TGT	TGT	rs150991429	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70053123_70053124insTGT	uc001opm.2	+	2						NM_003824	NP_003815			Fas-associated via death domain						activation of caspase activity|activation of pro-apoptotic gene products|cellular response to mechanical stimulus|defense response to virus|induction of apoptosis via death domain receptors|innate immune response|interspecies interaction between organisms|necrotic cell death|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-8 production|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tumor necrosis factor production|positive regulation of type I interferon-mediated signaling pathway|signal transduction	cytosol	death receptor binding|identical protein binding			ovary(1)|lung(1)|pancreas(1)	3	Esophageal squamous(2;1.19e-45)		LUSC - Lung squamous cell carcinoma(11;1.46e-14)|STAD - Stomach adenocarcinoma(18;0.0513)															---	---	---	---
Unknown	0	broad.mit.edu	37	11	70066571	70066571	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70066571delA								FADD (13063 upstream) : PPFIA1 (50252 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	70106331	70106331	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70106331delT								FADD (52823 upstream) : PPFIA1 (10492 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	70113693	70113696	+	IGR	DEL	AGGA	-	-	rs71974523		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70113693_70113696delAGGA								FADD (60185 upstream) : PPFIA1 (3127 downstream)																																			---	---	---	---
PPFIA1	8500	broad.mit.edu	37	11	70150125	70150125	+	Intron	DEL	A	-	-	rs111257665		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70150125delA	uc001opo.2	+						PPFIA1_uc001opn.1_Intron|PPFIA1_uc001opp.2_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	70249411	70249412	+	Intron	INS	-	AGCCTCCCA	AGCCTCCCA	rs139086598	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70249411_70249412insAGCCTCCCA	uc001opv.3	+						CTTN_uc001opu.2_Intron|CTTN_uc001opw.3_Intron	NM_005231	NP_005222			cortactin isoform a							cell cortex|cytoskeleton|lamellipodium|ruffle|soluble fraction	protein binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(2;4.34e-41)|LUSC - Lung squamous cell carcinoma(11;1.51e-13)|STAD - Stomach adenocarcinoma(18;0.0513)	Lung(977;0.0234)|LUSC - Lung squamous cell carcinoma(976;0.133)														---	---	---	---
SHANK2	22941	broad.mit.edu	37	11	70784126	70784126	+	Intron	DEL	T	-	-	rs143457672	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70784126delT	uc001oqc.2	-							NM_012309	NP_036441			SH3 and multiple ankyrin repeat domains 2						intracellular signal transduction	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane	GKAP/Homer scaffold activity|ionotropic glutamate receptor binding|SH3 domain binding			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5			LUSC - Lung squamous cell carcinoma(11;4.72e-09)|STAD - Stomach adenocarcinoma(18;0.071)															---	---	---	---
Unknown	0	broad.mit.edu	37	11	71091621	71091622	+	IGR	INS	-	GGGC	GGGC	rs72550567		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71091621_71091622insGGGC								SHANK2 (155813 upstream) : DHCR7 (53837 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	71851949	71851949	+	IGR	DEL	G	-	-	rs61633235		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71851949delG								FOLR3 (1015 upstream) : FOLR1 (48653 downstream)																																			---	---	---	---
INPPL1	3636	broad.mit.edu	37	11	71948748	71948748	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71948748delC	uc001osf.2	+	26	3607	c.3460delC	c.(3460-3462)CCCfs	p.P1154fs	INPPL1_uc001osg.2_Frame_Shift_Del_p.P912fs	NM_001567	NP_001558	O15357	SHIP2_HUMAN	inositol polyphosphate phosphatase-like 1	1154					actin filament organization|cell adhesion|endocytosis	actin cortical patch|cytosol	actin binding|SH2 domain binding|SH3 domain binding			skin(2)|ovary(1)|breast(1)	4																		---	---	---	---
PDE2A	5138	broad.mit.edu	37	11	72320159	72320159	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72320159delA	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)											OREG0021199	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
FCHSD2	9873	broad.mit.edu	37	11	72696936	72696936	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72696936delT	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)															---	---	---	---
FAM168A	23201	broad.mit.edu	37	11	73281432	73281432	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73281432delA	uc001otz.1	-						FAM168A_uc001oty.1_Intron|FAM168A_uc009ytp.1_Intron	NM_015159	NP_055974			hypothetical protein LOC23201												0																		---	---	---	---
FAM168A	23201	broad.mit.edu	37	11	73292772	73292772	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73292772delT	uc001otz.1	-						FAM168A_uc001oty.1_Intron|FAM168A_uc009ytp.1_Intron	NM_015159	NP_055974			hypothetical protein LOC23201												0																		---	---	---	---
DNAJB13	374407	broad.mit.edu	37	11	73675858	73675863	+	Intron	DEL	GCGCGC	-	-	rs77430927	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73675858_73675863delGCGCGC	uc001ouo.2	+							NM_153614	NP_705842			testis spermatogenesis apoptosis-related protein						apoptosis|protein folding|spermatogenesis		heat shock protein binding|unfolded protein binding				0	Breast(11;7.42e-05)															OREG0021218	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
UCP3	7352	broad.mit.edu	37	11	73712721	73712721	+	Intron	DEL	T	-	-	rs58267612		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73712721delT	uc001our.2	-							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	73756623	73756623	+	Intron	DEL	T	-	-	rs35986121		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73756623delT	uc001ouu.2	-						C2CD3_uc001out.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)																	---	---	---	---
XRRA1	143570	broad.mit.edu	37	11	74649905	74649905	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74649905delA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	74753118	74753118	+	IGR	DEL	A	-	-	rs72992610	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74753118delA								NEU3 (34377 upstream) : OR2AT4 (46679 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	74950887	74950887	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74950887delA								SLCO2B1 (33443 upstream) : ARRB1 (25595 downstream)																																			---	---	---	---
ARRB1	408	broad.mit.edu	37	11	74980343	74980343	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74980343delC	uc001owe.1	-						ARRB1_uc001owf.1_Intron	NM_004041	NP_004032			arrestin beta 1 isoform A						G-protein coupled receptor internalization|histone H4 acetylation|negative regulation of interleukin-6 production|negative regulation of interleukin-8 production|negative regulation of NF-kappaB transcription factor activity|negative regulation of protein ubiquitination|platelet activation|positive regulation of ERK1 and ERK2 cascade|positive regulation of histone acetylation|positive regulation of Rho protein signal transduction|positive regulation of transcription from RNA polymerase II promoter|post-Golgi vesicle-mediated transport|proteasomal ubiquitin-dependent protein catabolic process|protein transport|protein ubiquitination|signal transduction|stress fiber assembly|transcription from RNA polymerase II promoter	chromatin|coated pit|cytoplasmic vesicle membrane|cytosol|Golgi membrane|lysosomal membrane|membrane fraction|nucleus|plasma membrane|pseudopodium|soluble fraction	angiotensin receptor binding|enzyme inhibitor activity|GTPase activator activity|insulin-like growth factor receptor binding|transcription factor binding|transcription regulatory region DNA binding|ubiquitin protein ligase binding			breast(2)	2																		---	---	---	---
GDPD5	81544	broad.mit.edu	37	11	75153214	75153214	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75153214delT	uc001owo.3	-						GDPD5_uc001owp.3_Intron|GDPD5_uc001own.3_Intron|GDPD5_uc009yuc.2_Intron|GDPD5_uc009yud.2_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																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	75978009	75978009	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75978009delA								WNT11 (56206 upstream) : PRKRIR (82995 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	76022976	76022976	+	IGR	DEL	T	-	-	rs75799236		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76022976delT								WNT11 (101173 upstream) : PRKRIR (38028 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	76111051	76111052	+	Intron	DEL	AC	-	-	rs141655764		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76111051_76111052delAC	uc001oxi.1	+											Homo sapiens cDNA FLJ30390 fis, clone BRACE2008308.																														---	---	---	---
Unknown	0	broad.mit.edu	37	11	76485536	76485536	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76485536delT								GUCY2E (52703 upstream) : TSKU (8749 downstream)																																			---	---	---	---
MYO7A	4647	broad.mit.edu	37	11	76891308	76891309	+	Intron	INS	-	CTGCCAAATTATTTGG	CTGCCAAATTATTTGG	rs140333333	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76891308_76891309insCTGCCAAATTATTTGG	uc001oyb.2	+						MYO7A_uc010rsl.1_Intron|MYO7A_uc010rsm.1_Intron|MYO7A_uc001oyc.2_Intron|MYO7A_uc001oyd.2_Intron|MYO7A_uc009yus.1_Intron|MYO7A_uc009yut.1_Intron	NM_000260	NP_000251			myosin VIIA isoform 1						actin filament-based movement|equilibrioception|lysosome organization|sensory perception of sound|visual perception	cytosol|lysosomal membrane|myosin complex|photoreceptor inner segment|photoreceptor outer segment|synapse	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(3)|breast(1)	4																		---	---	---	---
MYO7A	4647	broad.mit.edu	37	11	76892834	76892835	+	Intron	INS	-	G	G	rs11371875		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76892834_76892835insG	uc001oyb.2	+						MYO7A_uc010rsl.1_Intron|MYO7A_uc010rsm.1_Intron|MYO7A_uc001oyc.2_Intron|MYO7A_uc001oyd.2_Intron|MYO7A_uc009yus.1_Intron|MYO7A_uc009yut.1_Intron	NM_000260	NP_000251			myosin VIIA isoform 1						actin filament-based movement|equilibrioception|lysosome organization|sensory perception of sound|visual perception	cytosol|lysosomal membrane|myosin complex|photoreceptor inner segment|photoreceptor outer segment|synapse	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(3)|breast(1)	4																		---	---	---	---
C11orf67	28971	broad.mit.edu	37	11	77557054	77557054	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77557054delT	uc001oyq.2	+						C11orf67_uc001oyp.2_Intron|C11orf67_uc001oyr.1_Intron	NM_024684	NP_078960			hypothetical protein LOC28971												0	all_cancers(14;5.69e-19)|all_epithelial(13;2.15e-21)|Breast(9;1.16e-15)|Ovarian(111;0.152)		Epithelial(5;1.37e-49)|all cancers(3;5.58e-46)|BRCA - Breast invasive adenocarcinoma(5;7.26e-31)															---	---	---	---
C11orf67	28971	broad.mit.edu	37	11	77586088	77586089	+	Intron	DEL	AA	-	-	rs3016157		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77586088_77586089delAA	uc001oyr.1	+						C11orf67_uc001oyp.2_Intron	NM_024684	NP_078960			hypothetical protein LOC28971												0	all_cancers(14;5.69e-19)|all_epithelial(13;2.15e-21)|Breast(9;1.16e-15)|Ovarian(111;0.152)		Epithelial(5;1.37e-49)|all cancers(3;5.58e-46)|BRCA - Breast invasive adenocarcinoma(5;7.26e-31)															---	---	---	---
KCTD14	65987	broad.mit.edu	37	11	77730072	77730073	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77730072_77730073insT	uc001oyw.3	-							NM_023930	NP_076419			potassium channel tetramerisation domain							voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(2)	2	all_cancers(14;4.53e-19)|all_epithelial(13;1.73e-21)|Breast(9;2.71e-16)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;1e-24)															---	---	---	---
Unknown	0	broad.mit.edu	37	11	80877662	80877663	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:80877662_80877663delAA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	81161412	81161412	+	IGR	DEL	A	-	-	rs75160462	byFrequency;by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:81161412delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	81639672	81639672	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:81639672delA	uc001ozo.1	-											Homo sapiens cDNA clone IMAGE:5298883.																														---	---	---	---
Unknown	0	broad.mit.edu	37	11	81690479	81690479	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:81690479delT	uc001ozo.1	-											Homo sapiens cDNA clone IMAGE:5298883.																														---	---	---	---
Unknown	0	broad.mit.edu	37	11	81732034	81732034	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:81732034delT	uc001ozo.1	-											Homo sapiens cDNA clone IMAGE:5298883.																														---	---	---	---
Unknown	0	broad.mit.edu	37	11	81735187	81735187	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:81735187delA	uc001ozo.1	-											Homo sapiens cDNA clone IMAGE:5298883.																														---	---	---	---
Unknown	0	broad.mit.edu	37	11	81895001	81895001	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:81895001delA	uc001ozo.1	-											Homo sapiens cDNA clone IMAGE:5298883.																														---	---	---	---
Unknown	0	broad.mit.edu	37	11	82058591	82058591	+	Intron	DEL	T	-	-	rs11350886		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82058591delT	uc001ozo.1	-											Homo sapiens cDNA clone IMAGE:5298883.																														---	---	---	---
Unknown	0	broad.mit.edu	37	11	82461433	82461433	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82461433delT								FAM181B (16527 upstream) : PRCP (73977 downstream)																																			---	---	---	---
C11orf82	220042	broad.mit.edu	37	11	82639612	82639612	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82639612delG	uc001ozt.2	+						C11orf82_uc010rsr.1_Intron|C11orf82_uc010rss.1_Intron|C11orf82_uc009yvd.2_Intron	NM_145018	NP_659455			nitric oxide-inducible gene protein						apoptosis|cell cycle arrest	cytoplasm|nucleus				ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	82790948	82790948	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82790948delA								RAB30 (8064 upstream) : PCF11 (77189 downstream)																																			---	---	---	---
DLG2	1740	broad.mit.edu	37	11	83197395	83197396	+	Intron	DEL	AA	-	-	rs112220223		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:83197395_83197396delAA	uc001paj.2	-						DLG2_uc001pai.2_Intron|DLG2_uc010rsy.1_Intron|DLG2_uc010rsz.1_Intron|DLG2_uc010rta.1_Intron|DLG2_uc001pak.2_Intron|DLG2_uc010rtb.1_Intron|DLG2_uc010rsw.1_Intron|DLG2_uc010rsx.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	83325060	83325061	+	Intron	INS	-	T	T	rs151045942	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:83325060_83325061insT	uc001paj.2	-						DLG2_uc001pai.2_Intron|DLG2_uc010rsy.1_Intron|DLG2_uc010rsz.1_Intron|DLG2_uc010rta.1_Intron|DLG2_uc001pak.2_Intron|DLG2_uc010rtb.1_Intron|DLG2_uc010rsw.1_Intron|DLG2_uc010rsx.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	83365474	83365475	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:83365474_83365475insT	uc001paj.2	-						DLG2_uc001pai.2_Intron|DLG2_uc010rsy.1_Intron|DLG2_uc010rsz.1_Intron|DLG2_uc010rta.1_Intron|DLG2_uc001pak.2_Intron|DLG2_uc010rtb.1_Intron|DLG2_uc001pal.1_Intron|DLG2_uc010rsw.1_Intron|DLG2_uc010rsx.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	83752325	83752325	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:83752325delA	uc001paj.2	-						DLG2_uc001pai.2_Intron|DLG2_uc010rsy.1_Intron|DLG2_uc010rsz.1_Intron|DLG2_uc010rta.1_Intron|DLG2_uc001pak.2_Intron|DLG2_uc010rtb.1_Intron|DLG2_uc001pal.1_Intron|DLG2_uc001pam.1_Intron	NM_001364	NP_001355			chapsyn-110 isoform 2							cell junction|postsynaptic density|postsynaptic membrane	guanylate kinase activity|protein binding|protein binding			ovary(3)|pancreas(2)|skin(1)	6		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)																---	---	---	---
DLG2	1740	broad.mit.edu	37	11	84186383	84186384	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:84186383_84186384insT	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	84902188	84902189	+	Intron	DEL	GC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:84902188_84902189delGC	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	85180998	85180998	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85180998delA	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)																---	---	---	---
Unknown	0	broad.mit.edu	37	11	86465663	86465663	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86465663delA								ME3 (81985 upstream) : PRSS23 (45828 downstream)																																			---	---	---	---
PRSS23	11098	broad.mit.edu	37	11	86597016	86597018	+	Intron	DEL	ATG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86597016_86597018delATG	uc001pcc.1	+						uc001pcd.2_Intron					Homo sapiens serine protease mRNA, complete cds.						proteolysis	extracellular region|nucleus	serine-type endopeptidase activity			central_nervous_system(1)|pancreas(1)	2		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)																---	---	---	---
TMEM135	65084	broad.mit.edu	37	11	86773054	86773054	+	Intron	DEL	T	-	-	rs141554783		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86773054delT	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	86846549	86846550	+	Intron	DEL	TA	-	-	rs4014717	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86846549_86846550delTA	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	86915081	86915081	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86915081delT	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)																---	---	---	---
TMEM135	65084	broad.mit.edu	37	11	86979717	86979717	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86979717delT	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	87105916	87105916	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:87105916delG								TMEM135 (71348 upstream) : RAB38 (740515 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	87135050	87135050	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:87135050delA								TMEM135 (100482 upstream) : RAB38 (711381 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	87759063	87759063	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:87759063delT								TMEM135 (724495 upstream) : RAB38 (87368 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	87785136	87785136	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:87785136delA								TMEM135 (750568 upstream) : RAB38 (61295 downstream)																																			---	---	---	---
GRM5	2915	broad.mit.edu	37	11	88532009	88532009	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:88532009delA	uc001pcq.2	-						GRM5_uc009yvm.2_Intron	NM_001143831	NP_001137303			glutamate receptor, metabotropic 5 isoform a						activation of phospholipase C activity by metabotropic glutamate receptor signaling pathway|synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			central_nervous_system(4)|ovary(2)|lung(2)|breast(1)	9		Acute lymphoblastic leukemia(157;2.54e-05)|all_hematologic(158;0.00834)			Acamprosate(DB00659)													---	---	---	---
NOX4	50507	broad.mit.edu	37	11	89312639	89312639	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89312639delA	uc009yvq.2	-							NM_001143837	NP_001137309			NADPH oxidase 4 isoform c						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)																---	---	---	---
TRIM49	57093	broad.mit.edu	37	11	89534022	89534022	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89534022delA	uc001pdb.2	-							NM_020358	NP_065091			ring finger protein 18							intracellular	zinc ion binding				0		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00556)																---	---	---	---
Unknown	0	broad.mit.edu	37	11	90288846	90288847	+	IGR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:90288846_90288847insA								CHORDC1 (332314 upstream) : MIR1261 (313442 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	91248288	91248289	+	IGR	INS	-	T	T	rs141602261	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:91248288_91248289insT								MIR1261 (645918 upstream) : FAT3 (836973 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	91558310	91558310	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:91558310delA								MIR1261 (955940 upstream) : FAT3 (526952 downstream)																																			---	---	---	---
FAT3	120114	broad.mit.edu	37	11	92312044	92312044	+	Intron	DEL	A	-	-	rs150419928	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92312044delA	uc001pdj.3	+							NM_001008781	NP_001008781			FAT tumor suppressor homolog 3						homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)	5		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)													TCGA Ovarian(4;0.039)			---	---	---	---
Unknown	0	broad.mit.edu	37	11	92690261	92690261	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92690261delT								FAT3 (60628 upstream) : MTNR1B (12528 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	92792755	92792755	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92792755delA								MTNR1B (76807 upstream) : SLC36A4 (88097 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	93031137	93031137	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93031137delT								SLC36A4 (100042 upstream) : CCDC67 (32019 downstream)																																			---	---	---	---
PANX1	24145	broad.mit.edu	37	11	93900164	93900165	+	Intron	INS	-	G	G	rs142100806	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93900164_93900165insG	uc001per.2	+						PANX1_uc001peq.2_Intron	NM_015368	NP_056183			pannexin 1						positive regulation of interleukin-1 beta secretion|protein hexamerization|synaptic transmission	bleb|endoplasmic reticulum membrane|gap junction|integral to membrane	calcium channel activity|gap junction hemi-channel activity|leak channel activity|receptor binding				0		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)																---	---	---	---
MRE11A	4361	broad.mit.edu	37	11	94225062	94225063	+	Intron	INS	-	A	A	rs144047125	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94225062_94225063insA	uc001peu.2	-						MRE11A_uc001pev.2_Intron|MRE11A_uc009ywj.2_Intron|ANKRD49_uc001pew.2_5'Flank|ANKRD49_uc001pex.2_5'Flank	NM_005591	NP_005582			meiotic recombination 11 homolog A isoform 1						DNA duplex unwinding|double-strand break repair via homologous recombination|double-strand break repair via nonhomologous end joining|negative regulation of DNA endoreduplication|positive regulation of kinase activity|positive regulation of protein autophosphorylation|reciprocal meiotic recombination|regulation of mitotic recombination|sister chromatid cohesion|telomere maintenance via telomerase	Mre11 complex|nucleoplasm	3'-5' exonuclease activity|double-stranded DNA binding|manganese ion binding|protein C-terminus binding|single-stranded DNA specific endodeoxyribonuclease activity			breast(4)|lung(1)	5		Acute lymphoblastic leukemia(157;2.37e-05)|all_hematologic(158;0.00824)											Homologous_recombination	Ataxia-Telangiectasia-Like_Disorder				---	---	---	---
Unknown	0	broad.mit.edu	37	11	95186494	95186494	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:95186494delT								SESN3 (220789 upstream) : FAM76B (315612 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	95202472	95202472	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:95202472delT								SESN3 (236767 upstream) : FAM76B (299634 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	95359027	95359027	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:95359027delT								SESN3 (393322 upstream) : FAM76B (143079 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	96483314	96483317	+	IGR	DEL	TGTT	-	-	rs147468109		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:96483314_96483317delTGTT								JRKL (356587 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	96574545	96574546	+	IGR	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:96574545_96574546delTG								JRKL (447818 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	96955307	96955308	+	IGR	INS	-	ACAC	ACAC	rs12269795		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:96955307_96955308insACAC								JRKL (828580 upstream) : None (None downstream)																																			---	---	---	---
CNTN5	53942	broad.mit.edu	37	11	98987502	98987502	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:98987502delT	uc001pga.2	+						CNTN5_uc009ywv.1_Intron|CNTN5_uc001pfz.2_Intron|CNTN5_uc001pgb.2_Intron	NM_014361	NP_055176			contactin 5 isoform long						cell adhesion	anchored to membrane|plasma membrane	protein binding			skin(3)|ovary(2)|pancreas(2)|breast(1)	8		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)														---	---	---	---
CNTN5	53942	broad.mit.edu	37	11	100123498	100123499	+	Intron	DEL	TC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:100123498_100123499delTC	uc001pga.2	+						CNTN5_uc001pfz.2_Intron|CNTN5_uc001pgb.2_Intron|CNTN5_uc010ruk.1_Intron	NM_014361	NP_055176			contactin 5 isoform long						cell adhesion	anchored to membrane|plasma membrane	protein binding			skin(3)|ovary(2)|pancreas(2)|breast(1)	8		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)														---	---	---	---
CNTN5	53942	broad.mit.edu	37	11	100222639	100222639	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:100222639delT	uc001pga.2	+						CNTN5_uc001pgb.2_Intron|CNTN5_uc010ruk.1_Intron	NM_014361	NP_055176			contactin 5 isoform long						cell adhesion	anchored to membrane|plasma membrane	protein binding			skin(3)|ovary(2)|pancreas(2)|breast(1)	8		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	100463018	100463019	+	IGR	DEL	AA	-	-	rs112726965		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:100463018_100463019delAA								CNTN5 (235546 upstream) : ARHGAP42 (95388 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	100486802	100486802	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:100486802delG								CNTN5 (259330 upstream) : ARHGAP42 (71605 downstream)																																			---	---	---	---
ARHGAP42	143872	broad.mit.edu	37	11	100576183	100576183	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:100576183delT	uc001pge.2	+							NM_152432	NP_689645			Rho-type GTPase-activating protein FLJ32810						filopodium assembly|signal transduction	intracellular	cytoskeletal adaptor activity|GTPase activator activity|SH3 domain binding				0																		---	---	---	---
PGR	5241	broad.mit.edu	37	11	100912944	100912944	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:100912944delA	uc001pgh.2	-						PGR_uc001pgg.2_Intron|PGR_uc001pgi.2_Intron|PGR_uc009yww.1_Intron|PGR_uc001pgj.2_Intron|PGR_uc009ywx.1_Intron	NM_000926	NP_000917			progesterone receptor						cell-cell signaling|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	cytoplasm|nucleoplasm	enzyme binding|receptor binding|sequence-specific DNA binding transcription factor activity|steroid binding|steroid hormone receptor activity|zinc ion binding			lung(1)|liver(1)|central_nervous_system(1)|pancreas(1)	4		Acute lymphoblastic leukemia(157;0.000885)|all_hematologic(158;0.014)		LUSC - Lung squamous cell carcinoma(1;0.0387)|BRCA - Breast invasive adenocarcinoma(274;0.124)|OV - Ovarian serous cystadenocarcinoma(223;0.148)|Lung(307;0.164)	Desogestrel(DB00304)|Drospirenone(DB01395)|Dydrogesterone(DB00378)|Ethynodiol Diacetate(DB00823)|Etonogestrel(DB00294)|Levonorgestrel(DB00367)|Medroxyprogesterone(DB00603)|Megestrol(DB00351)|Mifepristone(DB00834)|Norethindrone(DB00717)|Norgestimate(DB00957)|Norgestrel(DB00506)|Progesterone(DB00396)													---	---	---	---
Unknown	0	broad.mit.edu	37	11	101739872	101739872	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:101739872delA								TRPC6 (285213 upstream) : ANGPTL5 (21534 downstream)																																			---	---	---	---
KIAA1377	57562	broad.mit.edu	37	11	101835033	101835033	+	Intron	DEL	A	-	-	rs79464549		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:101835033delA	uc001pgm.2	+						KIAA1377_uc001pgn.2_Intron|KIAA1377_uc010run.1_Intron	NM_020802	NP_065853			hypothetical protein LOC57562								protein binding			breast(2)|ovary(1)|central_nervous_system(1)	4	all_epithelial(12;0.0104)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00931)		BRCA - Breast invasive adenocarcinoma(274;0.038)														---	---	---	---
YAP1	10413	broad.mit.edu	37	11	102009960	102009961	+	Intron	DEL	AA	-	-	rs113718885		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102009960_102009961delAA	uc001pgt.2	+						YAP1_uc001pgs.2_Intron|YAP1_uc001pgu.2_Intron|YAP1_uc001pgv.2_Intron|YAP1_uc010ruo.1_Intron|YAP1_uc001pgw.2_Intron	NM_001130145	NP_001123617			Yes-associated protein 1, 65kDa isoform 1						cell proliferation|cellular response to gamma radiation|contact inhibition|hippo signaling cascade|regulation of transcription, DNA-dependent|response to DNA damage stimulus|transcription, DNA-dependent	cytoplasm|nucleus	protein binding|transcription coactivator activity|transcription corepressor activity|transcription regulatory region DNA binding			ovary(1)|lung(1)|central_nervous_system(1)	3	all_cancers(8;0.000575)|all_epithelial(12;0.00564)	Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.00936)	Lung(13;0.245)	BRCA - Breast invasive adenocarcinoma(274;0.0189)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	102262975	102262976	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102262975_102262976delTT								BIRC2 (13581 upstream) : TMEM123 (4082 downstream)																																			---	---	---	---
DYNC2H1	79659	broad.mit.edu	37	11	103146851	103146851	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103146851delT	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	103176971	103176971	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103176971delA	uc001pho.2	+						DYNC2H1_uc001phn.1_Intron|DYNC2H1_uc009yxe.1_Intron	NM_001080463	NP_001073932			dynein, cytoplasmic 2, heavy chain 1						cell projection organization|Golgi organization|microtubule-based movement|multicellular organismal development	cilium axoneme|dynein complex|Golgi apparatus|microtubule|plasma membrane	ATP binding|ATPase activity|microtubule motor activity				0		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)														---	---	---	---
PDGFD	80310	broad.mit.edu	37	11	103992990	103992991	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103992990_103992991insT	uc001phq.2	-						PDGFD_uc001php.2_Intron	NM_025208	NP_079484			platelet derived growth factor D isoform 1						positive regulation of cell division	endoplasmic reticulum lumen|extracellular region|Golgi membrane	growth factor activity			upper_aerodigestive_tract(1)|large_intestine(1)	2		Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Melanoma(852;0.0563)|all_neural(303;0.165)		BRCA - Breast invasive adenocarcinoma(274;0.00136)|Epithelial(105;0.111)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	104215812	104215813	+	IGR	DEL	TT	-	-	rs10605994		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:104215812_104215813delTT								PDGFD (180785 upstream) : CASP12 (540629 downstream)																																			---	---	---	---
CASP5	838	broad.mit.edu	37	11	104872625	104872626	+	Intron	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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)														---	---	---	---
GRIA4	2893	broad.mit.edu	37	11	105604359	105604359	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:105604359delT	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	11	106266498	106266499	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:106266498_106266499insT								AASDHPPT (297079 upstream) : GUCY1A2 (291411 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	106913511	106913511	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:106913511delT								GUCY1A2 (24340 upstream) : CWF19L2 (283563 downstream)																																			---	---	---	---
CWF19L2	143884	broad.mit.edu	37	11	107299328	107299329	+	Intron	DEL	AA	-	-	rs35070417		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107299328_107299329delAA	uc010rvp.1	-						CWF19L2_uc001pjh.3_Intron|CWF19L2_uc009yxo.2_Intron	NM_152434	NP_689647			CWF19-like 2, cell cycle control								catalytic activity				0		Melanoma(852;1.75e-05)|all_epithelial(67;6.27e-05)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0258)		Epithelial(105;7.18e-06)|BRCA - Breast invasive adenocarcinoma(274;1.65e-05)|all cancers(92;1.76e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	107358567	107358567	+	IGR	DEL	A	-	-	rs11441978		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107358567delA								CWF19L2 (29995 upstream) : ALKBH8 (14887 downstream)																																			---	---	---	---
ALKBH8	91801	broad.mit.edu	37	11	107375331	107375331	+	3'UTR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107375331delT	uc010rvr.1	-	12					ALKBH8_uc001pjk.2_3'UTR|ALKBH8_uc010rvq.1_3'UTR|ALKBH8_uc009yxp.2_3'UTR|ALKBH8_uc001pjl.2_RNA	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)														---	---	---	---
ALKBH8	91801	broad.mit.edu	37	11	107385551	107385551	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107385551delA	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	107590792	107590792	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107590792delC								SLN (8005 upstream) : SLC35F2 (70928 downstream)																																			---	---	---	---
C11orf65	160140	broad.mit.edu	37	11	108335072	108335073	+	Intron	INS	-	A	A	rs139385986	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108335072_108335073insA	uc001pkh.2	-						C11orf65_uc010rvx.1_Intron|C11orf65_uc009yxu.1_Intron	NM_152587	NP_689800			hypothetical protein LOC160140											ovary(1)	1		all_cancers(61;1.38e-11)|all_epithelial(67;3.16e-07)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;8.21e-06)|BRCA - Breast invasive adenocarcinoma(274;1.01e-05)|all cancers(92;0.000189)|Colorectal(284;0.114)|OV - Ovarian serous cystadenocarcinoma(223;0.144)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	109711100	109711100	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:109711100delA								C11orf87 (411262 upstream) : ZC3H12C (252826 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	110361875	110361875	+	IGR	DEL	T	-	-	rs66478519		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110361875delT								FDX1 (26271 upstream) : ARHGAP20 (85891 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	110861419	110861419	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110861419delA								ARHGAP20 (277507 upstream) : C11orf53 (265288 downstream)																																			---	---	---	---
DLAT	1737	broad.mit.edu	37	11	111910356	111910356	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111910356delT	uc001pmo.2	+						DLAT_uc009yyk.1_Intron|DLAT_uc010rwr.1_Intron	NM_001931	NP_001922			dihydrolipoamide S-acetyltransferase precursor						glycolysis|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial pyruvate dehydrogenase complex	dihydrolipoyllysine-residue acetyltransferase activity|protein binding				0		all_cancers(61;4.53e-11)|all_epithelial(67;2.76e-06)|Melanoma(852;9.42e-06)|all_hematologic(158;0.000885)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0512)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)		Epithelial(105;4.87e-07)|BRCA - Breast invasive adenocarcinoma(274;6.83e-07)|all cancers(92;9.63e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.0557)	NADH(DB00157)													---	---	---	---
NCAM1	4684	broad.mit.edu	37	11	113091824	113091824	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113091824delA	uc009yyq.1	+						NCAM1_uc001pno.2_Intron	NM_001076682	NP_001070150			neural cell adhesion molecule 1 isoform 3						axon guidance|interferon-gamma-mediated signaling pathway	anchored to membrane|extracellular region|Golgi membrane|integral to membrane				ovary(1)	1		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)														---	---	---	---
ZW10	9183	broad.mit.edu	37	11	113639971	113639971	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113639971delA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	114124136	114124137	+	IGR	INS	-	A	A	rs147579474	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114124136_114124137insA								ZBTB16 (2742 upstream) : NNMT (4416 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	114297826	114297826	+	IGR	DEL	A	-	-	rs12146509	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114297826delA								RBM7 (18194 upstream) : REXO2 (12282 downstream)																																			---	---	---	---
FAM55A	120400	broad.mit.edu	37	11	114402229	114402229	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114402229delT	uc001ppa.2	-						FAM55A_uc010rxd.1_5'Flank|FAM55A_uc001ppb.1_Intron	NM_152315	NP_689528			hypothetical protein LOC120400							extracellular region					0		all_cancers(61;8.53e-16)|all_epithelial(67;1.71e-08)|all_hematologic(158;3.05e-05)|Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0194)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.0906)		BRCA - Breast invasive adenocarcinoma(274;3.02e-06)|Epithelial(105;0.000144)|all cancers(92;0.00106)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	114657903	114657903	+	IGR	DEL	A	-	-	rs71921778		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114657903delA								FAM55B (80251 upstream) : CADM1 (382050 downstream)																																			---	---	---	---
CADM1	23705	broad.mit.edu	37	11	115142798	115142799	+	Intron	DEL	TT	-	-	rs63495760		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:115142798_115142799delTT	uc001ppi.3	-						CADM1_uc001ppf.3_Intron|CADM1_uc001ppk.3_Intron|CADM1_uc001ppj.3_Intron|CADM1_uc001ppl.2_Intron	NM_014333	NP_055148			immunoglobulin superfamily, member 4D isoform 1						adherens junction organization|apoptosis|cell differentiation|cell junction assembly|cell recognition|detection of stimulus|heterophilic cell-cell adhesion|homophilic cell adhesion|multicellular organismal development|positive regulation of cytokine secretion|spermatogenesis|susceptibility to natural killer cell mediated cytotoxicity	basolateral plasma membrane|cell-cell junction|integral to membrane	PDZ domain binding|protein C-terminus binding|protein homodimerization activity|receptor binding			ovary(2)	2	all_hematologic(175;0.0628)	all_cancers(61;2.98e-14)|all_epithelial(67;2.64e-08)|all_hematologic(158;0.000154)|Melanoma(852;0.000952)|Acute lymphoblastic leukemia(157;0.00101)|Breast(348;0.0102)|Medulloblastoma(222;0.0429)|Prostate(24;0.145)|all_neural(223;0.237)		BRCA - Breast invasive adenocarcinoma(274;5.01e-06)|Epithelial(105;0.000305)|all cancers(92;0.00303)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	115549043	115549072	+	IGR	DEL	ACACACACACACACACACACACACACACAC	-	-	rs72100243		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:115549043_115549072delACACACACACACACACACACACACACACAC								CADM1 (173802 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	115964008	115964008	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:115964008delT								CADM1 (588767 upstream) : BUD13 (654880 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	116100118	116100120	+	IGR	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116100118_116100120delTTT								CADM1 (724877 upstream) : BUD13 (518768 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	116212553	116212553	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116212553delA								CADM1 (837312 upstream) : BUD13 (406335 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	116426597	116426599	+	IGR	DEL	AAC	-	-	rs34194194		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116426597_116426599delAAC								None (None upstream) : BUD13 (192289 downstream)																																			---	---	---	---
SIK3	23387	broad.mit.edu	37	11	116854244	116854244	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116854244delA	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																		---	---	---	---
RNF214	257160	broad.mit.edu	37	11	117129139	117129139	+	Intron	DEL	T	-	-	rs148722873		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117129139delT	uc001pqt.2	+						RNF214_uc001pqu.2_Intron|RNF214_uc010rxf.1_Intron	NM_207343	NP_997226			ring finger protein 214								zinc ion binding				0	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.88e-05)|Epithelial(105;0.000397)|all cancers(92;0.00258)														---	---	---	---
CEP164	22897	broad.mit.edu	37	11	117247903	117247904	+	Intron	INS	-	CA	CA	rs138346144	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117247903_117247904insCA	uc001prc.2	+						CEP164_uc001prb.2_Intron|CEP164_uc010rxk.1_Intron|CEP164_uc001prf.2_Intron|CEP164_uc009yzp.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	117300129	117300129	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117300129delT	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)														---	---	---	---
FXYD6	53826	broad.mit.edu	37	11	117729405	117729418	+	Intron	DEL	TCTTTCTTTCTTTC	-	-	rs66739036		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117729405_117729418delTCTTTCTTTCTTTC	uc001pro.1	-						FXYD6_uc001prp.1_Intron|FXYD6_uc001prq.1_Intron|FXYD6_uc001prr.1_Intron|FXYD6_uc009yzq.1_Intron	NM_022003	NP_071286			FXYD domain-containing ion transport regulator 6							integral to membrane|plasma membrane	ion channel activity			central_nervous_system(1)|skin(1)	2	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|Breast(348;0.111)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.89e-05)|Epithelial(105;0.00122)														---	---	---	---
TMPRSS13	84000	broad.mit.edu	37	11	117795316	117795316	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117795316delA	uc001prs.1	-						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	118053497	118053497	+	IGR	DEL	T	-	-	rs112086298		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118053497delT								SCN2B (6160 upstream) : AMICA1 (10945 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	119298106	119298106	+	Intron	DEL	C	-	-	rs35268881		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119298106delC	uc001pwo.2	+						uc001pwp.1_Intron					Homo sapiens cDNA FLJ40501 fis, clone TESTI2045171.																														---	---	---	---
Unknown	0	broad.mit.edu	37	11	119713800	119713800	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119713800delG								PVRL1 (114365 upstream) : TRIM29 (268195 downstream)																																			---	---	---	---
GRIK4	2900	broad.mit.edu	37	11	120490586	120490586	+	Intron	DEL	T	-	-	rs112524840		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120490586delT	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	120560719	120560719	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120560719delT	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	120980448	120980448	+	Intron	DEL	A	-	-	rs11346469		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120980448delA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	121090571	121090571	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121090571delG								TECTA (29058 upstream) : SC5DL (72817 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	122362878	122362881	+	IGR	DEL	CTTA	-	-	rs149281686		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122362878_122362881delCTTA								LOC399959 (124411 upstream) : UBASH3B (163517 downstream)																																			---	---	---	---
UBASH3B	84959	broad.mit.edu	37	11	122627167	122627167	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122627167delT	uc001pyi.3	+							NM_032873	NP_116262			ubiquitin associated and SH3 domain containing,							cytoplasm|nucleus	protein tyrosine phosphatase activity			central_nervous_system(1)	1		Breast(109;0.00254)|Medulloblastoma(222;0.00877)|Lung NSC(97;0.0183)|all_lung(97;0.0186)|all_neural(223;0.0381)|all_hematologic(192;0.104)		BRCA - Breast invasive adenocarcinoma(274;1.37e-05)|OV - Ovarian serous cystadenocarcinoma(99;0.0463)														---	---	---	---
ASAM	79827	broad.mit.edu	37	11	123068374	123068374	+	5'Flank	DEL	A	-	-	rs76456749	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123068374delA	uc001pyt.2	-							NM_024769	NP_079045			adipocyte-specific adhesion molecule precursor							integral to membrane|tight junction					0		Breast(109;0.0025)|Lung NSC(97;0.0179)|all_lung(97;0.0182)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.73e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0446)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	123712651	123712652	+	IGR	INS	-	T	T	rs141388936	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123712651_123712652insT								OR6M1 (35594 upstream) : TMEM225 (40983 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	123830165	123830165	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123830165delT								OR6T1 (15620 upstream) : OR10S1 (17238 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	124054116	124054117	+	5'Flank	INS	-	CTCTTTCTCT	CTCTTTCTCT	rs151301948	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124054116_124054117insCTCTTTCTCT	uc001pzv.1	+											H.sapiens mRNA HTPCRX09 for olfactory receptor.																														---	---	---	---
SIAE	54414	broad.mit.edu	37	11	124519316	124519317	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124519316_124519317delTT	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)														---	---	---	---
ROBO3	64221	broad.mit.edu	37	11	124739786	124739787	+	Intron	DEL	AT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124739786_124739787delAT	uc001qbc.2	+							NM_022370	NP_071765			roundabout, axon guidance receptor, homolog 3						axon midline choice point recognition	integral to membrane	receptor activity			breast(1)|central_nervous_system(1)	2	all_hematologic(175;0.215)	Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|Breast(109;0.0481)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0296)														---	---	---	---
SLC37A2	219855	broad.mit.edu	37	11	124944968	124944968	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124944968delA	uc001qbn.2	+						SLC37A2_uc010sau.1_Intron	NM_001145290	NP_001138762			solute carrier family 37 (glycerol-3-phosphate						carbohydrate transport|transmembrane transport	integral to membrane				ovary(2)	2	all_hematologic(175;0.215)	Breast(109;0.012)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.152)|all_lung(97;0.159)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0384)														---	---	---	---
PKNOX2	63876	broad.mit.edu	37	11	125077088	125077089	+	Intron	DEL	TC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125077088_125077089delTC	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	125185716	125185716	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125185716delC	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)														---	---	---	---
STT3A	3703	broad.mit.edu	37	11	125467144	125467144	+	Intron	DEL	C	-	-	rs513209	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125467144delC	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)														---	---	---	---
STT3A	3703	broad.mit.edu	37	11	125471519	125471519	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125471519delA	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	125696835	125696835	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125696835delT								PATE3 (35342 upstream) : PATE4 (6376 downstream)																																			---	---	---	---
RPUSD4	84881	broad.mit.edu	37	11	126080281	126080281	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126080281delT	uc001qde.2	-						FAM118B_uc001qdf.2_5'Flank|FAM118B_uc009zca.2_5'Flank|FAM118B_uc001qdg.2_5'Flank|RPUSD4_uc010sbl.1_5'Flank|RPUSD4_uc009zbz.2_Intron|RPUSD4_uc009zby.2_Intron	NM_032795	NP_116184			RNA pseudouridylate synthase domain containing 4						pseudouridine synthesis		protein binding|pseudouridine synthase activity|RNA binding			breast(1)	1	all_hematologic(175;0.145)	Breast(109;0.00867)|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;0.0761)														---	---	---	---
ST3GAL4	6484	broad.mit.edu	37	11	126250155	126250155	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126250155delA	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	126324057	126324059	+	Intron	DEL	CTT	-	-	rs72019155		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126324057_126324059delCTT	uc001qea.2	-						KIRREL3_uc001qeb.2_Intron|KIRREL3_uc001qec.1_Intron	NM_032531	NP_115920			kin of IRRE like 3 isoform 1						hemopoiesis	extracellular region|integral to membrane|plasma membrane	protein binding			ovary(3)	3	all_hematologic(175;0.145)	Lung NSC(97;0.0484)|all_lung(97;0.0522)|Medulloblastoma(222;0.0523)|Breast(109;0.0949)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;6.03e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.12)														---	---	---	---
KIRREL3	84623	broad.mit.edu	37	11	126526951	126526951	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126526951delA	uc001qea.2	-						KIRREL3_uc001qeb.2_Intron|KIRREL3_uc001qec.1_Intron|KIRREL3_uc001qed.3_Intron|uc009zcf.1_Intron	NM_032531	NP_115920			kin of IRRE like 3 isoform 1						hemopoiesis	extracellular region|integral to membrane|plasma membrane	protein binding			ovary(3)	3	all_hematologic(175;0.145)	Lung NSC(97;0.0484)|all_lung(97;0.0522)|Medulloblastoma(222;0.0523)|Breast(109;0.0949)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;6.03e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.12)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	127873579	127873579	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:127873579delT								None (None upstream) : ETS1 (455077 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	129126975	129126975	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129126975delA								ARHGAP32 (64882 upstream) : BARX2 (118906 downstream)																																			---	---	---	---
BARX2	8538	broad.mit.edu	37	11	129248739	129248739	+	Intron	DEL	A	-	-	rs36045160		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129248739delA	uc001qfc.3	+							NM_003658	NP_003649			BarH-like homeobox 2												0	all_hematologic(175;0.0749)	Lung NSC(97;0.000383)|all_lung(97;0.000824)|Breast(109;0.000962)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.00929)|Lung(977;0.0245)|LUSC - Lung squamous cell carcinoma(976;0.0253)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	129611876	129611877	+	IGR	INS	-	TTTG	TTTG	rs139336832	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129611876_129611877insTTTG								BARX2 (289703 upstream) : TMEM45B (73864 downstream)																																			---	---	---	---
TMEM45B	120224	broad.mit.edu	37	11	129729194	129729194	+	3'UTR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129729194delT	uc001qfe.1	+	6					TMEM45B_uc001qff.1_3'UTR	NM_138788	NP_620143			transmembrane protein 45B							integral to membrane					0	all_hematologic(175;0.0537)	Breast(109;0.00526)|Lung NSC(97;0.00901)|all_lung(97;0.018)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.012)|Lung(977;0.179)|LUSC - Lung squamous cell carcinoma(976;0.189)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	129877119	129877119	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129877119delA								NCRNA00167 (1738 upstream) : APLP2 (62597 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	129916124	129916125	+	IGR	DEL	TA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129916124_129916125delTA								NCRNA00167 (40743 upstream) : APLP2 (23591 downstream)																																			---	---	---	---
ZBTB44	29068	broad.mit.edu	37	11	130132635	130132635	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:130132635delA	uc001qga.2	-						ZBTB44_uc001qgb.3_Intron|ZBTB44_uc001qfx.2_Intron|ZBTB44_uc001qgc.1_Intron|ZBTB44_uc001qfz.2_5'Flank	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	130308386	130308387	+	IGR	DEL	CC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:130308386_130308387delCC								ADAMTS8 (9847 upstream) : ADAMTS15 (10482 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	130690972	130690972	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:130690972delG								ADAMTS15 (347257 upstream) : SNX19 (54795 downstream)																																			---	---	---	---
NTM	50863	broad.mit.edu	37	11	131874500	131874501	+	Intron	DEL	TC	-	-	rs148894261		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:131874500_131874501delTC	uc001qgp.2	+						NTM_uc001qgm.2_Intron|NTM_uc010sch.1_Intron|NTM_uc010sci.1_Intron|NTM_uc010scj.1_Intron|NTM_uc001qgo.2_Intron|NTM_uc001qgq.2_Intron	NM_016522	NP_057606			neurotrimin isoform 1						cell adhesion|neuron recognition	anchored to membrane|plasma membrane				ovary(4)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
OPCML	4978	broad.mit.edu	37	11	132409844	132409845	+	Intron	INS	-	TGA	TGA			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:132409844_132409845insTGA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	134517220	134517221	+	IGR	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134517220_134517221delTG								B3GAT1 (235408 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	169091	169094	+	IGR	DEL	CTGA	-	-	rs139655934		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:169091_169094delCTGA								FAM138D (19679 upstream) : IQSEC3 (7109 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	169299	169300	+	IGR	DEL	TA	-	-	rs59947182		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:169299_169300delTA								FAM138D (19887 upstream) : IQSEC3 (6903 downstream)																																			---	---	---	---
IQSEC3	440073	broad.mit.edu	37	12	176807	176807	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:176807delA	uc001qht.1	+							NM_015232	NP_056047			IQ motif and Sec7 domain 3						regulation of ARF protein signal transduction	cytoplasm	ARF guanyl-nucleotide exchange factor activity			central_nervous_system(2)|large_intestine(1)|skin(1)	4	all_cancers(10;0.016)|all_lung(10;0.0222)|all_epithelial(11;0.0262)|Lung NSC(10;0.031)		OV - Ovarian serous cystadenocarcinoma(31;0.00456)	LUAD - Lung adenocarcinoma(1;0.172)|Lung(1;0.179)														---	---	---	---
IQSEC3	440073	broad.mit.edu	37	12	247308	247309	+	5'Flank	INS	-	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:247308_247309insC	uc001qhw.1	+						IQSEC3_uc001qhu.1_Intron|IQSEC3_uc001qht.1_Intron|uc001qhv.1_Intron	NM_015232	NP_056047			IQ motif and Sec7 domain 3						regulation of ARF protein signal transduction	cytoplasm	ARF guanyl-nucleotide exchange factor activity			central_nervous_system(2)|large_intestine(1)|skin(1)	4	all_cancers(10;0.016)|all_lung(10;0.0222)|all_epithelial(11;0.0262)|Lung NSC(10;0.031)		OV - Ovarian serous cystadenocarcinoma(31;0.00456)	LUAD - Lung adenocarcinoma(1;0.172)|Lung(1;0.179)														---	---	---	---
KDM5A	5927	broad.mit.edu	37	12	463930	463931	+	Intron	INS	-	A	A	rs145302133	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:463930_463931insA	uc001qif.1	-						KDM5A_uc001qie.1_Intron|KDM5A_uc010sdn.1_Intron|KDM5A_uc010sdo.1_Intron	NM_001042603	NP_001036068			retinoblastoma binding protein 2 isoform 1						chromatin modification|multicellular organismal development|positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleolus	DNA binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)|ovary(1)	3								T 	NUP98	AML								---	---	---	---
CCDC77	84318	broad.mit.edu	37	12	522112	522112	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:522112delT	uc001qig.2	+						CCDC77_uc009zdk.2_Intron|CCDC77_uc010sdp.1_Intron|CCDC77_uc010sdq.1_Intron	NM_032358	NP_115734			coiled-coil domain containing 77 isoform a							centrosome				ovary(1)	1	all_cancers(10;0.0149)|all_epithelial(11;0.035)|all_lung(10;0.111)|Ovarian(42;0.142)|Lung NSC(10;0.156)		OV - Ovarian serous cystadenocarcinoma(31;0.00123)|BRCA - Breast invasive adenocarcinoma(9;0.033)															---	---	---	---
B4GALNT3	283358	broad.mit.edu	37	12	621871	621877	+	Intron	DEL	CCTTCCA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:621871_621877delCCTTCCA	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)															---	---	---	---
WNK1	65125	broad.mit.edu	37	12	917666	917667	+	Intron	INS	-	T	T	rs148456638	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:917666_917667insT	uc001qio.3	+						WNK1_uc001qin.2_Intron|WNK1_uc001qip.3_Intron	NM_018979	NP_061852			WNK lysine deficient protein kinase 1						intracellular protein kinase cascade|ion transport|neuron development	cytoplasm	ATP binding|protein binding|protein kinase inhibitor activity|protein serine/threonine kinase activity			stomach(6)|breast(6)|ovary(5)|lung(4)|large_intestine(1)|central_nervous_system(1)	23	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)															---	---	---	---
WNK1	65125	broad.mit.edu	37	12	985575	985575	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:985575delA	uc001qio.3	+						WNK1_uc001qip.3_Intron|WNK1_uc001qir.3_Intron	NM_018979	NP_061852			WNK lysine deficient protein kinase 1						intracellular protein kinase cascade|ion transport|neuron development	cytoplasm	ATP binding|protein binding|protein kinase inhibitor activity|protein serine/threonine kinase activity			stomach(6)|breast(6)|ovary(5)|lung(4)|large_intestine(1)|central_nervous_system(1)	23	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)															---	---	---	---
RAD52	5893	broad.mit.edu	37	12	1041662	1041662	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1041662delA	uc001qis.1	-						RAD52_uc001qit.1_Intron|RAD52_uc010sdt.1_Intron|RAD52_uc001qiu.1_Intron|RAD52_uc001qiv.1_Intron|RAD52_uc001qiw.1_Intron|RAD52_uc010sdu.1_Intron|RAD52_uc001qix.1_Intron	NM_134424	NP_602296			RAD52 homolog						DNA recombinase assembly|mitotic recombination|reciprocal meiotic recombination	nucleoplasm	DNA binding|protein binding			central_nervous_system(1)	1	all_cancers(10;0.0119)|all_epithelial(11;0.0171)|all_lung(10;0.0521)|Ovarian(42;0.0816)|Lung NSC(10;0.0987)		OV - Ovarian serous cystadenocarcinoma(31;0.00123)|BRCA - Breast invasive adenocarcinoma(9;0.0323)										Homologous_recombination					---	---	---	---
ERC1	23085	broad.mit.edu	37	12	1518153	1518153	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1518153delA	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	1543761	1543761	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1543761delC	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	12	1668142	1668143	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1668142_1668143delTT								ERC1 (63043 upstream) : FBXL14 (7017 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	1790404	1790404	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1790404delA								WNT5B (34027 upstream) : ADIPOR2 (9843 downstream)																																			---	---	---	---
CACNA1C	775	broad.mit.edu	37	12	2541286	2541286	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2541286delA	uc009zdu.1	+						CACNA1C_uc009zdv.1_Intron|CACNA1C_uc001qkb.2_Intron|CACNA1C_uc001qkc.2_Intron|CACNA1C_uc001qke.2_Intron|CACNA1C_uc001qkf.2_Intron|CACNA1C_uc001qjz.2_Intron|CACNA1C_uc001qkd.2_Intron|CACNA1C_uc001qkg.2_Intron|CACNA1C_uc009zdw.1_Intron|CACNA1C_uc001qkh.2_Intron|CACNA1C_uc001qkl.2_Intron|CACNA1C_uc001qkn.2_Intron|CACNA1C_uc001qko.2_Intron|CACNA1C_uc001qkp.2_Intron|CACNA1C_uc001qkr.2_Intron|CACNA1C_uc001qku.2_Intron|CACNA1C_uc001qkq.2_Intron|CACNA1C_uc001qks.2_Intron|CACNA1C_uc001qkt.2_Intron|CACNA1C_uc001qka.1_Intron|CACNA1C_uc001qki.1_Intron|CACNA1C_uc001qkj.1_Intron|CACNA1C_uc001qkk.1_Intron|CACNA1C_uc001qkm.1_Intron	NM_199460	NP_955630			calcium channel, voltage-dependent, L type,						axon guidance|calcium ion transport into cytosol|energy reserve metabolic process|regulation of insulin secretion	cytoplasm|postsynaptic density|voltage-gated calcium channel complex	calmodulin binding|voltage-gated calcium channel activity			ovary(10)|central_nervous_system(1)	11			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Nicardipine(DB00622)|Verapamil(DB00661)													---	---	---	---
Unknown	0	broad.mit.edu	37	12	2960330	2960331	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2960330_2960331delAA	uc009zdz.1	+											Homo sapiens cDNA clone IMAGE:40132675.																														---	---	---	---
Unknown	0	broad.mit.edu	37	12	2961536	2961536	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2961536delT	uc009zdz.1	+											Homo sapiens cDNA clone IMAGE:40132675.																														---	---	---	---
TULP3	7289	broad.mit.edu	37	12	3032984	3032984	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3032984delA	uc010seh.1	+						TULP3_uc010sef.1_Intron|TULP3_uc009zec.1_Intron|TULP3_uc010seg.1_Intron|TULP3_uc001qlj.2_Intron|TULP3_uc010sei.1_Intron	NM_003324	NP_003315			tubby like protein 3 isoform 1						G-protein coupled receptor protein signaling pathway|regulation of transcription, DNA-dependent	cytoplasm|extracellular region|nucleus|plasma membrane	phosphatidylinositol-4,5-bisphosphate binding				0			OV - Ovarian serous cystadenocarcinoma(31;0.000818)															---	---	---	---
TULP3	7289	broad.mit.edu	37	12	3036533	3036533	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3036533delT	uc010seh.1	+						TULP3_uc010sef.1_Intron|TULP3_uc009zec.1_Intron|TULP3_uc010seg.1_Intron|TULP3_uc001qlj.2_Intron|TULP3_uc010sei.1_Intron	NM_003324	NP_003315			tubby like protein 3 isoform 1						G-protein coupled receptor protein signaling pathway|regulation of transcription, DNA-dependent	cytoplasm|extracellular region|nucleus|plasma membrane	phosphatidylinositol-4,5-bisphosphate binding				0			OV - Ovarian serous cystadenocarcinoma(31;0.000818)															---	---	---	---
Unknown	0	broad.mit.edu	37	12	3058904	3058905	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3058904_3058905delTT								TULP3 (8598 upstream) : TEAD4 (9591 downstream)																																			---	---	---	---
TSPAN9	10867	broad.mit.edu	37	12	3202673	3202673	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3202673delG	uc001qlp.2	+							NM_006675	NP_006666			tetraspanin 9							integral to plasma membrane|membrane fraction				ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(31;0.00153)|COAD - Colon adenocarcinoma(12;0.0831)															---	---	---	---
PRMT8	56341	broad.mit.edu	37	12	3665840	3665840	+	Intron	DEL	A	-	-	rs112790280		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3665840delA	uc001qmf.2	+						PRMT8_uc009zed.2_Intron|PRMT8_uc009zee.1_Intron	NM_019854	NP_062828			HMT1 hnRNP methyltransferase-like 4						regulation of protein binding	cytoplasm|plasma membrane	histone-arginine N-methyltransferase activity|protein heterodimerization activity|protein homodimerization activity|protein-arginine omega-N asymmetric methyltransferase activity|protein-arginine omega-N monomethyltransferase activity			ovary(3)|central_nervous_system(1)|skin(1)	5			OV - Ovarian serous cystadenocarcinoma(31;0.0109)|COAD - Colon adenocarcinoma(12;0.0264)															---	---	---	---
EFCAB4B	84766	broad.mit.edu	37	12	3726431	3726432	+	Intron	INS	-	TTG	TTG			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3726431_3726432insTTG	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	4166023	4166023	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4166023delT								PARP11 (183415 upstream) : CCND2 (216879 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	4260608	4260608	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4260608delA								PARP11 (278000 upstream) : CCND2 (122294 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	5102496	5102496	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5102496delA								KCNA1 (75076 upstream) : KCNA5 (50589 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	5357763	5357763	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5357763delT								KCNA5 (201815 upstream) : NTF3 (183517 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	5444861	5444861	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5444861delA								KCNA5 (288913 upstream) : NTF3 (96419 downstream)																																			---	---	---	---
PLEKHG6	55200	broad.mit.edu	37	12	6432569	6432569	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6432569delT	uc001qnr.2	+						PLEKHG6_uc010sew.1_Intron|PLEKHG6_uc010sex.1_Intron	NM_018173	NP_060643			pleckstrin homology domain-containing family G						regulation of Rho protein signal transduction	cleavage furrow|cytoplasm|spindle pole	GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			large_intestine(1)|skin(1)	2																OREG0021621	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
IFFO1	25900	broad.mit.edu	37	12	6662498	6662498	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6662498delA	uc001qpd.1	-						IFFO1_uc001qoy.2_5'Flank|IFFO1_uc001qpb.1_5'Flank|IFFO1_uc001qpe.1_Intron|IFFO1_uc010sfe.1_Intron|IFFO1_uc001qpf.1_Intron|IFFO1_uc001qpc.1_Intron	NM_080730	NP_542768			intermediate filament family orphan isoform 2							intermediate filament					0																		---	---	---	---
ATN1	1822	broad.mit.edu	37	12	7032948	7032949	+	5'Flank	INS	-	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7032948_7032949insG	uc001qrw.1	+							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																OREG0021640	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	12	7832194	7832194	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7832194delT								APOBEC1 (7406 upstream) : GDF3 (10188 downstream)																																			---	---	---	---
SLC2A3	6515	broad.mit.edu	37	12	8082586	8082589	+	Intron	DEL	TTTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8082586_8082589delTTTT	uc001qtr.2	-						SLC2A3_uc001qts.2_3'UTR	NM_006931	NP_008862			solute carrier family 2 (facilitated glucose						carbohydrate metabolic process|water-soluble vitamin metabolic process	integral to membrane|plasma membrane	D-glucose transmembrane transporter activity|dehydroascorbic acid transporter activity			ovary(3)|pancreas(1)	4				Kidney(36;0.0866)														---	---	---	---
SLC2A3	6515	broad.mit.edu	37	12	8084184	8084184	+	Intron	DEL	T	-	-	rs76797177		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8084184delT	uc001qtr.2	-						SLC2A3_uc001qts.2_Intron	NM_006931	NP_008862			solute carrier family 2 (facilitated glucose						carbohydrate metabolic process|water-soluble vitamin metabolic process	integral to membrane|plasma membrane	D-glucose transmembrane transporter activity|dehydroascorbic acid transporter activity			ovary(3)|pancreas(1)	4				Kidney(36;0.0866)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	8415807	8415808	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8415807_8415808delTT	uc001quj.1	+											full-length cDNA clone CS0DB004YI02 of Neuroblastoma Cot 10-normalized of Homo sapiens (human).																														---	---	---	---
A2ML1	144568	broad.mit.edu	37	12	9001077	9001077	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9001077delA	uc001quz.3	+						A2ML1_uc001qva.1_Intron|A2ML1_uc010sgm.1_Intron	NM_144670	NP_653271			alpha-2-macroglobulin-like 1 precursor							extracellular space	endopeptidase inhibitor activity			ovary(2)|skin(1)	3																		---	---	---	---
KLRG1	10219	broad.mit.edu	37	12	9148002	9148002	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9148002delG	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																		---	---	---	---
KLRF1	51348	broad.mit.edu	37	12	9994746	9994747	+	Intron	INS	-	TG	TG	rs139435558	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9994746_9994747insTG	uc010sgw.1	+						KLRF1_uc009zgw.2_Intron|KLRF1_uc009zgx.2_Intron|KLRF1_uc001qwm.2_Intron|KLRF1_uc009zgy.2_Intron|KLRF1_uc009zgz.2_Intron|KLRF1_uc009zha.2_Intron	NM_016523	NP_057607			killer cell lectin-like receptor subfamily F,						cell surface receptor linked signaling pathway	integral to plasma membrane	MHC class I receptor activity|sugar binding			large_intestine(1)	1																		---	---	---	---
CLEC2A	387836	broad.mit.edu	37	12	10065487	10065487	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10065487delT	uc009zhb.2	-							NM_001130711	NP_001124183			C-type lectin domain family 2, member A						natural killer cell mediated cytotoxicity	integral to membrane|plasma membrane	protein homodimerization activity|receptor activity|sugar binding				0																		---	---	---	---
OLR1	4973	broad.mit.edu	37	12	10319126	10319126	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10319126delA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	10392021	10392033	+	IGR	DEL	ATCCTTCCTTCCT	-	-	rs11053697		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10392021_10392033delATCCTTCCTTCCT								GABARAPL1 (16299 upstream) : KLRD1 (65017 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	10732374	10732374	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10732374delT								KLRC1 (125390 upstream) : KLRA1 (8704 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	11557289	11557289	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11557289delG								PRB2 (8791 upstream) : ETV6 (245499 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	11795897	11795898	+	IGR	INS	-	AC	AC	rs145270278	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11795897_11795898insAC								PRB2 (247399 upstream) : ETV6 (6890 downstream)																																			---	---	---	---
ETV6	2120	broad.mit.edu	37	12	11946706	11946706	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11946706delT	uc001qzz.2	+							NM_001987	NP_001978			ets variant 6							cytoplasm|nucleolus	protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		ETV6/NTRK3(234)|ETV6/JAK2(11)	soft_tissue(85)|kidney(66)|breast(55)|salivary_gland(26)|haematopoietic_and_lymphoid_tissue(13)|ovary(2)|upper_aerodigestive_tract(1)|skin(1)|pancreas(1)	250		all_cancers(2;1.88e-12)|Acute lymphoblastic leukemia(2;6.91e-39)|all_hematologic(2;2.7e-36)						T	NTRK3|RUNX1|PDGFRB|ABL1|MN1|ABL2|FACL6|CHIC2|ARNT|JAK2|EVI1|CDX2|STL|HLXB9|MDS2|PER1|SYK|TTL|FGFR3|PAX5	congenital fibrosarcoma|multiple leukemia and lymphoma| secretory breast|MDS|ALL								---	---	---	---
ETV6	2120	broad.mit.edu	37	12	12180082	12180082	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12180082delA	uc001raa.1	+							NM_001987	NP_001978			ets variant 6							cytoplasm|nucleolus	protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		ETV6/NTRK3(234)|ETV6/JAK2(11)	soft_tissue(85)|kidney(66)|breast(55)|salivary_gland(26)|haematopoietic_and_lymphoid_tissue(13)|ovary(2)|upper_aerodigestive_tract(1)|skin(1)|pancreas(1)	250		all_cancers(2;1.88e-12)|Acute lymphoblastic leukemia(2;6.91e-39)|all_hematologic(2;2.7e-36)						T	NTRK3|RUNX1|PDGFRB|ABL1|MN1|ABL2|FACL6|CHIC2|ARNT|JAK2|EVI1|CDX2|STL|HLXB9|MDS2|PER1|SYK|TTL|FGFR3|PAX5	congenital fibrosarcoma|multiple leukemia and lymphoma| secretory breast|MDS|ALL								---	---	---	---
Unknown	0	broad.mit.edu	37	12	12442156	12442157	+	IGR	DEL	AA	-	-	rs113301605		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12442156_12442157delAA								LRP6 (22345 upstream) : MANSC1 (40061 downstream)																																			---	---	---	---
MANSC1	54682	broad.mit.edu	37	12	12482821	12482822	+	3'UTR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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)														---	---	---	---
DUSP16	80824	broad.mit.edu	37	12	12641194	12641195	+	Intron	INS	-	TTTG	TTTG	rs150291708	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12641194_12641195insTTTG	uc001rao.1	-						DUSP16_uc001ran.1_Intron	NM_030640	NP_085143			dual specificity phosphatase 16						inactivation of MAPK activity|MAPK export from nucleus|MAPK phosphatase export from nucleus, leptomycin B sensitive	cytoplasmic membrane-bounded vesicle|nucleus	MAP kinase tyrosine/serine/threonine phosphatase activity|protein tyrosine phosphatase activity				0		Prostate(47;0.0687)		BRCA - Breast invasive adenocarcinoma(232;0.0203)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	13037697	13037698	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13037697_13037698delAA								RPL13AP20 (8628 upstream) : GPRC5A (6258 downstream)																																			---	---	---	---
HTR7P1	93164	broad.mit.edu	37	12	13161406	13161406	+	Intron	DEL	T	-	-	rs12821282		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13161406delT	uc001rbh.2	+											Homo sapiens cDNA FLJ43688 fis, clone TBAES2003492.												0																		---	---	---	---
GRIN2B	2904	broad.mit.edu	37	12	13753434	13753435	+	Intron	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13753434_13753435delTG	uc001rbt.2	-							NM_000834	NP_000825			N-methyl-D-aspartate receptor subunit 2B						response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	glycine binding|N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			central_nervous_system(4)|ovary(3)|skin(3)|lung(2)	12					Felbamate(DB00949)|Haloperidol(DB00502)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)													---	---	---	---
GRIN2B	2904	broad.mit.edu	37	12	13948902	13948902	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13948902delA	uc001rbt.2	-							NM_000834	NP_000825			N-methyl-D-aspartate receptor subunit 2B						response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	glycine binding|N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			central_nervous_system(4)|ovary(3)|skin(3)|lung(2)	12					Felbamate(DB00949)|Haloperidol(DB00502)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)													---	---	---	---
GRIN2B	2904	broad.mit.edu	37	12	14000549	14000549	+	Intron	DEL	G	-	-	rs144700853	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14000549delG	uc001rbt.2	-							NM_000834	NP_000825			N-methyl-D-aspartate receptor subunit 2B						response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	glycine binding|N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			central_nervous_system(4)|ovary(3)|skin(3)|lung(2)	12					Felbamate(DB00949)|Haloperidol(DB00502)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)													---	---	---	---
Unknown	0	broad.mit.edu	37	12	14180921	14180921	+	IGR	DEL	A	-	-	rs11345767		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14180921delA								GRIN2B (47899 upstream) : ATF7IP (337690 downstream)																																			---	---	---	---
PLBD1	79887	broad.mit.edu	37	12	14723732	14723733	+	5'Flank	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14723732_14723733insT	uc001rcc.1	-							NM_024829	NP_079105			phospholipase B domain containing 1						lipid catabolic process	extracellular region	hydrolase activity				0																		---	---	---	---
ART4	420	broad.mit.edu	37	12	14983054	14983057	+	Intron	DEL	GTGT	-	-	rs113436435		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14983054_14983057delGTGT	uc001rcl.1	-						ART4_uc009zid.1_Intron|ART4_uc009zie.1_Intron	NM_021071	NP_066549			ADP-ribosyltransferase 4 precursor						arginine metabolic process|protein ADP-ribosylation	anchored to membrane|plasma membrane	NAD(P)+-protein-arginine ADP-ribosyltransferase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	15147884	15147885	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:15147884_15147885delTT								PDE6H (13087 upstream) : RERG (112833 downstream)																																			---	---	---	---
RERG	85004	broad.mit.edu	37	12	15366929	15366930	+	Intron	DEL	TA	-	-	rs59153894		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:15366929_15366930delTA	uc001rcs.2	-						RERG_uc001rct.2_Intron|RERG_uc010shu.1_Intron	NM_032918	NP_116307			RAS-like, estrogen-regulated, growth inhibitor						negative regulation of cell growth|negative regulation of cell proliferation|response to hormone stimulus|small GTPase mediated signal transduction	cytosol|membrane|nucleus	estrogen receptor binding|GDP binding|GTP binding|GTPase activity			lung(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	15419272	15419272	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:15419272delA								RERG (44968 upstream) : PTPRO (56215 downstream)																																			---	---	---	---
PTPRO	5800	broad.mit.edu	37	12	15733058	15733058	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:15733058delA	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)																---	---	---	---
Unknown	0	broad.mit.edu	37	12	16361043	16361044	+	IGR	INS	-	A	A	rs138725452	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:16361043_16361044insA								DERA (170729 upstream) : MGST1 (139032 downstream)																																			---	---	---	---
PIK3C2G	5288	broad.mit.edu	37	12	18576079	18576082	+	Intron	DEL	GAGT	-	-	rs9634089	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:18576079_18576082delGAGT	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	18687633	18687635	+	Intron	DEL	AAG	-	-	rs79457561	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:18687633_18687635delAAG	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)																---	---	---	---
Unknown	0	broad.mit.edu	37	12	18810001	18810001	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:18810001delA								PIK3C2G (8650 upstream) : PLCZ1 (26115 downstream)																																			---	---	---	---
PLEKHA5	54477	broad.mit.edu	37	12	19459013	19459013	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:19459013delA	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	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	19491542	19491542	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:19491542delA	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	20371056	20371056	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:20371056delG								AEBP2 (695883 upstream) : PDE3A (151141 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	20472881	20472881	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:20472881delT								AEBP2 (797708 upstream) : PDE3A (49316 downstream)																																			---	---	---	---
PDE3A	5139	broad.mit.edu	37	12	20812406	20812407	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:20812406_20812407insT	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	21011361	21011361	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21011361delT	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	21047462	21047463	+	Intron	INS	-	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21047462_21047463insC	uc001rek.2	+						SLCO1B3_uc001rel.2_Intron|SLCO1B3_uc010sil.1_Intron|LST-3TM12_uc010sim.1_Intron|SLCO1B3_uc001reo.2_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)																	---	---	---	---
SLCO1A2	6579	broad.mit.edu	37	12	21459010	21459010	+	Intron	DEL	A	-	-	rs113164589	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21459010delA	uc001rer.2	-						SLCO1A2_uc001res.2_Intron|SLCO1A2_uc010siq.1_Intron|SLCO1A2_uc010sio.1_Intron|SLCO1A2_uc010sip.1_Intron|SLCO1A2_uc001ret.2_Intron|SLCO1A2_uc001reu.2_Intron	NM_021094	NP_066580			organic anion transporting polypeptide A						bile acid metabolic process|sodium-independent organic anion transport	integral to membrane|plasma membrane	bile acid transmembrane transporter activity|organic anion transmembrane transporter activity			large_intestine(1)|pancreas(1)|ovary(1)|skin(1)	4																		---	---	---	---
RECQL	5965	broad.mit.edu	37	12	21629742	21629742	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21629742delT	uc001rex.2	-						RECQL_uc001rey.2_Intron	NM_032941	NP_116559			RecQ protein-like						DNA recombination|DNA repair|DNA replication	nucleus	ATP binding|ATP-dependent 3'-5' DNA helicase activity|DNA strand annealing activity|protein binding			ovary(1)|lung(1)	2													Direct_reversal_of_damage|Other_identified_genes_with_known_or_suspected_DNA_repair_function					---	---	---	---
GYS2	2998	broad.mit.edu	37	12	21727271	21727271	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21727271delA	uc001rfb.2	-							NM_021957	NP_068776			glycogen synthase 2						glucose metabolic process|glycogen biosynthetic process|response to glucose stimulus	cortical actin cytoskeleton|cytosol|ectoplasm|insoluble fraction|soluble fraction	glycogen (starch) synthase activity|protein homodimerization activity			lung(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	22723685	22723686	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22723685_22723686delAA								KIAA0528 (26233 upstream) : ETNK1 (54390 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	22745992	22745992	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22745992delT								KIAA0528 (48540 upstream) : ETNK1 (32084 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	23362767	23362767	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:23362767delA								ETNK1 (519160 upstream) : SOX5 (322465 downstream)																																			---	---	---	---
SOX5	6660	broad.mit.edu	37	12	23934196	23934196	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:23934196delT	uc001rfw.2	-						SOX5_uc001rfx.2_Intron|SOX5_uc001rfy.2_Intron|SOX5_uc010siv.1_Intron|SOX5_uc010siw.1_Intron|SOX5_uc001rfz.1_Intron|SOX5_uc001rga.2_Intron	NM_006940	NP_008871			SRY (sex determining region Y)-box 5 isoform a						transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(5)|lung(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	24893521	24893522	+	IGR	DEL	AA	-	-	rs10719084		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:24893521_24893522delAA								SOX5 (178141 upstream) : BCAT1 (70759 downstream)																																			---	---	---	---
BCAT1	586	broad.mit.edu	37	12	24994675	24994676	+	Intron	DEL	AA	-	-	rs34990218		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:24994675_24994676delAA	uc001rgd.3	-						BCAT1_uc001rgc.2_Intron|BCAT1_uc010six.1_Intron|BCAT1_uc010siy.1_Intron|BCAT1_uc001rge.3_Intron	NM_005504	NP_005495			branched chain aminotransferase 1, cytosolic						branched chain family amino acid biosynthetic process|branched chain family amino acid catabolic process|cell proliferation|G1/S transition of mitotic cell cycle	cytosol	L-isoleucine transaminase activity|L-leucine transaminase activity|L-valine transaminase activity			lung(1)|breast(1)	2	Acute lymphoblastic leukemia(6;0.00112)|all_hematologic(7;0.00152)|Ovarian(17;0.107)|Colorectal(261;0.196)				Gabapentin(DB00996)|L-Glutamic Acid(DB00142)|L-Isoleucine(DB00167)|L-Leucine(DB00149)|L-Valine(DB00161)|Pyridoxal Phosphate(DB00114)													---	---	---	---
BCAT1	586	broad.mit.edu	37	12	25075098	25075098	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25075098delT	uc001rgd.3	-						BCAT1_uc010siy.1_Intron|BCAT1_uc001rge.3_Intron	NM_005504	NP_005495			branched chain aminotransferase 1, cytosolic						branched chain family amino acid biosynthetic process|branched chain family amino acid catabolic process|cell proliferation|G1/S transition of mitotic cell cycle	cytosol	L-isoleucine transaminase activity|L-leucine transaminase activity|L-valine transaminase activity			lung(1)|breast(1)	2	Acute lymphoblastic leukemia(6;0.00112)|all_hematologic(7;0.00152)|Ovarian(17;0.107)|Colorectal(261;0.196)				Gabapentin(DB00996)|L-Glutamic Acid(DB00142)|L-Isoleucine(DB00167)|L-Leucine(DB00149)|L-Valine(DB00161)|Pyridoxal Phosphate(DB00114)													---	---	---	---
Unknown	0	broad.mit.edu	37	12	25163581	25163581	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25163581delT								C12orf77 (13208 upstream) : LRMP (41660 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	25188276	25188276	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25188276delT								C12orf77 (37903 upstream) : LRMP (16965 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	25813711	25813711	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25813711delT								IFLTD1 (12223 upstream) : RASSF8 (298258 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	25943691	25943708	+	IGR	DEL	ACACACACACACACACAG	-	-	rs66482114		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25943691_25943708delACACACACACACACACAG								IFLTD1 (142203 upstream) : RASSF8 (168261 downstream)																																			---	---	---	---
ITPR2	3709	broad.mit.edu	37	12	26684616	26684617	+	Intron	DEL	AA	-	-	rs71069250		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26684616_26684617delAA	uc001rhg.2	-							NM_002223	NP_002214			inositol 1,4,5-triphosphate receptor, type 2						activation of phospholipase C activity|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	integral to membrane|plasma membrane enriched fraction|platelet dense tubular network membrane|sarcoplasmic reticulum membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity			kidney(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	14	Colorectal(261;0.0847)																	---	---	---	---
C12orf11	55726	broad.mit.edu	37	12	27080152	27080152	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27080152delG	uc001rhk.3	-						C12orf11_uc010sjk.1_Intron	NM_018164	NP_060634			hypothetical protein LOC55726						cell division|mitosis|regulation of mitotic cell cycle		protein binding			large_intestine(1)|ovary(1)|central_nervous_system(1)	3	Colorectal(261;0.0847)																	---	---	---	---
MRPS35	60488	broad.mit.edu	37	12	27901735	27901735	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27901735delA	uc001rih.2	+						MRPS35_uc001rii.2_Intron	NM_021821	NP_068593			mitochondrial ribosomal protein S35 precursor						DNA damage response, detection of DNA damage	mitochondrial small ribosomal subunit					0	Lung SC(9;0.0873)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	28090026	28090030	+	IGR	DEL	AAAAA	-	-	rs112352149		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:28090026_28090030delAAAAA								KLHDC5 (134054 upstream) : PTHLH (20988 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	28944160	28944161	+	IGR	INS	-	CA	CA	rs143943331	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:28944160_28944161insCA								CCDC91 (241062 upstream) : FAR2 (358071 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	30411860	30411861	+	IGR	INS	-	AG	AG	rs145358955	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:30411860_30411861insAG								TMTC1 (474168 upstream) : IPO8 (370062 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	30454937	30454937	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:30454937delT								TMTC1 (517245 upstream) : IPO8 (326986 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	30494080	30494083	+	IGR	DEL	TTTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:30494080_30494083delTTTT								TMTC1 (556388 upstream) : IPO8 (287840 downstream)																																			---	---	---	---
TSPAN11	441631	broad.mit.edu	37	12	31097849	31097849	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31097849delA	uc010sju.1	+						TSPAN11_uc001rjp.2_Intron|TSPAN11_uc010sjv.1_Intron	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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	31519293	31519296	+	Intron	DEL	TTTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31519293_31519296delTTTT	uc001rkg.3	-											Homo sapiens cDNA clone IMAGE:5532261, partial cds.																														---	---	---	---
DENND5B	160518	broad.mit.edu	37	12	31585981	31585981	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31585981delT	uc001rki.1	-						DENND5B_uc001rkh.1_Intron|DENND5B_uc009zjq.1_Intron|DENND5B_uc001rkj.2_3'UTR	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	31619287	31619287	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31619287delA	uc001rki.1	-						DENND5B_uc001rkh.1_Intron|DENND5B_uc009zjq.1_Intron|DENND5B_uc001rkj.2_Intron|DENND5B_uc001rkk.1_Intron	NM_144973	NP_659410			DENN/MADD domain containing 5B							integral to membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
DENND5B	160518	broad.mit.edu	37	12	31642689	31642690	+	Intron	DEL	TA	-	-	rs141374770		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31642689_31642690delTA	uc001rki.1	-						DENND5B_uc001rkh.1_Intron|DENND5B_uc001rkj.2_Intron|DENND5B_uc001rkk.1_Intron	NM_144973	NP_659410			DENN/MADD domain containing 5B							integral to membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	32242418	32242418	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32242418delT								C12orf35 (96387 upstream) : BICD1 (17767 downstream)																																			---	---	---	---
BICD1	636	broad.mit.edu	37	12	32520461	32520461	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32520461delA	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	34102906	34102906	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:34102906delT								SYT10 (510152 upstream) : ALG10 (72310 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	34480679	34480679	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:34480679delT								ALG10 (299445 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	34493561	34493562	+	IGR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:34493561_34493562insA								ALG10 (312327 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	34609955	34609955	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:34609955delT								ALG10 (428721 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	38580906	38580907	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:38580906_38580907delAA								None (None upstream) : ALG10B (129650 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	38794867	38794868	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:38794867_38794868delAA								ALG10B (71340 upstream) : CPNE8 (251134 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	38881627	38881627	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:38881627delA								ALG10B (158100 upstream) : CPNE8 (164375 downstream)																																			---	---	---	---
CPNE8	144402	broad.mit.edu	37	12	39233328	39233328	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:39233328delA	uc001rls.1	-							NM_153634	NP_705898			copine VIII											pancreas(1)	1	Esophageal squamous(101;0.187)	Lung NSC(34;0.137)|Melanoma(24;0.152)|all_lung(34;0.157)																---	---	---	---
Unknown	0	broad.mit.edu	37	12	39473936	39473937	+	IGR	INS	-	C	C	rs17547738		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:39473936_39473937insC								CPNE8 (174516 upstream) : KIF21A (213094 downstream)																																			---	---	---	---
KIF21A	55605	broad.mit.edu	37	12	39722071	39722071	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:39722071delC	uc001rly.2	-						KIF21A_uc001rlv.2_Intron|KIF21A_uc001rlw.2_Intron|KIF21A_uc001rlx.2_Intron|KIF21A_uc001rlz.2_Intron|KIF21A_uc010skl.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)																---	---	---	---
KIF21A	55605	broad.mit.edu	37	12	39814288	39814288	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:39814288delA	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)																---	---	---	---
LRRK2	120892	broad.mit.edu	37	12	40671669	40671669	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40671669delT	uc001rmg.3	+						LRRK2_uc001rmh.1_Intron	NM_198578	NP_940980			leucine-rich repeat kinase 2						activation of MAPKK activity|determination of adult lifespan|exploration behavior|intracellular distribution of mitochondria|negative regulation of branching morphogenesis of a nerve|negative regulation of dendritic spine morphogenesis|negative regulation of neuroblast proliferation|negative regulation of neuron maturation|neuromuscular junction development|neuron death|peptidyl-serine phosphorylation|positive regulation of autophagy|positive regulation of dopamine receptor signaling pathway|positive regulation of programmed cell death|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein phosphorylation|positive regulation of protein ubiquitination|protein autophosphorylation|regulation of kidney size|regulation of locomotion|regulation of membrane potential|response to oxidative stress|small GTPase mediated signal transduction|tangential migration from the subventricular zone to the olfactory bulb	external side of mitochondrial outer membrane	ATP binding|GTP binding|GTP-dependent protein kinase activity|GTPase activator activity|MAP kinase kinase activity|protein homodimerization activity|tubulin binding			ovary(12)|stomach(5)|upper_aerodigestive_tract(2)|lung(2)|large_intestine(1)|urinary_tract(1)|pancreas(1)	24	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)																---	---	---	---
LRRK2	120892	broad.mit.edu	37	12	40724839	40724839	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40724839delT	uc001rmg.3	+						LRRK2_uc009zjw.2_Intron|LRRK2_uc001rmi.2_Intron	NM_198578	NP_940980			leucine-rich repeat kinase 2						activation of MAPKK activity|determination of adult lifespan|exploration behavior|intracellular distribution of mitochondria|negative regulation of branching morphogenesis of a nerve|negative regulation of dendritic spine morphogenesis|negative regulation of neuroblast proliferation|negative regulation of neuron maturation|neuromuscular junction development|neuron death|peptidyl-serine phosphorylation|positive regulation of autophagy|positive regulation of dopamine receptor signaling pathway|positive regulation of programmed cell death|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein phosphorylation|positive regulation of protein ubiquitination|protein autophosphorylation|regulation of kidney size|regulation of locomotion|regulation of membrane potential|response to oxidative stress|small GTPase mediated signal transduction|tangential migration from the subventricular zone to the olfactory bulb	external side of mitochondrial outer membrane	ATP binding|GTP binding|GTP-dependent protein kinase activity|GTPase activator activity|MAP kinase kinase activity|protein homodimerization activity|tubulin binding			ovary(12)|stomach(5)|upper_aerodigestive_tract(2)|lung(2)|large_intestine(1)|urinary_tract(1)|pancreas(1)	24	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)																---	---	---	---
Unknown	0	broad.mit.edu	37	12	42174610	42174610	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42174610delT								PDZRN4 (206226 upstream) : GXYLT1 (301040 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	42213911	42213911	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42213911delC								PDZRN4 (245527 upstream) : GXYLT1 (261739 downstream)																																			---	---	---	---
PPHLN1	51535	broad.mit.edu	37	12	42671922	42671925	+	Intron	DEL	AGGG	-	-	rs12322512	by1000genomes;by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42671922_42671925delAGGG	uc001rmy.2	+							NM_201439	NP_958847			periphilin 1 isoform 3						keratinization	cytoplasm|nucleus				ovary(1)|breast(1)	2	all_cancers(12;0.00049)|Breast(8;0.165)	Lung NSC(34;0.123)		GBM - Glioblastoma multiforme(48;0.0875)														---	---	---	---
PRICKLE1	144165	broad.mit.edu	37	12	42975141	42975141	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42975141delA	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	43286158	43286158	+	IGR	DEL	A	-	-	rs35521259		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:43286158delA								PRICKLE1 (302586 upstream) : ADAMTS20 (461855 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	43737417	43737417	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:43737417delT								PRICKLE1 (753845 upstream) : ADAMTS20 (10596 downstream)																																			---	---	---	---
ADAMTS20	80070	broad.mit.edu	37	12	43920261	43920261	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:43920261delA	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)														---	---	---	---
ANO6	196527	broad.mit.edu	37	12	45726077	45726078	+	Intron	DEL	TC	-	-	rs71437716		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:45726077_45726078delTC	uc001roo.2	+						ANO6_uc010sld.1_Intron|ANO6_uc010sle.1_Intron|ANO6_uc010slf.1_Intron|ANO6_uc010slg.1_Intron	NM_001025356	NP_001020527			anoctamin 6 isoform a						activation of blood coagulation via clotting cascade|phosphatidylserine exposure on blood platelet	chloride channel complex|plasma membrane	chloride channel activity			ovary(1)|kidney(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	46501146	46501146	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46501146delT								SFRS2IP (115243 upstream) : SLC38A1 (75697 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	46894747	46894747	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46894747delA								SLC38A2 (128102 upstream) : SLC38A4 (263797 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	47092251	47092252	+	IGR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:47092251_47092252insA								SLC38A2 (325606 upstream) : SLC38A4 (66292 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	47121851	47121851	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:47121851delT								SLC38A2 (355206 upstream) : SLC38A4 (36693 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	47279028	47279029	+	IGR	DEL	CT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:47279028_47279029delCT								SLC38A4 (59248 upstream) : AMIGO2 (190462 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	47412067	47412067	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:47412067delT								SLC38A4 (192287 upstream) : AMIGO2 (57424 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	47775427	47775427	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:47775427delT								FAM113B (144986 upstream) : RPAP3 (280289 downstream)																																			---	---	---	---
RPAP3	79657	broad.mit.edu	37	12	48070719	48070719	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48070719delA	uc001rpr.2	-						RPAP3_uc010slk.1_Intron|RPAP3_uc001rps.2_Intron	NM_024604	NP_078880			RNA polymerase II associated protein 3 isoform								binding			ovary(1)	1	Lung SC(27;0.192)																	---	---	---	---
VDR	7421	broad.mit.edu	37	12	48269816	48269816	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48269816delA	uc001rqm.2	-						VDR_uc001rql.2_Intron|VDR_uc001rqn.2_Intron|VDR_uc010slq.1_Intron	NM_001017535	NP_001017535			vitamin D (1,25-dihydroxyvitamin D3) receptor						decidualization|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of vitamin D 24-hydroxylase activity|regulation of calcidiol 1-monooxygenase activity|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	retinoid X receptor binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|vitamin D3 receptor activity|zinc ion binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Acute lymphoblastic leukemia(13;0.109)|all_hematologic(14;0.214)		GBM - Glioblastoma multiforme(48;0.17)	Calcidiol(DB00146)|Calcipotriol(DB02300)|Calcitriol(DB00136)|Dihydrotachysterol(DB01070)|Ergocalciferol(DB00153)|Paricalcitol(DB00910)													---	---	---	---
Unknown	0	broad.mit.edu	37	12	48580935	48580935	+	IGR	DEL	A	-	-	rs11358735		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48580935delA								C12orf68 (1226 upstream) : OR10AD1 (15187 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	48840997	48840998	+	IGR	INS	-	TGTGTA	TGTGTA	rs71998992		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48840997_48840998insTGTGTA								ZNF641 (95976 upstream) : ANP32D (25450 downstream)																																			---	---	---	---
LALBA	3906	broad.mit.edu	37	12	48963167	48963167	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48963167delA	uc001rrt.2	-							NM_002289	NP_002280			lactalbumin, alpha- precursor						cell-cell signaling|defense response to bacterium|induction of apoptosis|lactose biosynthetic process|signal transduction	extracellular space	calcium ion binding|lactose synthase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	49011936	49011938	+	IGR	DEL	TTG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49011936_49011938delTTG								LALBA (48107 upstream) : C12orf41 (35057 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	49603214	49603214	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49603214delT								TUBA1A (20353 upstream) : TUBA1C (18495 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	49674452	49674453	+	IGR	DEL	AA	-	-	rs76252542		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49674452_49674453delAA								TUBA1C (7339 upstream) : PRPH (14456 downstream)																																			---	---	---	---
TMBIM6	7009	broad.mit.edu	37	12	50151816	50151817	+	Intron	INS	-	A	A	rs80171037		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50151816_50151817insA	uc001rux.2	+						TMBIM6_uc010sml.1_Intron|TMBIM6_uc001ruy.2_Intron|TMBIM6_uc001ruz.2_Intron	NM_003217	NP_003208			testis enhanced gene transcript (BAX inhibitor						apoptosis|negative regulation of apoptosis	endoplasmic reticulum|insoluble fraction|integral to plasma membrane|nucleus					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	50177437	50177437	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50177437delT								TMBIM6 (18720 upstream) : NCKAP5L (7492 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	50180117	50180117	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50180117delT								TMBIM6 (21400 upstream) : NCKAP5L (4812 downstream)																																			---	---	---	---
LIMA1	51474	broad.mit.edu	37	12	50632657	50632657	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50632657delA	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	50829550	50829550	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50829550delT	uc001rwp.1	+						LARP4_uc001rwo.1_Intron|LARP4_uc001rwq.1_Intron|LARP4_uc001rwr.1_Intron|LARP4_uc001rws.1_Intron|LARP4_uc009zlr.1_5'Flank|LARP4_uc001rwm.2_Intron|LARP4_uc001rwn.2_Intron	NM_052879	NP_443111			c-Mpl binding protein isoform a								nucleotide binding|RNA binding			ovary(1)	1																		---	---	---	---
LARP4	113251	broad.mit.edu	37	12	50833559	50833559	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50833559delT	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_5'Flank|LARP4_uc001rwm.2_Intron|LARP4_uc001rwn.2_Intron	NM_052879	NP_443111			c-Mpl binding protein isoform a								nucleotide binding|RNA binding			ovary(1)	1																		---	---	---	---
DIP2B	57609	broad.mit.edu	37	12	50977085	50977085	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50977085delT	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																		---	---	---	---
SLC4A8	9498	broad.mit.edu	37	12	51825389	51825389	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51825389delT	uc001rys.1	+						SLC4A8_uc010sni.1_Intron|SLC4A8_uc001rym.2_Intron|SLC4A8_uc001ryn.2_Intron|SLC4A8_uc001ryo.2_Intron|SLC4A8_uc001ryp.1_Intron|SLC4A8_uc010snj.1_Intron|SLC4A8_uc001ryq.3_Intron|SLC4A8_uc001ryr.2_Intron|SLC4A8_uc010snk.1_Intron	NM_001039960	NP_001035049			solute carrier family 4, sodium bicarbonate						bicarbonate transport|sodium ion transport	integral to membrane|plasma membrane	inorganic anion exchanger activity			ovary(3)|pancreas(1)|skin(1)	5				BRCA - Breast invasive adenocarcinoma(357;0.15)														---	---	---	---
SLC4A8	9498	broad.mit.edu	37	12	51864783	51864783	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51864783delT	uc001rys.1	+						SLC4A8_uc010sni.1_Intron|SLC4A8_uc001rym.2_Intron|SLC4A8_uc001ryn.2_Intron|SLC4A8_uc001ryo.2_Intron|SLC4A8_uc010snj.1_Intron|SLC4A8_uc001ryq.3_Intron|SLC4A8_uc001ryr.2_Intron|SLC4A8_uc010snk.1_Intron	NM_001039960	NP_001035049			solute carrier family 4, sodium bicarbonate						bicarbonate transport|sodium ion transport	integral to membrane|plasma membrane	inorganic anion exchanger activity			ovary(3)|pancreas(1)|skin(1)	5				BRCA - Breast invasive adenocarcinoma(357;0.15)														---	---	---	---
SCN8A	6334	broad.mit.edu	37	12	52018709	52018709	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52018709delT	uc001ryw.2	+							NM_014191	NP_055006			sodium channel, voltage gated, type VIII, alpha						axon guidance|myelination|peripheral nervous system development	cytoplasmic membrane-bounded vesicle|node of Ranvier	ATP binding|voltage-gated sodium channel activity			ovary(7)	7				BRCA - Breast invasive adenocarcinoma(357;0.181)	Lamotrigine(DB00555)													---	---	---	---
SCN8A	6334	broad.mit.edu	37	12	52076670	52076670	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52076670delA	uc001ryw.2	+							NM_014191	NP_055006			sodium channel, voltage gated, type VIII, alpha						axon guidance|myelination|peripheral nervous system development	cytoplasmic membrane-bounded vesicle|node of Ranvier	ATP binding|voltage-gated sodium channel activity			ovary(7)	7				BRCA - Breast invasive adenocarcinoma(357;0.181)	Lamotrigine(DB00555)													---	---	---	---
Unknown	0	broad.mit.edu	37	12	52729450	52729451	+	IGR	DEL	GA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52729450_52729451delGA								KRT83 (14268 upstream) : KRT85 (24341 downstream)																																			---	---	---	---
KRT79	338785	broad.mit.edu	37	12	53223675	53223675	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53223675delA	uc001sbb.2	-						KRT79_uc001sba.2_Intron	NM_175834	NP_787028			keratin 6L							keratin filament	structural molecule activity			ovary(2)|skin(2)	4																		---	---	---	---
ZNF740	283337	broad.mit.edu	37	12	53577275	53577275	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53577275delT	uc001scb.3	+						CSAD_uc010snx.1_5'Flank|CSAD_uc001sby.2_5'Flank|CSAD_uc001sbz.2_5'Flank|CSAD_uc009zmu.2_5'Flank|CSAD_uc001sca.3_5'Flank|CSAD_uc010sny.1_5'Flank	NM_001004304	NP_001004304			zinc finger protein 740						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|protein binding|zinc ion binding				0																		---	---	---	---
ESPL1	9700	broad.mit.edu	37	12	53665468	53665468	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53665468delA	uc001sck.2	+						ESPL1_uc001scj.2_Intron	NM_012291	NP_036423			separase						apoptosis|cytokinesis|establishment of mitotic spindle localization|mitotic sister chromatid segregation|negative regulation of sister chromatid cohesion|positive regulation of mitotic metaphase/anaphase transition|proteolysis	centrosome|nucleus	cysteine-type peptidase activity|protein binding			lung(1)|kidney(1)|skin(1)	3																		---	---	---	---
ESPL1	9700	broad.mit.edu	37	12	53669989	53669989	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53669989delA	uc001sck.2	+						ESPL1_uc001scj.2_Intron	NM_012291	NP_036423			separase						apoptosis|cytokinesis|establishment of mitotic spindle localization|mitotic sister chromatid segregation|negative regulation of sister chromatid cohesion|positive regulation of mitotic metaphase/anaphase transition|proteolysis	centrosome|nucleus	cysteine-type peptidase activity|protein binding			lung(1)|kidney(1)|skin(1)	3																		---	---	---	---
SP1	6667	broad.mit.edu	37	12	53784467	53784467	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53784467delA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	54844837	54844839	+	IGR	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54844837_54844839delTTT								ITGA5 (31787 upstream) : GTSF1 (4898 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	55060766	55060768	+	IGR	DEL	TTT	-	-	rs63410060		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55060766_55060768delTTT								DCD (18617 upstream) : MUCL1 (187531 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	55152768	55152768	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55152768delT								DCD (110619 upstream) : MUCL1 (95531 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	55290651	55290651	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55290651delT								MUCL1 (38479 upstream) : KIAA0748 (53214 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	55445362	55445362	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55445362delC								NEUROD4 (21562 upstream) : OR9K2 (78191 downstream)																																			---	---	---	---
SMARCC2	6601	broad.mit.edu	37	12	56558553	56558553	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56558553delA	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)															---	---	---	---
SMARCC2	6601	broad.mit.edu	37	12	56570266	56570266	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56570266delT	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	12	56891571	56891573	+	IGR	DEL	TTG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56891571_56891573delTTG								GLS2 (9390 upstream) : RBMS2 (24036 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	58065357	58065358	+	IGR	INS	-	AAAG	AAAG	rs150140755		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:58065357_58065358insAAAG								B4GALNT1 (38372 upstream) : OS9 (22528 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	58571293	58571293	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:58571293delT								XRCC6BP1 (220242 upstream) : LRIG3 (694645 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	60281024	60281025	+	IGR	INS	-	AT	AT	rs138279523	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:60281024_60281025insAT								SLC16A7 (105617 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	60712177	60712177	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:60712177delG								SLC16A7 (536770 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	61116003	61116004	+	IGR	DEL	TG	-	-	rs10538905		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:61116003_61116004delTG								SLC16A7 (940596 upstream) : FAM19A2 (986039 downstream)																																			---	---	---	---
USP15	9958	broad.mit.edu	37	12	62659119	62659119	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:62659119delC	uc001src.1	+						USP15_uc001srb.1_Intron|USP15_uc010ssj.1_Intron|USP15_uc010ssk.1_Intron|USP15_uc001sra.2_Intron	NM_006313	NP_006304			ubiquitin specific peptidase 15						protein deubiquitination|ubiquitin-dependent protein catabolic process		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(2)|lung(1)	3			GBM - Glioblastoma multiforme(1;0.000276)	GBM - Glioblastoma multiforme(28;0.0622)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	63010801	63010801	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:63010801delT								MIRLET7I (13252 upstream) : PPM1H (26962 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	63022370	63022370	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:63022370delT								MIRLET7I (24821 upstream) : PPM1H (15393 downstream)																																			---	---	---	---
PPM1H	57460	broad.mit.edu	37	12	63119665	63119665	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:63119665delC	uc001srk.3	-							NM_020700	NP_065751			protein phosphatase 1H (PP2C domain containing)								phosphoprotein phosphatase activity			lung(3)|ovary(1)	4			GBM - Glioblastoma multiforme(1;0.000443)|BRCA - Breast invasive adenocarcinoma(9;0.209)	GBM - Glioblastoma multiforme(28;0.0126)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	65295208	65295208	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65295208delT	uc001ssj.1	+											Homo sapiens cDNA FLJ41278 fis, clone BRAMY2037147.																														---	---	---	---
LEMD3	23592	broad.mit.edu	37	12	65604874	65604874	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65604874delA	uc001ssl.1	+						LEMD3_uc009zqo.1_Intron	NM_014319	NP_055134			LEM domain containing 3						negative regulation of activin receptor signaling pathway|negative regulation of BMP signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway	integral to nuclear inner membrane|membrane fraction	DNA binding|nucleotide binding|protein binding			central_nervous_system(3)|ovary(1)	4			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.0104)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	65902591	65902591	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65902591delT								MSRB3 (41911 upstream) : RPSAP52 (249212 downstream)																																			---	---	---	---
TMBIM4	51643	broad.mit.edu	37	12	66544004	66544004	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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)														---	---	---	---
GRIP1	23426	broad.mit.edu	37	12	67057886	67057887	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:67057886_67057887delTT	uc001stk.2	-						GRIP1_uc010sta.1_Intron|GRIP1_uc001stm.2_Intron	NM_021150	NP_066973			glutamate receptor interacting protein 1						androgen receptor signaling pathway|intracellular signal transduction|positive regulation of transcription, DNA-dependent|synaptic transmission	cell junction|cytoplasmic membrane-bounded vesicle|cytosol|endoplasmic reticulum|postsynaptic membrane	androgen receptor binding|beta-catenin binding|protein C-terminus binding|receptor signaling complex scaffold activity|transcription coactivator activity			ovary(2)	2			GBM - Glioblastoma multiforme(2;0.00069)	GBM - Glioblastoma multiforme(28;0.0933)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	67232227	67232227	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:67232227delA								GRIP1 (34333 upstream) : CAND1 (430834 downstream)																																			---	---	---	---
CAND1	55832	broad.mit.edu	37	12	67679756	67679756	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:67679756delT	uc001stn.2	+							NM_018448	NP_060918			TIP120 protein						cell differentiation|negative regulation of catalytic activity|protein ubiquitination|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|ubiquitin ligase complex	protein binding			central_nervous_system(1)|skin(1)	2			GBM - Glioblastoma multiforme(1;1.13e-10)|Lung(24;0.000342)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(28;0.0279)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	67840216	67840216	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:67840216delT								CAND1 (131828 upstream) : DYRK2 (202296 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	68750152	68750152	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:68750152delA								MDM1 (23991 upstream) : RAP1B (254500 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	68784459	68784459	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:68784459delA								MDM1 (58298 upstream) : RAP1B (220193 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	68803899	68803899	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:68803899delG								MDM1 (77738 upstream) : RAP1B (200753 downstream)																																			---	---	---	---
NUP107	57122	broad.mit.edu	37	12	69127702	69127703	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69127702_69127703insA	uc001suf.2	+						NUP107_uc001sug.2_Intron|NUP107_uc010stj.1_Intron	NM_020401	NP_065134			nucleoporin 107kDa						carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA export from nucleus|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|Nup107-160 complex	nucleocytoplasmic transporter activity|protein binding			skin(1)	1	Breast(13;6.25e-06)		Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.00694)															---	---	---	---
Unknown	0	broad.mit.edu	37	12	69454927	69454927	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69454927delA								CPM (97907 upstream) : CPSF6 (178390 downstream)																																			---	---	---	---
CPSF6	11052	broad.mit.edu	37	12	69647964	69647965	+	Intron	DEL	AA	-	-	rs72496006		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69647964_69647965delAA	uc001sut.3	+						CPSF6_uc001suu.3_Intron	NM_007007	NP_008938			cleavage and polyadenylation specific factor 6,						mRNA polyadenylation|protein tetramerization	mRNA cleavage factor complex|paraspeckles|ribonucleoprotein complex	mRNA binding|nucleotide binding|protein binding				0	all_epithelial(5;2.47e-36)|Lung NSC(4;1.1e-32)|all_lung(4;6.26e-31)|Breast(13;1.59e-06)|Esophageal squamous(21;0.187)		Epithelial(6;4.89e-17)|BRCA - Breast invasive adenocarcinoma(5;8.5e-10)|Lung(24;6.04e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.0151)|LUSC - Lung squamous cell carcinoma(43;0.171)|Kidney(9;0.241)															---	---	---	---
FRS2	10818	broad.mit.edu	37	12	69890222	69890222	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69890222delA	uc001suy.2	+						FRS2_uc001suz.2_Intron|FRS2_uc009zrj.2_Intron|FRS2_uc009zrk.2_Intron	NM_006654	NP_006645			fibroblast growth factor receptor substrate 2						activation of MAPKK activity|activation of phospholipase C activity|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|transmembrane receptor protein tyrosine phosphatase signaling pathway	endomembrane system|endosome|integral to plasma membrane|membrane fraction	fibroblast growth factor receptor binding|insulin receptor binding|phosphatase activator activity|transmembrane receptor protein tyrosine kinase adaptor activity			prostate(1)|kidney(1)	2	Breast(13;2.15e-06)|Esophageal squamous(21;0.187)		Epithelial(6;2.94e-18)|Lung(24;9.68e-05)|OV - Ovarian serous cystadenocarcinoma(12;0.000984)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.0151)|Kidney(9;0.143)|LUSC - Lung squamous cell carcinoma(43;0.24)															---	---	---	---
Unknown	0	broad.mit.edu	37	12	70825572	70825572	+	RNA	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70825572delT	uc001svy.1	+	1		c.56delT								Homo sapiens cDNA FLJ30122 fis, clone BRACE1000087.																														---	---	---	---
PTPRR	5801	broad.mit.edu	37	12	71043557	71043558	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:71043557_71043558insT	uc001swi.1	-						PTPRR_uc001swf.1_Intron|PTPRR_uc001swg.1_Intron|PTPRR_uc001swh.1_Intron|PTPRR_uc009zrs.2_Intron|PTPRR_uc010stq.1_Intron	NM_002849	NP_002840			protein tyrosine phosphatase, receptor type, R						in utero embryonic development	cell surface|Golgi apparatus|integral to membrane|nucleus|perinuclear region of cytoplasm|plasma membrane	protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			skin(2)|ovary(1)	3			GBM - Glioblastoma multiforme(2;5.67e-07)|Lung(24;0.00283)|OV - Ovarian serous cystadenocarcinoma(12;0.00578)|LUSC - Lung squamous cell carcinoma(43;0.132)	COAD - Colon adenocarcinoma(1;0.136)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	71384907	71384907	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:71384907delT								PTPRR (70323 upstream) : TSPAN8 (133970 downstream)																																			---	---	---	---
LGR5	8549	broad.mit.edu	37	12	71939373	71939373	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:71939373delT	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																		---	---	---	---
TBC1D15	64786	broad.mit.edu	37	12	72258268	72258269	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:72258268_72258269delTT	uc001swu.2	+						TBC1D15_uc009zrv.2_Intron|TBC1D15_uc010stt.1_Intron|TBC1D15_uc001swv.2_Intron|TBC1D15_uc001sww.2_Intron	NM_022771	NP_073608			TBC1 domain family, member 15 isoform 1								protein binding|Rab GTPase activator activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	73525141	73525143	+	IGR	DEL	AAG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:73525141_73525143delAAG								TRHDE (465720 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	73657020	73657021	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:73657020_73657021delTT								TRHDE (597599 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	73713150	73713150	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:73713150delT								TRHDE (653729 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	73953077	73953078	+	IGR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:73953077_73953078insA								TRHDE (893656 upstream) : ATXN7L3B (978473 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	74099939	74099940	+	IGR	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:74099939_74099940delAC								None (None upstream) : ATXN7L3B (831611 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	74343925	74343928	+	IGR	DEL	AAAA	-	-	rs76297247		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:74343925_74343928delAAAA								None (None upstream) : ATXN7L3B (587623 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	74530048	74530048	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:74530048delT	uc009zrx.1	-											Homo sapiens cDNA clone IMAGE:3926153, partial cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	12	76296945	76296946	+	IGR	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76296945_76296946delTG								KRR1 (391527 upstream) : PHLDA1 (122282 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	76332281	76332282	+	IGR	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76332281_76332282delAC								KRR1 (426863 upstream) : PHLDA1 (86946 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	76378548	76378549	+	IGR	INS	-	GA	GA			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76378548_76378549insGA								KRR1 (473130 upstream) : PHLDA1 (40679 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	76548235	76548235	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76548235delA								NAP1L1 (69497 upstream) : BBS10 (190031 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	76554249	76554249	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76554249delT								NAP1L1 (75511 upstream) : BBS10 (184017 downstream)																																			---	---	---	---
OSBPL8	114882	broad.mit.edu	37	12	76846781	76846784	+	Intron	DEL	TTTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76846781_76846784delTTTT	uc001sye.1	-						OSBPL8_uc001syf.1_Intron|OSBPL8_uc001syg.1_Intron	NM_020841	NP_065892			oxysterol-binding protein-like protein 8 isoform						lipid transport		lipid binding			ovary(1)	1																		---	---	---	---
ZDHHC17	23390	broad.mit.edu	37	12	77195024	77195024	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:77195024delT	uc001syk.1	+						ZDHHC17_uc001syi.1_Intron|ZDHHC17_uc001syj.2_Intron	NM_015336	NP_056151			huntingtin interacting protein 14						lipoprotein transport|positive regulation of I-kappaB kinase/NF-kappaB cascade	Golgi-associated vesicle membrane|integral to membrane	magnesium ion transmembrane transporter activity|protein binding|protein-cysteine S-palmitoleyltransferase activity|signal transducer activity|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	77794618	77794619	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:77794618_77794619insT								E2F7 (335258 upstream) : NAV3 (430450 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	77821057	77821057	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:77821057delA								E2F7 (361697 upstream) : NAV3 (404012 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	78119715	78119715	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:78119715delT								E2F7 (660355 upstream) : NAV3 (105354 downstream)																																			---	---	---	---
SYT1	6857	broad.mit.edu	37	12	79431064	79431064	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:79431064delT	uc001sys.2	+						SYT1_uc001syt.2_Intron|SYT1_uc001syu.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																		---	---	---	---
SYT1	6857	broad.mit.edu	37	12	79732367	79732367	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:79732367delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	80450439	80450442	+	IGR	DEL	CTGT	-	-	rs142348069		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80450439_80450442delCTGT								PPP1R12A (121204 upstream) : PTPRQ (387684 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	80810302	80810302	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80810302delA								PPP1R12A (481067 upstream) : PTPRQ (27824 downstream)																																			---	---	---	---
LIN7A	8825	broad.mit.edu	37	12	81309531	81309531	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81309531delT	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	81488563	81488564	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81488563_81488564insA	uc001szl.1	+						ACSS3_uc001szm.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																		---	---	---	---
PPFIA2	8499	broad.mit.edu	37	12	81688219	81688226	+	Intron	DEL	AGGAAGGA	-	-	rs72104251		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81688219_81688226delAGGAAGGA	uc001szo.1	-						PPFIA2_uc010sue.1_Intron|PPFIA2_uc010sug.1_Intron|PPFIA2_uc010suh.1_Intron|PPFIA2_uc010sui.1_Intron|PPFIA2_uc010suj.1_Intron|PPFIA2_uc009zsi.1_Intron|PPFIA2_uc010suf.1_Intron|PPFIA2_uc009zsh.2_Intron	NM_003625	NP_003616			PTPRF interacting protein alpha 2											ovary(3)|lung(2)|pancreas(1)	6																		---	---	---	---
PPFIA2	8499	broad.mit.edu	37	12	81885904	81885905	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81885904_81885905delTT	uc001szo.1	-						PPFIA2_uc010sue.1_Intron|PPFIA2_uc010sug.1_Intron|PPFIA2_uc010suh.1_Intron|PPFIA2_uc010sui.1_Intron|PPFIA2_uc010suj.1_Intron|PPFIA2_uc009zsi.1_Intron	NM_003625	NP_003616			PTPRF interacting protein alpha 2											ovary(3)|lung(2)|pancreas(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	82506644	82506647	+	IGR	DEL	TTTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:82506644_82506647delTTTT								PPFIA2 (353535 upstream) : CCDC59 (239443 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	82671902	82671902	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:82671902delT								PPFIA2 (518793 upstream) : CCDC59 (74188 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	82684465	82684465	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:82684465delT								PPFIA2 (531356 upstream) : CCDC59 (61625 downstream)																																			---	---	---	---
TMTC2	160335	broad.mit.edu	37	12	83290562	83290562	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:83290562delT	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	83514394	83514394	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:83514394delG	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	84299314	84299315	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:84299314_84299315delTT								TMTC2 (771251 upstream) : SLC6A15 (953954 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	84727735	84727735	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:84727735delA								None (None upstream) : SLC6A15 (525534 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	85158529	85158529	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:85158529delT								None (None upstream) : SLC6A15 (94740 downstream)																																			---	---	---	---
ALX1	8092	broad.mit.edu	37	12	85681231	85681232	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:85681231_85681232insT	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	85978051	85978051	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:85978051delT								ALX1 (282492 upstream) : RASSF9 (220280 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	87842991	87842991	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:87842991delA								MGAT4C (610310 upstream) : C12orf50 (530825 downstream)																																			---	---	---	---
C12orf50	160419	broad.mit.edu	37	12	88388162	88388163	+	Intron	DEL	CA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88388162_88388163delCA	uc001tam.1	-						C12orf50_uc001tan.2_Intron	NM_152589	NP_689802			hypothetical protein LOC160419											skin(2)|ovary(1)	3																		---	---	---	---
CEP290	80184	broad.mit.edu	37	12	88513833	88513833	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88513833delA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	89328637	89328637	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:89328637delT								KITLG (354399 upstream) : DUSP6 (413202 downstream)																																			---	---	---	---
POC1B	282809	broad.mit.edu	37	12	89836707	89836707	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:89836707delA	uc001tbc.2	-						POC1B_uc001tba.2_Intron|POC1B_uc001tbb.2_Intron|POC1B_uc010sun.1_Intron|POC1B_uc009zsp.2_Intron|POC1B_uc009zsq.2_Intron	NM_172240	NP_758440			WD repeat domain 51B						cell projection organization	centriole|microtubule basal body				ovary(1)	1																		---	---	---	---
POC1B	282809	broad.mit.edu	37	12	89846185	89846185	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:89846185delT	uc001tbc.2	-						POC1B_uc001tba.2_Intron|POC1B_uc001tbb.2_Intron|POC1B_uc010sun.1_Intron|POC1B_uc009zsp.2_Intron|POC1B_uc009zsq.2_Intron	NM_172240	NP_758440			WD repeat domain 51B						cell projection organization	centriole|microtubule basal body				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	90319786	90319786	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:90319786delA								LOC338758 (214058 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	90705242	90705242	+	IGR	DEL	A	-	-	rs138438097		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:90705242delA								LOC338758 (599514 upstream) : C12orf12 (640751 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	91668732	91668732	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:91668732delT								DCN (91926 upstream) : BTG1 (710134 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	92113588	92113589	+	IGR	INS	-	AGGA	AGGA	rs28728429		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:92113588_92113589insAGGA								DCN (536782 upstream) : BTG1 (265277 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	92372844	92372845	+	IGR	INS	-	CA	CA			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:92372844_92372845insCA								DCN (796038 upstream) : BTG1 (6021 downstream)																																			---	---	---	---
BTG1	694	broad.mit.edu	37	12	92517982	92517982	+	Intron	DEL	A	-	-	rs56158608		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:92517982delA	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								---	---	---	---
BTG1	694	broad.mit.edu	37	12	92529828	92529828	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:92529828delA	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	93054903	93054904	+	IGR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93054903_93054904insA								CLLU1 (177447 upstream) : C12orf74 (41936 downstream)																																			---	---	---	---
EEA1	8411	broad.mit.edu	37	12	93216346	93216347	+	Intron	INS	-	C	C	rs147852680	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93216346_93216347insC	uc001tck.2	-							NM_003566	NP_003557			early endosome antigen 1, 162kD						early endosome to late endosome transport|synaptic vesicle to endosome fusion|vesicle fusion	cytosol|early endosome membrane|extrinsic to plasma membrane|membrane fraction	1-phosphatidylinositol binding|calmodulin binding|GTP-dependent protein binding|protein homodimerization activity|zinc ion binding			ovary(2)|skin(1)	3																		---	---	---	---
EEA1	8411	broad.mit.edu	37	12	93251373	93251373	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93251373delA	uc001tck.2	-							NM_003566	NP_003557			early endosome antigen 1, 162kD						early endosome to late endosome transport|synaptic vesicle to endosome fusion|vesicle fusion	cytosol|early endosome membrane|extrinsic to plasma membrane|membrane fraction	1-phosphatidylinositol binding|calmodulin binding|GTP-dependent protein binding|protein homodimerization activity|zinc ion binding			ovary(2)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	93401225	93401226	+	IGR	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93401225_93401226delAC								EEA1 (78118 upstream) : NUDT4 (370475 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	93614213	93614213	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93614213delA								EEA1 (291106 upstream) : NUDT4 (157488 downstream)																																			---	---	---	---
NUDT4	11163	broad.mit.edu	37	12	93778545	93778545	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93778545delT	uc001tcm.2	+						NUDT4_uc010sup.1_Intron|NUDT4_uc001tcn.2_Intron|NUDT4_uc010suq.1_Intron|NUDT4_uc001tco.2_Intron	NM_019094	NP_061967			nudix-type motif 4 isoform alpha						calcium-mediated signaling|cyclic nucleotide metabolic process|cyclic-nucleotide-mediated signaling|intracellular transport|regulation of RNA export from nucleus	cytoplasm	diphosphoinositol-polyphosphate diphosphatase activity|metal ion binding				0																		---	---	---	---
CRADD	8738	broad.mit.edu	37	12	94073976	94073976	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94073976delA	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	94274053	94274053	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94274053delT	uc010sur.1	+						CRADD_uc010sus.1_Intron	NM_003805	NP_003796			CASP2 and RIPK1 domain containing adaptor with						apoptosis|cellular response to mechanical stimulus|induction of apoptosis via death domain receptors|signal transduction	intracellular	death domain binding|protease binding|protein binding, bridging			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	94389370	94389370	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94389370delA								CRADD (100754 upstream) : PLXNC1 (153129 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	94517554	94517554	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94517554delT								CRADD (228938 upstream) : PLXNC1 (24945 downstream)																																			---	---	---	---
CCDC41	51134	broad.mit.edu	37	12	94736561	94736561	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94736561delA	uc001tdd.2	-						CCDC41_uc001tde.2_Intron|CCDC41_uc009zsw.1_Intron	NM_016122	NP_057206			NY-REN-58 antigen												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	95158910	95158910	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95158910delC								TMCC3 (114586 upstream) : MIR492 (69264 downstream)																																			---	---	---	---
NR2C1	7181	broad.mit.edu	37	12	95451201	95451201	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95451201delA	uc001tdm.3	-						NR2C1_uc010suu.1_Intron|NR2C1_uc001tdo.3_Intron|NR2C1_uc001tdn.3_Intron	NM_003297	NP_003288			nuclear receptor subfamily 2, group C, member 1						regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	PML body	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	95761558	95761558	+	IGR	DEL	A	-	-	rs80194517		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95761558delA								MIR331 (59269 upstream) : METAP2 (106264 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	96046936	96046936	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96046936delT								USP44 (101673 upstream) : NTN4 (4648 downstream)																																			---	---	---	---
CCDC38	120935	broad.mit.edu	37	12	96284754	96284755	+	Intron	DEL	GA	-	-	rs142196054		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96284754_96284755delGA	uc001tek.1	-							NM_182496	NP_872302			coiled-coil domain containing 38											skin(1)	1																		---	---	---	---
CCDC38	120935	broad.mit.edu	37	12	96330081	96330081	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96330081delT	uc001tek.1	-							NM_182496	NP_872302			coiled-coil domain containing 38											skin(1)	1																		---	---	---	---
CDK17	5128	broad.mit.edu	37	12	96685788	96685789	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96685788_96685789insA	uc001tep.1	-						CDK17_uc009ztk.2_Intron|CDK17_uc010svb.1_Intron	NM_002595	NP_002586			PCTAIRE protein kinase 2								ATP binding|cyclin-dependent protein kinase activity			ovary(3)|lung(2)|kidney(1)|central_nervous_system(1)	7																		---	---	---	---
RMST	196475	broad.mit.edu	37	12	97952867	97952870	+	Intron	DEL	TCTC	-	-	rs67214788		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:97952867_97952870delTCTC	uc001tez.1	+						RMST_uc001tfa.1_Intron					Homo sapiens C23up NCRMS mRNA, partial sequence; alternatively spliced.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	97981647	97981647	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:97981647delA								RMST (22854 upstream) : LOC100128191 (925106 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	98074023	98074023	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:98074023delA								RMST (115230 upstream) : LOC100128191 (832730 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	98115345	98115346	+	Intron	INS	-	TGTT	TGTT	rs144355305	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:98115345_98115346insTGTT	uc001tfc.1	-											Homo sapiens cDNA FLJ25775 fis, clone TST06543.																														---	---	---	---
Unknown	0	broad.mit.edu	37	12	98443606	98443606	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:98443606delT								RMST (484813 upstream) : LOC100128191 (463147 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	98680925	98680926	+	IGR	INS	-	TGTC	TGTC	rs151003793	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:98680925_98680926insTGTC								RMST (722132 upstream) : LOC100128191 (225827 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	98740223	98740223	+	IGR	DEL	T	-	-	rs34506925		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:98740223delT								RMST (781430 upstream) : LOC100128191 (166530 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	98902853	98902853	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:98902853delA								RMST (944060 upstream) : LOC100128191 (3900 downstream)																																			---	---	---	---
TMPO	7112	broad.mit.edu	37	12	98920832	98920832	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:98920832delT	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	99233173	99233174	+	Intron	INS	-	TATC	TATC	rs150720158	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:99233173_99233174insTATC	uc001tge.1	-						ANKS1B_uc001tgf.1_Intron|ANKS1B_uc001tgk.2_Intron|ANKS1B_uc010svd.1_Intron|ANKS1B_uc001tgd.1_Intron|ANKS1B_uc010sve.1_Intron|ANKS1B_uc001tgh.3_Intron|ANKS1B_uc001tgi.2_Intron|ANKS1B_uc009ztr.2_Intron|ANKS1B_uc001tgj.2_Intron|ANKS1B_uc009ztp.2_Intron|ANKS1B_uc010svf.1_Intron|ANKS1B_uc001tgg.3_Intron|ANKS1B_uc010svg.1_Intron|ANKS1B_uc009zts.1_Intron|ANKS1B_uc001tgm.1_Intron	NM_152788	NP_690001			cajalin 2 isoform a							Cajal body|cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane					0		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)														---	---	---	---
ANKS1B	56899	broad.mit.edu	37	12	99234075	99234075	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:99234075delA	uc001tge.1	-						ANKS1B_uc001tgf.1_Intron|ANKS1B_uc001tgk.2_Intron|ANKS1B_uc010svd.1_Intron|ANKS1B_uc001tgd.1_Intron|ANKS1B_uc010sve.1_Intron|ANKS1B_uc001tgh.3_Intron|ANKS1B_uc001tgi.2_Intron|ANKS1B_uc009ztr.2_Intron|ANKS1B_uc001tgj.2_Intron|ANKS1B_uc009ztp.2_Intron|ANKS1B_uc010svf.1_Intron|ANKS1B_uc001tgg.3_Intron|ANKS1B_uc010svg.1_Intron|ANKS1B_uc009zts.1_Intron|ANKS1B_uc001tgm.1_Intron	NM_152788	NP_690001			cajalin 2 isoform a							Cajal body|cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane					0		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)														---	---	---	---
GAS2L3	283431	broad.mit.edu	37	12	101012976	101012976	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101012976delT	uc001thu.2	+						GAS2L3_uc009zty.2_Intron|GAS2L3_uc001thv.2_Intron	NM_174942	NP_777602			growth arrest-specific 2 like 3						cell cycle arrest					skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	101059082	101059085	+	IGR	DEL	TGTG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101059082_101059085delTGTG								GAS2L3 (40399 upstream) : ANO4 (52219 downstream)																																			---	---	---	---
ANO4	121601	broad.mit.edu	37	12	101315846	101315847	+	Intron	DEL	TT	-	-	rs77520774		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101315846_101315847delTT	uc010svm.1	+						ANO4_uc010svl.1_Intron|ANO4_uc001thw.2_Intron|ANO4_uc001thx.2_Intron	NM_178826	NP_849148			anoctamin 4							chloride channel complex	chloride channel activity			ovary(4)|skin(2)	6															HNSCC(74;0.22)			---	---	---	---
ANO4	121601	broad.mit.edu	37	12	101393661	101393663	+	Intron	DEL	AAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101393661_101393663delAAA	uc010svm.1	+						ANO4_uc010svl.1_Intron|ANO4_uc001thw.2_Intron|ANO4_uc001thx.2_Intron	NM_178826	NP_849148			anoctamin 4							chloride channel complex	chloride channel activity			ovary(4)|skin(2)	6															HNSCC(74;0.22)			---	---	---	---
UTP20	27340	broad.mit.edu	37	12	101700103	101700103	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101700103delT	uc001tia.1	+							NM_014503	NP_055318			down-regulated in metastasis						endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|negative regulation of cell proliferation	90S preribosome|cytoplasm|nucleolus|nucleoplasm|preribosome, small subunit precursor|small-subunit processome	protein binding			ovary(2)|breast(2)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	101913547	101913547	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101913547delT								SPIC (32773 upstream) : MYBPC1 (75200 downstream)																																			---	---	---	---
CCDC53	51019	broad.mit.edu	37	12	102409069	102409070	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102409069_102409070delAA	uc010svw.1	-						CCDC53_uc010svx.1_Intron|CCDC53_uc010svy.1_Intron|CCDC53_uc010svz.1_Intron	NM_016053	NP_057137			coiled-coil domain containing 53							WASH complex	protein binding				0																		---	---	---	---
NUP37	79023	broad.mit.edu	37	12	102512025	102512025	+	Intron	DEL	T	-	-	rs67225375		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102512025delT	uc001tjc.2	-						NUP37_uc009zub.1_Intron|C12orf48_uc001tjd.2_5'Flank|C12orf48_uc001tje.2_5'Flank|C12orf48_uc001tjg.2_5'Flank|C12orf48_uc010swa.1_5'Flank|C12orf48_uc001tjf.2_5'Flank|C12orf48_uc001tjh.2_5'Flank|C12orf48_uc010swb.1_5'Flank|C12orf48_uc001tji.2_5'Flank	NM_024057	NP_076962			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	103019502	103019502	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:103019502delT								IGF1 (145124 upstream) : PAH (212602 downstream)																																			---	---	---	---
LOC253724	253724	broad.mit.edu	37	12	104262896	104262898	+	5'Flank	DEL	AAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104262896_104262898delAAA	uc001tjy.3	-						LOC253724_uc010swf.1_Intron					Homo sapiens Grp94 neighboring nucleotidase pseudogene, mRNA (cDNA clone IMAGE:4373107).												0																		---	---	---	---
LOC253724	253724	broad.mit.edu	37	12	104279140	104279140	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104279140delT	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																		---	---	---	---
HCFC2	29915	broad.mit.edu	37	12	104463809	104463809	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104463809delT	uc001tkj.3	+						HCFC2_uc009zul.2_Intron	NM_013320	NP_037452			host cell factor C2						regulation of transcription from RNA polymerase II promoter|viral reproduction	cytoplasm|nucleus	transcription coactivator activity			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	104564890	104564890	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104564890delT								NFYB (32850 upstream) : TXNRD1 (41598 downstream)																																			---	---	---	---
TXNRD1	7296	broad.mit.edu	37	12	104676397	104676398	+	Intron	INS	-	TG	TG	rs138149408	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104676397_104676398insTG	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																		---	---	---	---
CHST11	50515	broad.mit.edu	37	12	104885242	104885243	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104885242_104885243delTT	uc001tkx.1	+						CHST11_uc001tky.2_Intron	NM_018413	NP_060883			carbohydrate sulfotransferase 11						chondroitin sulfate biosynthetic process	Golgi membrane|integral to membrane	chondroitin 4-sulfotransferase activity|N-acetylgalactosamine 4-O-sulfotransferase activity				0																		---	---	---	---
CHST11	50515	broad.mit.edu	37	12	105018305	105018306	+	Intron	INS	-	GGT	GGT	rs10636834		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105018305_105018306insGGT	uc001tkx.1	+						CHST11_uc001tky.2_Intron	NM_018413	NP_060883			carbohydrate sulfotransferase 11						chondroitin sulfate biosynthetic process	Golgi membrane|integral to membrane	chondroitin 4-sulfotransferase activity|N-acetylgalactosamine 4-O-sulfotransferase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	105357679	105357680	+	IGR	DEL	CT	-	-	rs111773140		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105357679_105357680delCT								SLC41A2 (35207 upstream) : C12orf45 (22418 downstream)																																			---	---	---	---
C12orf75	387882	broad.mit.edu	37	12	105757103	105757103	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105757103delC	uc001tlh.3	+						C12orf75_uc001tli.3_Intron	NM_001145199	NP_001138671			hypothetical protein LOC387882												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	105775714	105775714	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105775714delA								C12orf75 (10419 upstream) : NUAK1 (681411 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	105807085	105807086	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105807085_105807086insT								C12orf75 (41790 upstream) : NUAK1 (650039 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	105997624	105997624	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105997624delT								C12orf75 (232329 upstream) : NUAK1 (459501 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	106199826	106199826	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106199826delG								C12orf75 (434531 upstream) : NUAK1 (257299 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	106742388	106742388	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106742388delT								TCP11L2 (1598 upstream) : POLR3B (9048 downstream)																																			---	---	---	---
POLR3B	55703	broad.mit.edu	37	12	106892453	106892453	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106892453delG	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																		---	---	---	---
RFX4	5992	broad.mit.edu	37	12	107082962	107082962	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:107082962delC	uc001tlr.2	+						RFX4_uc010swv.1_Intron|RFX4_uc001tls.2_Intron|RFX4_uc001tlt.2_Intron|RFX4_uc001tlv.2_Intron	NM_213594	NP_998759			regulatory factor X4 isoform c						transcription, DNA-dependent	nucleus	DNA binding			upper_aerodigestive_tract(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	107520187	107520187	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:107520187delT								CRY1 (32589 upstream) : BTBD11 (192010 downstream)																																			---	---	---	---
BTBD11	121551	broad.mit.edu	37	12	107732427	107732428	+	Intron	INS	-	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:107732427_107732428insG	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	108497052	108497053	+	IGR	INS	-	CTT	CTT	rs151326682	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108497052_108497053insCTT								ASCL4 (326632 upstream) : WSCD2 (26458 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	108799642	108799642	+	IGR	DEL	A	-	-	rs75566384		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108799642delA								CMKLR1 (66548 upstream) : FICD (109409 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	108823439	108823439	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108823439delT								CMKLR1 (90345 upstream) : FICD (85612 downstream)																																			---	---	---	---
SSH1	54434	broad.mit.edu	37	12	109187175	109187178	+	Intron	DEL	TTTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109187175_109187178delTTTT	uc001tnm.2	-						SSH1_uc001tnl.2_Intron|SSH1_uc010sxg.1_Intron|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																		---	---	---	---
ACACB	32	broad.mit.edu	37	12	109594175	109594175	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109594175delA	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)													---	---	---	---
FOXN4	121643	broad.mit.edu	37	12	109720254	109720255	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109720254_109720255delAA	uc001toe.3	-						FOXN4_uc009zvg.2_Intron|FOXN4_uc001tof.3_Intron	NM_213596	NP_998761			forkhead box N4						axon extension|embryo development|organ development|pattern specification process|regulation of heart contraction|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			ovary(1)|lung(1)	2																		---	---	---	---
TCHP	84260	broad.mit.edu	37	12	110362550	110362551	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110362550_110362551insA	uc001tpo.1	+							NM_032300				trichoplein						apoptosis|negative regulation of cell growth	apical cortex|centrosome|keratin filament|mitochondrion|plasma membrane	protein binding			skin(1)	1																		---	---	---	---
GIT2	9815	broad.mit.edu	37	12	110435377	110435380	+	5'Flank	DEL	AGAG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110435377_110435380delAGAG	uc001tps.2	-						GIT2_uc001tpq.2_5'Flank|GIT2_uc001tpv.2_5'Flank|GIT2_uc001tpu.2_5'Flank|GIT2_uc001tpt.2_5'Flank|GIT2_uc010sxu.1_5'Flank|GIT2_uc001tpw.2_5'Flank|GIT2_uc010sxv.1_5'Flank|ANKRD13A_uc009zvl.1_5'Flank|ANKRD13A_uc009zvm.1_5'Flank|ANKRD13A_uc001tpx.2_5'Flank|ANKRD13A_uc010sxw.1_5'Flank	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																		---	---	---	---
IFT81	28981	broad.mit.edu	37	12	110591799	110591799	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110591799delT	uc001tqi.2	+						IFT81_uc001tqh.2_Intron|IFT81_uc001tqj.2_Intron|IFT81_uc001tqg.2_Intron	NM_001143779	NP_001137251			intraflagellar transport 81-like isoform 1						cell differentiation|multicellular organismal development|spermatogenesis	intraflagellar transport particle B|microtubule-based flagellum				ovary(1)	1																		---	---	---	---
IFT81	28981	broad.mit.edu	37	12	110633679	110633679	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110633679delT	uc001tqi.2	+						IFT81_uc001tqh.2_Intron|IFT81_uc001tqj.2_Intron	NM_001143779	NP_001137251			intraflagellar transport 81-like isoform 1						cell differentiation|multicellular organismal development|spermatogenesis	intraflagellar transport particle B|microtubule-based flagellum				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	110705615	110705617	+	IGR	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110705615_110705617delTTT								IFT81 (49016 upstream) : ATP2A2 (13415 downstream)																																			---	---	---	---
ATP2A2	488	broad.mit.edu	37	12	110732977	110732977	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110732977delT	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																		---	---	---	---
ATP2A2	488	broad.mit.edu	37	12	110747958	110747959	+	Intron	DEL	TT	-	-	rs113324660		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110747958_110747959delTT	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																		---	---	---	---
PPTC7	160760	broad.mit.edu	37	12	110999746	110999746	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110999746delA	uc001trh.1	-							NM_139283	NP_644812			T-cell activation protein phosphatase 2C								metal ion binding|phosphoprotein phosphatase activity				0																		---	---	---	---
CUX2	23316	broad.mit.edu	37	12	111705857	111705857	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111705857delT	uc001tsa.1	+						CUX2_uc001tsb.1_Intron	NM_015267	NP_056082			cut-like 2							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)|skin(2)|breast(1)	6																		---	---	---	---
ATXN2	6311	broad.mit.edu	37	12	111917660	111917662	+	Intron	DEL	AAA	-	-	rs34924253		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111917660_111917662delAAA	uc001tsj.2	-						ATXN2_uc001tsh.2_Intron|ATXN2_uc001tsi.2_Intron|ATXN2_uc001tsk.2_Intron|ATXN2_uc001tsg.2_Intron	NM_002973	NP_002964			ataxin 2						cell death|cytoplasmic mRNA processing body assembly|regulation of translation|RNA metabolic process|RNA transport|stress granule assembly	nucleus|perinuclear region of cytoplasm|polysome|stress granule|trans-Golgi network	protein C-terminus binding|RNA binding			ovary(1)|breast(1)	2																		---	---	---	---
ALDH2	217	broad.mit.edu	37	12	112245090	112245091	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112245090_112245091delAA	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								---	---	---	---
Unknown	0	broad.mit.edu	37	12	112249271	112249272	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112249271_112249272delTT								ALDH2 (1489 upstream) : C12orf47 (28301 downstream)																																			---	---	---	---
NAA25	80018	broad.mit.edu	37	12	112529508	112529510	+	Intron	DEL	AAA	-	-	rs78263591		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112529508_112529510delAAA	uc001ttm.2	-						NAA25_uc001ttn.3_Intron|NAA25_uc009zvz.1_Intron|NAA25_uc009zwa.1_Intron	NM_024953	NP_079229			mitochondrial distribution and morphology 20							cytoplasm	protein binding			ovary(1)|breast(1)|pancreas(1)	3																		---	---	---	---
C12orf51	283450	broad.mit.edu	37	12	112685782	112685787	+	Intron	DEL	ACACAC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112685782_112685787delACACAC	uc009zwc.2	-							NM_001109662	NP_001103132			chromosome 12 open reading frame 51											ovary(1)|lung(1)	2																		---	---	---	---
C12orf51	283450	broad.mit.edu	37	12	112700740	112700740	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112700740delT	uc009zwc.2	-						C12orf51_uc010syk.1_Intron|C12orf51_uc001tts.2_Intron|C12orf51_uc001ttt.3_Intron	NM_001109662	NP_001103132			chromosome 12 open reading frame 51											ovary(1)|lung(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	113578821	113578821	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113578821delT								RASAL1 (4792 upstream) : CCDC42B (8842 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	114654488	114654488	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114654488delA								RBM19 (250312 upstream) : TBX5 (137248 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	114773534	114773534	+	IGR	DEL	G	-	-	rs57317323	byFrequency;by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114773534delG								RBM19 (369358 upstream) : TBX5 (18202 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	115493363	115493364	+	IGR	DEL	TC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115493363_115493364delTC								TBX3 (371394 upstream) : MED13L (903019 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	116030327	116030327	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116030327delT								TBX3 (908358 upstream) : MED13L (366056 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	116282689	116282689	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116282689delC								None (None upstream) : MED13L (113694 downstream)																																			---	---	---	---
MED13L	23389	broad.mit.edu	37	12	116559317	116559317	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116559317delA	uc001tvw.2	-							NM_015335	NP_056150			mediator complex subunit 13-like						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent					skin(4)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)	8	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)														---	---	---	---
MED13L	23389	broad.mit.edu	37	12	116675101	116675101	+	Intron	DEL	A	-	-	rs144743515	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116675101delA	uc001tvw.2	-							NM_015335	NP_056150			mediator complex subunit 13-like						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent					skin(4)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)	8	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	116757664	116757667	+	IGR	DEL	AAAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116757664_116757667delAAAA								MED13L (42673 upstream) : NCRNA00173 (213560 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	116820290	116820293	+	IGR	DEL	ACTC	-	-	rs72358621		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116820290_116820293delACTC								MED13L (105299 upstream) : NCRNA00173 (150934 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	117089632	117089632	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117089632delA								MAP1LC3B2 (75207 upstream) : C12orf49 (63964 downstream)																																			---	---	---	---
FBXW8	26259	broad.mit.edu	37	12	117459730	117459731	+	Intron	INS	-	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117459730_117459731insC	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)														---	---	---	---
FBXO21	23014	broad.mit.edu	37	12	117618435	117618435	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117618435delT	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)														---	---	---	---
RFC5	5985	broad.mit.edu	37	12	118465477	118465478	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:118465477_118465478delAA	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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	118994327	118994327	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:118994327delG								SUDS3 (138488 upstream) : SRRM4 (425069 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	119212636	119212637	+	IGR	DEL	GA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119212636_119212637delGA								SUDS3 (356797 upstream) : SRRM4 (206759 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	119635751	119635752	+	IGR	DEL	TT	-	-	rs72055095		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119635751_119635752delTT								HSPB8 (3201 upstream) : LOC144742 (85878 downstream)																																			---	---	---	---
CCDC60	160777	broad.mit.edu	37	12	119833752	119833752	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119833752delT	uc001txe.2	+						uc001txf.2_Intron	NM_178499	NP_848594			coiled-coil domain containing 60											ovary(2)|upper_aerodigestive_tract(1)	3	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.207)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	120007771	120007772	+	Intron	INS	-	TG	TG	rs150658130	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120007771_120007772insTG	uc001txf.2	-											Homo sapiens full length insert cDNA clone ZD48A05.																														---	---	---	---
PRKAB1	5564	broad.mit.edu	37	12	120110460	120110461	+	Intron	DEL	AG	-	-	rs150497180		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120110460_120110461delAG	uc009zwu.2	+						PRKAB1_uc001txg.2_Intron	NM_006253	NP_006244			AMP-activated protein kinase beta 1						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)													---	---	---	---
CIT	11113	broad.mit.edu	37	12	120171833	120171833	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120171833delT	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)														---	---	---	---
CIT	11113	broad.mit.edu	37	12	120281826	120281828	+	Intron	DEL	TTT	-	-	rs113598683		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120281826_120281828delTTT	uc001txi.1	-						CIT_uc001txj.1_Intron	NM_007174	NP_009105			citron						intracellular signal transduction		ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity			ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1)	10	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)	Myeloproliferative disorder(1001;0.0255)		BRCA - Breast invasive adenocarcinoma(302;0.211)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	120369021	120369022	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120369021_120369022delAA								CIT (53929 upstream) : CCDC64 (58626 downstream)																																			---	---	---	---
CCDC64	92558	broad.mit.edu	37	12	120428948	120428948	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120428948delA	uc001txl.1	+						CCDC64_uc001txk.2_Intron|CCDC64_uc009zwv.1_Intron	NM_207311	NP_997194			coiled-coil domain containing 64						Golgi to secretory granule transport|neuron projection development	centrosome	dynactin binding|Rab GTPase binding			ovary(2)	2	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
MSI1	4440	broad.mit.edu	37	12	120802094	120802094	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120802094delG	uc001tye.1	-							NM_002442	NP_002433			musashi 1						nervous system development	cytoplasm|nucleus	nucleotide binding			central_nervous_system(2)|breast(1)	3	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
COQ5	84274	broad.mit.edu	37	12	120959812	120959813	+	Intron	DEL	AG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120959812_120959813delAG	uc001tyn.2	-						COQ5_uc001tyo.2_Intron|COQ5_uc010szj.1_Intron	NM_032314	NP_115690			coenzyme Q5 homolog, methyltransferase						ubiquinone biosynthetic process	mitochondrion	methyltransferase activity			ovary(1)	1	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	121490280	121490280	+	IGR	DEL	A	-	-	rs76567137		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121490280delA								OASL (13500 upstream) : P2RX7 (80398 downstream)																																			---	---	---	---
TMEM120B	144404	broad.mit.edu	37	12	122185990	122185991	+	Intron	DEL	CA	-	-	rs72024648		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122185990_122185991delCA	uc001ubc.3	+						TMEM120B_uc009zxh.2_Intron	NM_001080825	NP_001074294			transmembrane protein 120B							integral to membrane					0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;5.75e-05)|Epithelial(86;0.000128)|BRCA - Breast invasive adenocarcinoma(302;0.238)														---	---	---	---
HPD	3242	broad.mit.edu	37	12	122281970	122281970	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122281970delT	uc001ubj.2	-						HPD_uc001ubk.2_Intron	NM_002150	NP_002141			4-hydroxyphenylpyruvate dioxygenase						L-phenylalanine catabolic process|tyrosine catabolic process	cytosol	4-hydroxyphenylpyruvate dioxygenase activity|metal ion binding				0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000105)|Epithelial(86;0.000352)|BRCA - Breast invasive adenocarcinoma(302;0.225)	Nitisinone(DB00348)													---	---	---	---
PSMD9	5715	broad.mit.edu	37	12	122327828	122327828	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122327828delT	uc001ubl.2	+						HPD_uc001ubk.2_5'Flank|PSMD9_uc009zxj.2_Intron|PSMD9_uc001ubm.2_Intron	NM_002813	NP_002804			proteasome 26S non-ATPase subunit 9						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of insulin secretion|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of insulin secretion|positive regulation of transcription, DNA-dependent|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|proteasome regulatory particle assembly|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	nucleus|proteasome regulatory particle	bHLH transcription factor binding|transcription coactivator activity				0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000117)|Epithelial(86;0.000415)|BRCA - Breast invasive adenocarcinoma(302;0.231)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	122507192	122507193	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122507192_122507193delTT								BCL7A (7244 upstream) : MLXIP (9567 downstream)																																			---	---	---	---
RSRC2	65117	broad.mit.edu	37	12	123003697	123003697	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123003697delA	uc001ucr.2	-						RSRC2_uc001uco.2_Intron|RSRC2_uc001ucp.2_Intron|RSRC2_uc001ucq.2_Intron|RSRC2_uc001ucs.2_Intron|RSRC2_uc001uct.2_Intron|RSRC2_uc001ucu.2_Intron	NM_023012	NP_075388			arginine/serine-rich coiled-coil 2 isoform a											ovary(1)	1	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;5.14e-05)|Epithelial(86;0.000183)|BRCA - Breast invasive adenocarcinoma(302;0.201)														---	---	---	---
KNTC1	9735	broad.mit.edu	37	12	123031923	123031923	+	Intron	DEL	A	-	-	rs74554972		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123031923delA	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-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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	123085218	123085219	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123085218_123085219insT	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	123088048	123088048	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123088048delT	uc001ucv.2	+						KNTC1_uc010taf.1_Intron	NM_014708	NP_055523			Rough Deal homolog, centromere/kinetochore						cell division|mitotic cell cycle checkpoint|mitotic prometaphase|protein complex assembly|regulation of exit from mitosis	condensed chromosome kinetochore|cytosol|kinetochore microtubule|nucleus|spindle pole	protein binding			ovary(5)|kidney(3)|lung(1)|central_nervous_system(1)	10	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.21e-05)|Epithelial(86;0.000178)|BRCA - Breast invasive adenocarcinoma(302;0.217)														---	---	---	---
GPR81	27198	broad.mit.edu	37	12	123162123	123162123	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123162123delT	uc001ucw.1	-							NM_032554				G protein-coupled receptor 81						response to estradiol stimulus	integral to membrane|plasma membrane	G-protein coupled receptor activity				0	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.14e-05)|Epithelial(86;3.25e-05)|BRCA - Breast invasive adenocarcinoma(302;0.197)														---	---	---	---
GPR81	27198	broad.mit.edu	37	12	123177751	123177751	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123177751delT	uc001ucw.1	-							NM_032554				G protein-coupled receptor 81						response to estradiol stimulus	integral to membrane|plasma membrane	G-protein coupled receptor activity				0	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.14e-05)|Epithelial(86;3.25e-05)|BRCA - Breast invasive adenocarcinoma(302;0.197)														---	---	---	---
PITPNM2	57605	broad.mit.edu	37	12	123484601	123484601	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123484601delG	uc001uej.1	-						PITPNM2_uc001uek.1_Intron	NM_020845	NP_065896			phosphatidylinositol transfer protein,						metabolic process|transport	endomembrane system|integral to membrane|intracellular membrane-bounded organelle	calcium ion binding|lipid binding			ovary(1)|central_nervous_system(1)|skin(1)	3	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.55e-05)|Epithelial(86;8.43e-05)|BRCA - Breast invasive adenocarcinoma(302;0.123)														---	---	---	---
MPHOSPH9	10198	broad.mit.edu	37	12	123666278	123666278	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123666278delA	uc001uel.2	-						MPHOSPH9_uc010tal.1_Intron|MPHOSPH9_uc010tam.1_Intron|MPHOSPH9_uc001uem.2_Intron	NM_022782	NP_073619			M-phase phosphoprotein 9						M phase of mitotic cell cycle	centriole|Golgi membrane					0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000182)|Epithelial(86;0.00046)|BRCA - Breast invasive adenocarcinoma(302;0.169)														---	---	---	---
SBNO1	55206	broad.mit.edu	37	12	123826244	123826244	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123826244delT	uc010tap.1	-						SBNO1_uc010tao.1_Intron|SBNO1_uc010taq.1_Intron|SBNO1_uc001uet.2_Intron|SBNO1_uc001ueu.2_Intron|SBNO1_uc001uev.2_Intron|SBNO1_uc009zxy.1_Intron	NM_018183	NP_060653			sno, strawberry notch homolog 1								ATP binding|DNA binding|hydrolase activity			breast(5)|skin(2)|ovary(1)|kidney(1)	9	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000701)|Epithelial(86;0.00197)														---	---	---	---
SETD8	387893	broad.mit.edu	37	12	123878091	123878091	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123878091delT	uc001uew.2	+						SETD8_uc001uex.2_Intron	NM_020382	NP_065115			SET domain-containing 8						cell division|mitosis|negative regulation of transcription from RNA polymerase II promoter|peptidyl-lysine monomethylation|regulation of DNA damage response, signal transduction by p53 class mediator|transcription, DNA-dependent	chromosome|nucleus	histone-lysine N-methyltransferase activity|p53 binding|transcription corepressor activity				0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.00101)|Epithelial(86;0.00425)														---	---	---	---
RILPL1	353116	broad.mit.edu	37	12	123995806	123995807	+	Intron	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123995806_123995807delTG	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)														---	---	---	---
DDX55	57696	broad.mit.edu	37	12	124102563	124102563	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124102563delT	uc001ufi.2	+						DDX55_uc001ufh.2_Intron|DDX55_uc001ufj.1_3'UTR|DDX55_uc001ufk.2_Intron|DDX55_uc001ufl.2_5'Flank	NM_020936	NP_065987			DEAD (Asp-Glu-Ala-Asp) box polypeptide 55								ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)	1	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000142)|Epithelial(86;0.000637)|all cancers(50;0.00772)												OREG0022230	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
EIF2B1	1967	broad.mit.edu	37	12	124109526	124109526	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124109526delT	uc001ufm.2	-						EIF2B1_uc001ufn.2_Intron	NM_001414	NP_001405			eukaryotic translation initiation factor 2B,						cellular response to stimulus|oligodendrocyte development|regulation of translational initiation|response to glucose stimulus|response to heat|response to peptide hormone stimulus	cytosol|eukaryotic translation initiation factor 2B complex|membrane fraction|plasma membrane	protein binding|translation initiation factor activity				0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.67e-05)|Epithelial(86;0.000353)|all cancers(50;0.00489)														---	---	---	---
TCTN2	79867	broad.mit.edu	37	12	124182408	124182409	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124182408_124182409delTT	uc001ufp.2	+						TCTN2_uc009zya.2_Intron	NM_024809	NP_079085			tectonic family member 2 isoform 1						cilium assembly|smoothened signaling pathway	integral to membrane				ovary(1)	1	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000163)|Epithelial(86;0.000502)|all cancers(50;0.00451)														---	---	---	---
ATP6V0A2	23545	broad.mit.edu	37	12	124201455	124201456	+	Intron	INS	-	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124201455_124201456insC	uc001ufr.2	+						ATP6V0A2_uc001ufq.1_Intron	NM_012463	NP_036595			ATPase, H+ transporting, lysosomal V0 subunit						ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|immune response|insulin receptor signaling pathway|transferrin transport	endosome membrane|integral to membrane|plasma membrane|proton-transporting two-sector ATPase complex, proton-transporting domain	hydrogen ion transmembrane transporter activity|protein binding			ovary(2)	2	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000224)|Epithelial(86;0.000625)|all cancers(50;0.00775)														---	---	---	---
ATP6V0A2	23545	broad.mit.edu	37	12	124219689	124219690	+	Intron	INS	-	GTGTGT	GTGTGT	rs138945980	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124219689_124219690insGTGTGT	uc001ufr.2	+						ATP6V0A2_uc001ufq.1_Intron	NM_012463	NP_036595			ATPase, H+ transporting, lysosomal V0 subunit						ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|immune response|insulin receptor signaling pathway|transferrin transport	endosome membrane|integral to membrane|plasma membrane|proton-transporting two-sector ATPase complex, proton-transporting domain	hydrogen ion transmembrane transporter activity|protein binding			ovary(2)	2	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000224)|Epithelial(86;0.000625)|all cancers(50;0.00775)														---	---	---	---
DNAH10	196385	broad.mit.edu	37	12	124371042	124371043	+	Intron	DEL	GT	-	-	rs67952135		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124371042_124371043delGT	uc001uft.3	+							NM_207437	NP_997320			dynein, axonemal, heavy chain 10						microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(3)|skin(2)|central_nervous_system(1)	6	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)														---	---	---	---
CCDC92	80212	broad.mit.edu	37	12	124443870	124443870	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124443870delT	uc001ufw.1	-						CCDC92_uc001ufx.1_Intron|CCDC92_uc001ufy.1_Intron	NM_025140	NP_079416			coiled-coil domain containing 92												0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			Epithelial(86;0.0002)|OV - Ovarian serous cystadenocarcinoma(86;0.000222)|all cancers(50;0.00129)|BRCA - Breast invasive adenocarcinoma(302;0.242)														---	---	---	---
NCOR2	9612	broad.mit.edu	37	12	124895811	124895812	+	Intron	INS	-	AC	AC			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124895811_124895812insAC	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	124923291	124923292	+	Intron	DEL	AG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124923291_124923292delAG	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	124947573	124947574	+	Intron	INS	-	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124947573_124947574insC	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	124991753	124991753	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124991753delG	uc010tay.1	-						NCOR2_uc010taz.1_Intron|NCOR2_uc010tbc.1_Intron|NCOR2_uc001ugj.1_Intron|NCOR2_uc001ugk.1_Intron	NM_006312	NP_006303			nuclear receptor co-repressor 2 isoform 1						cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter|transcription, DNA-dependent	nuclear body|nucleus|transcriptional repressor complex	DNA binding|histone deacetylase binding|Notch binding|protein N-terminus binding|transcription corepressor activity			skin(3)|ovary(1)	4	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	125068567	125068567	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125068567delC								NCOR2 (16557 upstream) : SCARB1 (193608 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	125102878	125102878	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125102878delT								NCOR2 (50868 upstream) : SCARB1 (159297 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	125163074	125163074	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125163074delG								NCOR2 (111064 upstream) : SCARB1 (99101 downstream)																																			---	---	---	---
SCARB1	949	broad.mit.edu	37	12	125322005	125322008	+	Intron	DEL	GAAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125322005_125322008delGAAA	uc001ugo.3	-						SCARB1_uc001ugn.3_Intron|SCARB1_uc001ugm.3_Intron|SCARB1_uc010tbd.1_Intron|SCARB1_uc010tbe.1_Intron|SCARB1_uc001ugp.3_Intron	NM_005505	NP_005496			scavenger receptor class B, member 1 isoform 1						adhesion to symbiont|cell adhesion|cholesterol efflux|cholesterol homeostasis|cholesterol import|detection of lipopolysaccharide|high-density lipoprotein particle clearance|high-density lipoprotein particle remodeling|lipopolysaccharide transport|lipoprotein metabolic process|positive regulation of cholesterol storage|positive regulation of endothelial cell migration|positive regulation of nitric-oxide synthase activity|recognition of apoptotic cell|reverse cholesterol transport|triglyceride homeostasis|wound healing	caveola	1-phosphatidylinositol binding|apolipoprotein A-I binding|high-density lipoprotein particle receptor activity|lipopolysaccharide receptor activity|low-density lipoprotein particle binding|phosphatidylserine binding|transporter activity			kidney(1)	1	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000116)|Epithelial(86;0.000415)|all cancers(50;0.00395)	Phosphatidylserine(DB00144)													---	---	---	---
DHX37	57647	broad.mit.edu	37	12	125465270	125465272	+	In_Frame_Del	DEL	CTC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125465270_125465272delCTC	uc001ugy.2	-	4	601_603	c.502_504delGAG	c.(502-504)GAGdel	p.E168del		NM_032656	NP_116045	Q8IY37	DHX37_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 37	168							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	125651630	125651631	+	IGR	DEL	AT	-	-	rs11058060	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125651630_125651631delAT								AACS (23758 upstream) : TMEM132B (159531 downstream)																																			---	---	---	---
TMEM132B	114795	broad.mit.edu	37	12	125938937	125938938	+	Intron	DEL	TT	-	-	rs36015767		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125938937_125938938delTT	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	126001011	126001011	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:126001011delA	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	126270307	126270307	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:126270307delA								TMEM132B (126718 upstream) : LOC100128554 (656720 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	126611428	126611428	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:126611428delT								TMEM132B (467839 upstream) : LOC100128554 (315599 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	127303003	127303004	+	IGR	DEL	TT	-	-	rs5801687		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:127303003_127303004delTT								LOC100128554 (345673 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	127532918	127532918	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:127532918delT	uc001uho.2	-											Homo sapiens cDNA clone IMAGE:4829480.																														---	---	---	---
Unknown	0	broad.mit.edu	37	12	127968011	127968011	+	IGR	DEL	G	-	-	rs139529223		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:127968011delG								None (None upstream) : TMEM132C (931280 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	128471349	128471350	+	IGR	INS	-	CACA	CACA	rs139401600	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:128471349_128471350insCACA								None (None upstream) : TMEM132C (427941 downstream)																																			---	---	---	---
TMEM132C	92293	broad.mit.edu	37	12	129170147	129170148	+	Intron	INS	-	T	T	rs143726479	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129170147_129170148insT	uc001uhs.3	+							NM_001136103	NP_001129575			transmembrane protein 132C							integral to membrane				central_nervous_system(1)	1																		---	---	---	---
SLC15A4	121260	broad.mit.edu	37	12	129310943	129310944	+	5'Flank	DEL	AT	-	-	rs41341547		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129310943_129310944delAT	uc001uhu.2	-						SLC15A4_uc001uhv.2_5'Flank	NM_145648	NP_663623			solute carrier family 15, member 4						oligopeptide transport|protein transport	integral to membrane|lysosomal membrane	peptide:hydrogen symporter activity				0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.69e-06)|Epithelial(86;1.17e-05)|all cancers(50;5.07e-05)														---	---	---	---
GLT1D1	144423	broad.mit.edu	37	12	129347070	129347070	+	5'Flank	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129347070delC	uc010tbh.1	+						GLT1D1_uc001uhx.1_Intron|GLT1D1_uc001uhy.1_Intron	NM_144669	NP_653270			glycosyltransferase 1 domain containing 1						biosynthetic process	extracellular region	transferase activity, transferring glycosyl groups				0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;3.97e-06)|Epithelial(86;3.97e-05)|all cancers(50;0.00019)														---	---	---	---
TMEM132D	121256	broad.mit.edu	37	12	129604433	129604433	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129604433delG	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	129760577	129760578	+	Intron	INS	-	GTTT	GTTT	rs141331434	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129760577_129760578insGTTT	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	130379721	130379721	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130379721delC	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	130497958	130497959	+	IGR	INS	-	T	T	rs144311756	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130497958_130497959insT								TMEM132D (109746 upstream) : LOC100190940 (20040 downstream)																																			---	---	---	---
RIMBP2	23504	broad.mit.edu	37	12	130924068	130924069	+	Intron	DEL	GT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130924068_130924069delGT	uc001uil.2	-						RIMBP2_uc001uim.2_Intron|RIMBP2_uc001uin.1_Intron	NM_015347	NP_056162			RIM-binding protein 2							cell junction|synapse				upper_aerodigestive_tract(3)|ovary(3)|large_intestine(2)|central_nervous_system(2)|pancreas(1)	11	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)														---	---	---	---
RIMBP2	23504	broad.mit.edu	37	12	130971257	130971257	+	Intron	DEL	A	-	-	rs67716959		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130971257delA	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)														---	---	---	---
RIMBP2	23504	broad.mit.edu	37	12	131143022	131143022	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131143022delA	uc001uim.2	-											RecName: Full=RIMS-binding protein 2;          Short=RIM-BP2;							cell junction|synapse				upper_aerodigestive_tract(3)|ovary(3)|large_intestine(2)|central_nervous_system(2)|pancreas(1)	11	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)														---	---	---	---
GPR133	283383	broad.mit.edu	37	12	131472441	131472442	+	Intron	INS	-	G	G	rs140298373	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131472441_131472442insG	uc001uit.3	+						GPR133_uc010tbm.1_Intron	NM_198827	NP_942122			G protein-coupled receptor 133 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			pancreas(5)|ovary(3)|skin(2)	10	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.68e-06)|all cancers(50;2.71e-06)|Epithelial(86;6.75e-06)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	131906564	131906566	+	IGR	DEL	TCC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131906564_131906566delTCC								LOC116437 (209089 upstream) : SFRS8 (289069 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	131929361	131929361	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131929361delC								LOC116437 (231886 upstream) : SFRS8 (266274 downstream)																																			---	---	---	---
SFRS8	6433	broad.mit.edu	37	12	132277638	132277640	+	Intron	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132277638_132277640delTTT	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)														---	---	---	---
MMP17	4326	broad.mit.edu	37	12	132315237	132315237	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132315237delT	uc001ujc.1	+							NM_016155	NP_057239			matrix metalloproteinase 17 preproprotein						proteolysis	anchored to membrane|integral to plasma membrane|proteinaceous extracellular matrix	calcium ion binding|enzyme activator activity|metalloendopeptidase activity|zinc ion binding				0	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.82e-07)|Epithelial(86;1.51e-06)|all cancers(50;2.35e-05)														---	---	---	---
GALNT9	50614	broad.mit.edu	37	12	132871244	132871245	+	Intron	INS	-	G	G	rs144362969	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132871244_132871245insG	uc001ukc.3	-						GALNT9_uc009zys.2_Intron	NM_001122636	NP_001116108			UDP-N-acetyl-alpha-D-galactosamine:polypeptide						protein O-linked glycosylation	Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding				0	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.241)		OV - Ovarian serous cystadenocarcinoma(86;7.49e-08)|Epithelial(86;3.55e-07)|all cancers(50;2.09e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	19102833	19102834	+	IGR	INS	-	GC	GC	rs142670767	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19102833_19102834insGC								None (None upstream) : LOC284232 (305709 downstream)																																			---	---	---	---
DKFZp686A1627	266695	broad.mit.edu	37	13	19646950	19646950	+	Intron	DEL	T	-	-	rs36089073		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19646950delT	uc001umb.1	-							NR_002801				Homo sapiens mRNA; cDNA DKFZp686A1627 (from clone DKFZp686A1627).												0																		---	---	---	---
ZMYM5	9205	broad.mit.edu	37	13	20433273	20433273	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20433273delA	uc010tcn.1	-						ZMYM5_uc001umn.2_Intron|ZMYM5_uc001umo.2_Intron	NM_001142684	NP_001136156			zinc finger protein 237 isoform 3							nucleus	zinc ion binding				0		all_cancers(29;2.96e-22)|all_epithelial(30;3.76e-20)|all_lung(29;4.38e-20)|Lung NSC(5;5.8e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.61e-05)|Epithelial(112;4.89e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00171)|Lung(94;0.00942)|LUSC - Lung squamous cell carcinoma(192;0.0431)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	20472378	20472380	+	IGR	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20472378_20472380delTTT								ZMYM5 (34602 upstream) : ZMYM2 (60430 downstream)																																			---	---	---	---
CRYL1	51084	broad.mit.edu	37	13	21036237	21036238	+	Intron	INS	-	G	G	rs141513062	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21036237_21036238insG	uc001une.2	-						CRYL1_uc001unf.2_Intron|CRYL1_uc001ung.2_Intron	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	21254221	21254221	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21254221delT	uc001unh.2	+						IFT88_uc001uni.2_Intron|IFT88_uc001unj.2_Intron|IFT88_uc010tcq.1_Intron	NM_175605	NP_783195			intraflagellar transport 88 homolog isoform 1						cilium morphogenesis	centriole|intraflagellar transport particle B|microtubule basal body|microtubule-based flagellum	protein binding			ovary(1)	1		all_cancers(29;5.79e-25)|all_epithelial(30;2.57e-20)|all_lung(29;3.13e-16)|Lung SC(185;0.0262)|Ovarian(182;0.0825)|Hepatocellular(188;0.244)		all cancers(112;0.000667)|Epithelial(112;0.00119)|OV - Ovarian serous cystadenocarcinoma(117;0.0141)|Lung(94;0.0183)|LUSC - Lung squamous cell carcinoma(192;0.0528)														---	---	---	---
SKA3	221150	broad.mit.edu	37	13	21741918	21741919	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21741918_21741919insA	uc001unt.2	-						SKA3_uc001unv.2_Intron|SKA3_uc001unu.2_Intron	NM_145061	NP_659498			SKA3						cell division|chromosome segregation|mitosis|regulation of microtubule polymerization or depolymerization	condensed chromosome outer kinetochore|cytoplasm|spindle microtubule	protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	13	22051190	22051191	+	IGR	INS	-	CA	CA	rs138222083	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22051190_22051191insCA								ZDHHC20 (17767 upstream) : EFHA1 (15649 downstream)																																	OREG0022287	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	13	22288749	22288749	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22288749delT								FGF9 (10109 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	22832126	22832127	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22832126_22832127insT	uc001uoi.2	+						uc001uoj.2_Intron					Homo sapiens cDNA FLJ30283 fis, clone BRACE2002807.																														---	---	---	---
Unknown	0	broad.mit.edu	37	13	23380554	23380554	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23380554delT								None (None upstream) : SGCG (374506 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	23493872	23493877	+	IGR	DEL	TGTGTG	-	-	rs36047826		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23493872_23493877delTGTGTG								None (None upstream) : SGCG (261183 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	23498788	23498788	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23498788delA								None (None upstream) : SGCG (256272 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	23556453	23556453	+	IGR	DEL	T	-	-	rs71902764		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23556453delT								None (None upstream) : SGCG (198607 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	23580499	23580500	+	IGR	INS	-	T	T	rs140062191	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23580499_23580500insT								None (None upstream) : SGCG (174560 downstream)																																			---	---	---	---
SACS	26278	broad.mit.edu	37	13	23922956	23922956	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23922956delA	uc001uon.2	-						SACS_uc001uoo.2_Intron|SACS_uc001uop.1_Intron|SACS_uc001uoq.1_Intron	NM_014363	NP_055178			sacsin						cell death|negative regulation of inclusion body assembly|protein folding	axon|cell body fiber|dendrite|mitochondrion|nucleus	ATP binding|chaperone binding|Hsp70 protein binding|proteasome binding			ovary(7)|skin(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	12		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	24936034	24936034	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24936034delC								C1QTNF9 (39369 upstream) : PARP4 (59041 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	24989737	24989742	+	IGR	DEL	GTGTGT	-	-	rs3082324		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24989737_24989742delGTGTGT								C1QTNF9 (93072 upstream) : PARP4 (5333 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	25296630	25296630	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25296630delA								ATP12A (10713 upstream) : RNF17 (41671 downstream)																																			---	---	---	---
TPTE2P1	646405	broad.mit.edu	37	13	25541679	25541679	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25541679delT	uc010tdh.1	-						TPTE2P1_uc001upx.3_Intron	NR_026730				RecName: Full=C2 tensin-type domain-containing protein ENSP00000371290;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	13	25562052	25562052	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25562052delT								TPTE2P1 (19445 upstream) : PABPC3 (108224 downstream)																																			---	---	---	---
ATP8A2	51761	broad.mit.edu	37	13	26486880	26486880	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:26486880delT	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	26695779	26695779	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:26695779delA								SHISA2 (70581 upstream) : RNF6 (10474 downstream)																																			---	---	---	---
WASF3	10810	broad.mit.edu	37	13	27170717	27170717	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:27170717delT	uc001uqv.2	+						WASF3_uc001uqw.2_Intron	NM_006646	NP_006637			WAS protein family, member 3						actin filament polymerization	cytoplasm|cytoskeleton	actin binding			pancreas(1)	1	Colorectal(5;0.000247)	Lung SC(185;0.0156)|Breast(139;0.147)		all cancers(112;0.0114)|Epithelial(112;0.046)|OV - Ovarian serous cystadenocarcinoma(117;0.0547)|Lung(94;0.105)|LUSC - Lung squamous cell carcinoma(192;0.155)														---	---	---	---
WASF3	10810	broad.mit.edu	37	13	27241435	27241435	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:27241435delA	uc001uqv.2	+						WASF3_uc001uqw.2_Intron	NM_006646	NP_006637			WAS protein family, member 3						actin filament polymerization	cytoplasm|cytoskeleton	actin binding			pancreas(1)	1	Colorectal(5;0.000247)	Lung SC(185;0.0156)|Breast(139;0.147)		all cancers(112;0.0114)|Epithelial(112;0.046)|OV - Ovarian serous cystadenocarcinoma(117;0.0547)|Lung(94;0.105)|LUSC - Lung squamous cell carcinoma(192;0.155)														---	---	---	---
USP12	219333	broad.mit.edu	37	13	27648543	27648544	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:27648543_27648544delAA	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)														---	---	---	---
RPL21	6144	broad.mit.edu	37	13	27830554	27830554	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:27830554delT	uc001ura.2	+							NM_000982	NP_000973			ribosomal protein L21						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit	RNA binding|structural constituent of ribosome				0		Lung SC(185;0.0156)	Colorectal(13;0.00042)|READ - Rectum adenocarcinoma(15;0.105)	all cancers(112;0.0287)|OV - Ovarian serous cystadenocarcinoma(117;0.118)|Epithelial(112;0.139)|GBM - Glioblastoma multiforme(144;0.21)														---	---	---	---
FLT3	2322	broad.mit.edu	37	13	28587074	28587074	+	Intron	DEL	A	-	-	rs113567190		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28587074delA	uc001urw.2	-						FLT3_uc010aao.2_Intron|FLT3_uc010tdn.1_Intron	NM_004119	NP_004110			fms-related tyrosine kinase 3 precursor						positive regulation of cell proliferation	integral to plasma membrane	ATP binding|vascular endothelial growth factor receptor activity			haematopoietic_and_lymphoid_tissue(8536)|lung(7)|ovary(3)|stomach(1)|central_nervous_system(1)|skin(1)	8549	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0156)|Ovarian(182;0.0392)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.00154)|all cancers(112;0.00459)|GBM - Glioblastoma multiforme(144;0.00562)|Epithelial(112;0.0959)|Lung(94;0.212)	Sorafenib(DB00398)|Sunitinib(DB01268)			Mis|O		AML|ALL								---	---	---	---
FLT3	2322	broad.mit.edu	37	13	28609082	28609082	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28609082delA	uc001urw.2	-						FLT3_uc010aao.2_Intron|FLT3_uc010tdn.1_Intron	NM_004119	NP_004110			fms-related tyrosine kinase 3 precursor						positive regulation of cell proliferation	integral to plasma membrane	ATP binding|vascular endothelial growth factor receptor activity			haematopoietic_and_lymphoid_tissue(8536)|lung(7)|ovary(3)|stomach(1)|central_nervous_system(1)|skin(1)	8549	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0156)|Ovarian(182;0.0392)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.00154)|all cancers(112;0.00459)|GBM - Glioblastoma multiforme(144;0.00562)|Epithelial(112;0.0959)|Lung(94;0.212)	Sorafenib(DB00398)|Sunitinib(DB01268)			Mis|O		AML|ALL								---	---	---	---
FLT3	2322	broad.mit.edu	37	13	28635910	28635910	+	Intron	DEL	A	-	-	rs78564726		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28635910delA	uc001urw.2	-						FLT3_uc010aao.2_Intron|FLT3_uc010tdn.1_Intron	NM_004119	NP_004110			fms-related tyrosine kinase 3 precursor						positive regulation of cell proliferation	integral to plasma membrane	ATP binding|vascular endothelial growth factor receptor activity			haematopoietic_and_lymphoid_tissue(8536)|lung(7)|ovary(3)|stomach(1)|central_nervous_system(1)|skin(1)	8549	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0156)|Ovarian(182;0.0392)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.00154)|all cancers(112;0.00459)|GBM - Glioblastoma multiforme(144;0.00562)|Epithelial(112;0.0959)|Lung(94;0.212)	Sorafenib(DB00398)|Sunitinib(DB01268)			Mis|O		AML|ALL								---	---	---	---
FLT1	2321	broad.mit.edu	37	13	28886057	28886057	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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)													---	---	---	---
Unknown	0	broad.mit.edu	37	13	31008815	31008816	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31008815_31008816insT								LOC100188949 (60779 upstream) : HMGB1 (24065 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	31652513	31652520	+	IGR	DEL	AAGAAAGA	-	-	rs7986217		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31652513_31652520delAAGAAAGA								C13orf26 (103362 upstream) : HSPH1 (58245 downstream)																																			---	---	---	---
FRY	10129	broad.mit.edu	37	13	32770717	32770718	+	Intron	DEL	GT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32770717_32770718delGT	uc001utx.2	+						FRY_uc010tdw.1_Intron	NM_023037	NP_075463			furry homolog						regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to membrane				ovary(5)|large_intestine(1)|skin(1)	7		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)														---	---	---	---
FRY	10129	broad.mit.edu	37	13	32818080	32818080	+	Intron	DEL	A	-	-	rs138165196	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32818080delA	uc001utx.2	+						FRY_uc010tdw.1_Intron	NM_023037	NP_075463			furry homolog						regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to membrane				ovary(5)|large_intestine(1)|skin(1)	7		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)														---	---	---	---
PDS5B	23047	broad.mit.edu	37	13	33337568	33337568	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33337568delT	uc010abf.2	+						PDS5B_uc010abg.2_Intron	NM_015032	NP_055847			PDS5, regulator of cohesion maintenance, homolog						cell division|cell proliferation|mitotic sister chromatid cohesion|negative regulation of cell proliferation	chromatin|nucleus	ATP binding|DNA binding|identical protein binding			ovary(2)|lung(1)|pancreas(1)	4		Lung SC(185;0.0367)		all cancers(112;5.55e-06)|Epithelial(112;2.7e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00303)|BRCA - Breast invasive adenocarcinoma(63;0.0204)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	33440753	33440753	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33440753delA								PDS5B (88598 upstream) : KL (149448 downstream)																																			---	---	---	---
STARD13	90627	broad.mit.edu	37	13	33698854	33698855	+	Intron	INS	-	A	A	rs142303903	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33698854_33698855insA	uc001uuw.2	-						STARD13_uc001uuu.2_Intron|STARD13_uc001uuv.2_Intron|STARD13_uc001uux.2_Intron|STARD13_uc010tec.1_Intron	NM_178006	NP_821074			StAR-related lipid transfer (START) domain						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|lipid particle|mitochondrial membrane	GTPase activator activity|protein binding			ovary(2)|pancreas(1)|skin(1)	4	all_epithelial(80;0.155)	Lung SC(185;0.0367)		all cancers(112;1.31e-05)|Epithelial(112;0.000142)|BRCA - Breast invasive adenocarcinoma(63;0.00936)|OV - Ovarian serous cystadenocarcinoma(117;0.0533)|Lung(94;0.143)|GBM - Glioblastoma multiforme(144;0.143)														---	---	---	---
STARD13	90627	broad.mit.edu	37	13	33869658	33869658	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33869658delT	uc001uux.2	-						STARD13_uc010abh.1_Intron	NM_052851	NP_443083			StAR-related lipid transfer (START) domain						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|lipid particle|mitochondrial membrane	GTPase activator activity|protein binding			ovary(2)|pancreas(1)|skin(1)	4	all_epithelial(80;0.155)	Lung SC(185;0.0367)		all cancers(112;1.31e-05)|Epithelial(112;0.000142)|BRCA - Breast invasive adenocarcinoma(63;0.00936)|OV - Ovarian serous cystadenocarcinoma(117;0.0533)|Lung(94;0.143)|GBM - Glioblastoma multiforme(144;0.143)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	34911820	34911821	+	IGR	INS	-	AAG	AAG	rs140926526	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:34911820_34911821insAAG								RFC3 (371126 upstream) : NBEA (604635 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	34970570	34970570	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:34970570delA								RFC3 (429876 upstream) : NBEA (545886 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	35202881	35202882	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:35202881_35202882delTT								RFC3 (662187 upstream) : NBEA (313574 downstream)																																			---	---	---	---
NBEA	26960	broad.mit.edu	37	13	35569752	35569752	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:35569752delA	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)														---	---	---	---
NBEA	26960	broad.mit.edu	37	13	35581220	35581220	+	Intron	DEL	T	-	-	rs11308753		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:35581220delT	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)														---	---	---	---
DCLK1	9201	broad.mit.edu	37	13	36398087	36398087	+	Intron	DEL	T	-	-	rs5019502	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:36398087delT	uc001uvf.2	-						DCLK1_uc001uve.3_Intron|DCLK1_uc010teh.1_Intron|DCLK1_uc010abk.2_Intron	NM_004734	NP_004725			doublecortin-like kinase 1						cell differentiation|central nervous system development|endosome transport|intracellular signal transduction|response to virus	integral to plasma membrane	ATP binding|protein serine/threonine kinase activity|receptor signaling protein activity			stomach(6)|ovary(2)|skin(1)	9		Breast(139;0.0147)|Lung SC(185;0.0685)|Prostate(109;0.122)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.72e-06)|Epithelial(112;4.24e-05)|BRCA - Breast invasive adenocarcinoma(63;0.00159)|OV - Ovarian serous cystadenocarcinoma(117;0.0158)|GBM - Glioblastoma multiforme(144;0.0638)														---	---	---	---
DCLK1	9201	broad.mit.edu	37	13	36516315	36516316	+	Intron	INS	-	T	T	rs148014415	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:36516315_36516316insT	uc001uvf.2	-							NM_004734	NP_004725			doublecortin-like kinase 1						cell differentiation|central nervous system development|endosome transport|intracellular signal transduction|response to virus	integral to plasma membrane	ATP binding|protein serine/threonine kinase activity|receptor signaling protein activity			stomach(6)|ovary(2)|skin(1)	9		Breast(139;0.0147)|Lung SC(185;0.0685)|Prostate(109;0.122)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.72e-06)|Epithelial(112;4.24e-05)|BRCA - Breast invasive adenocarcinoma(63;0.00159)|OV - Ovarian serous cystadenocarcinoma(117;0.0158)|GBM - Glioblastoma multiforme(144;0.0638)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	37034628	37034628	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37034628delC								CCNA1 (17610 upstream) : C13orf36 (213421 downstream)																																			---	---	---	---
POSTN	10631	broad.mit.edu	37	13	38170904	38170904	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38170904delC	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	38228697	38228697	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38228697delA	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	38534797	38534798	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38534797_38534798delAA								TRPC4 (90858 upstream) : UFM1 (389144 downstream)																																			---	---	---	---
FREM2	341640	broad.mit.edu	37	13	39452807	39452808	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39452807_39452808insA	uc001uwv.2	+							NM_207361	NP_997244			FRAS1-related extracellular matrix protein 2						cell communication|homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(7)|pancreas(1)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1)	11		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)														---	---	---	---
C13orf23	80209	broad.mit.edu	37	13	39598729	39598729	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39598729delA	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	39633818	39633818	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39633818delA								NHLRC3 (9576 upstream) : LHFP (283212 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	39908834	39908834	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39908834delA								NHLRC3 (284592 upstream) : LHFP (8196 downstream)																																			---	---	---	---
LHFP	10186	broad.mit.edu	37	13	40036520	40036520	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:40036520delA	uc001uxf.2	-							NM_005780	NP_005771			lipoma HMGIC fusion partner precursor							integral to membrane	DNA binding		HMGA2/LHFP(2)	soft_tissue(2)|lung(1)|breast(1)	4		Lung NSC(96;3.55e-06)|Breast(139;0.00408)|Ovarian(182;0.0107)|Prostate(109;0.0118)|Lung SC(185;0.0719)|Hepatocellular(188;0.114)		OV - Ovarian serous cystadenocarcinoma(117;6.48e-46)|Epithelial(112;8.43e-42)|all cancers(112;1.42e-36)|GBM - Glioblastoma multiforme(144;0.00187)|BRCA - Breast invasive adenocarcinoma(63;0.00886)|KIRC - Kidney renal clear cell carcinoma(186;0.048)|Kidney(163;0.0601)|LUSC - Lung squamous cell carcinoma(192;0.105)				T	HMGA2	lipoma								---	---	---	---
LHFP	10186	broad.mit.edu	37	13	40104848	40104848	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:40104848delT	uc001uxf.2	-						uc001uxg.2_RNA	NM_005780	NP_005771			lipoma HMGIC fusion partner precursor							integral to membrane	DNA binding		HMGA2/LHFP(2)	soft_tissue(2)|lung(1)|breast(1)	4		Lung NSC(96;3.55e-06)|Breast(139;0.00408)|Ovarian(182;0.0107)|Prostate(109;0.0118)|Lung SC(185;0.0719)|Hepatocellular(188;0.114)		OV - Ovarian serous cystadenocarcinoma(117;6.48e-46)|Epithelial(112;8.43e-42)|all cancers(112;1.42e-36)|GBM - Glioblastoma multiforme(144;0.00187)|BRCA - Breast invasive adenocarcinoma(63;0.00886)|KIRC - Kidney renal clear cell carcinoma(186;0.048)|Kidney(163;0.0601)|LUSC - Lung squamous cell carcinoma(192;0.105)				T	HMGA2	lipoma								---	---	---	---
LOC646982	646982	broad.mit.edu	37	13	41011866	41011866	+	Intron	DEL	T	-	-	rs4943778		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41011866delT	uc010tfa.1	-						LOC646982_uc001uxj.3_Intron	NR_024507				Homo sapiens cDNA, FLJ17553.												0																		---	---	---	---
SUGT1L1	283507	broad.mit.edu	37	13	41418474	41418474	+	Intron	DEL	A	-	-	rs150676993		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41418474delA	uc001uxp.1	-							NR_003365				Homo sapiens cDNA FLJ35913 fis, clone TESTI2010239.												0																		---	---	---	---
ELF1	1997	broad.mit.edu	37	13	41575115	41575118	+	Intron	DEL	TTTT	-	-	rs71797488		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41575115_41575118delTTTT	uc001uxs.2	-							NM_172373	NP_758961			E74-like factor 1 (ets domain transcription						positive regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Lung NSC(96;8.3e-05)|Prostate(109;0.0233)|Breast(139;0.0296)|Lung SC(185;0.0367)		all cancers(112;1.87e-08)|Epithelial(112;8.45e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000202)|GBM - Glioblastoma multiforme(144;0.00266)|BRCA - Breast invasive adenocarcinoma(63;0.072)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	41869699	41869699	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41869699delA								MTRF1 (31957 upstream) : NAA16 (15642 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	41873240	41873241	+	IGR	INS	-	GTGT	GTGT	rs151084477	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41873240_41873241insGTGT								MTRF1 (35498 upstream) : NAA16 (12100 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	42101183	42101183	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42101183delC								C13orf15 (56170 upstream) : KIAA0564 (39779 downstream)																																			---	---	---	---
KIAA0564	23078	broad.mit.edu	37	13	42191255	42191255	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42191255delT	uc001uyj.2	-							NM_015058	NP_055873			hypothetical protein LOC23078 isoform a							extracellular region	ATP binding|ATPase activity			ovary(3)|upper_aerodigestive_tract(1)|kidney(1)|skin(1)	6		Lung NSC(96;4.61e-06)|Prostate(109;0.0167)|Lung SC(185;0.0262)|Breast(139;0.0854)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000368)|GBM - Glioblastoma multiforme(144;0.0033)|BRCA - Breast invasive adenocarcinoma(63;0.0969)														---	---	---	---
KIAA0564	23078	broad.mit.edu	37	13	42267149	42267152	+	Intron	DEL	TTTT	-	-	rs71706492		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42267149_42267152delTTTT	uc001uyj.2	-							NM_015058	NP_055873			hypothetical protein LOC23078 isoform a							extracellular region	ATP binding|ATPase activity			ovary(3)|upper_aerodigestive_tract(1)|kidney(1)|skin(1)	6		Lung NSC(96;4.61e-06)|Prostate(109;0.0167)|Lung SC(185;0.0262)|Breast(139;0.0854)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000368)|GBM - Glioblastoma multiforme(144;0.0033)|BRCA - Breast invasive adenocarcinoma(63;0.0969)														---	---	---	---
KIAA0564	23078	broad.mit.edu	37	13	42368222	42368222	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42368222delT	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	42625141	42625141	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42625141delA	uc001uyl.1	+						DGKH_uc010tfh.1_Intron|DGKH_uc001uym.1_Intron	NM_178009	NP_821077			diacylglycerol kinase, eta isoform 2						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation|protein oligomerization	endosome|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding			ovary(2)	2		Lung NSC(96;1.02e-05)|Prostate(109;0.0168)|Lung SC(185;0.0262)|Breast(139;0.0709)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;5.88e-05)|GBM - Glioblastoma multiforme(144;0.000935)|BRCA - Breast invasive adenocarcinoma(63;0.109)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	43412552	43412552	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:43412552delA								C13orf30 (46869 upstream) : EPSTI1 (49570 downstream)																																			---	---	---	---
EPSTI1	94240	broad.mit.edu	37	13	43496003	43496003	+	Intron	DEL	A	-	-	rs34619320		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:43496003delA	uc001uyw.1	-						EPSTI1_uc001uyx.1_Intron	NM_001002264	NP_001002264			epithelial stromal interaction 1 isoform 1											ovary(1)	1		Lung NSC(96;3.6e-06)|Breast(139;0.00869)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		GBM - Glioblastoma multiforme(144;0.000528)|BRCA - Breast invasive adenocarcinoma(63;0.0858)														---	---	---	---
ENOX1	55068	broad.mit.edu	37	13	44172342	44172342	+	Intron	DEL	A	-	-	rs35703508		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:44172342delA	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	44464083	44464083	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:44464083delT	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)														---	---	---	---
GTF2F2	2963	broad.mit.edu	37	13	45776575	45776576	+	Intron	INS	-	GT	GT	rs141320459	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45776575_45776576insGT	uc001uzw.2	+						GTF2F2_uc001uzv.2_Intron|KCTD4_uc001uzx.3_5'Flank	NM_004128	NP_004119			general transcription factor IIF, polypeptide 2,						mRNA capping|nuclear mRNA splicing, via spliceosome|positive regulation of viral transcription|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	microtubule cytoskeleton|transcription factor TFIIF complex	ATP binding|ATP-dependent helicase activity|DNA binding|protein binding				0		Lung NSC(96;0.00115)|Prostate(109;0.00578)|Breast(139;0.0192)|Lung SC(185;0.0367)|Hepatocellular(98;0.133)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000647)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	46014472	46014472	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46014472delA								SLC25A30 (21956 upstream) : COG3 (24599 downstream)																																			---	---	---	---
C13orf18	80183	broad.mit.edu	37	13	46935559	46935559	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46935559delT	uc010acl.2	-						C13orf18_uc001vbf.3_Intron|C13orf18_uc001vbg.3_Intron|C13orf18_uc010tfz.1_Intron|C13orf18_uc010acm.2_Intron|C13orf18_uc010acn.2_Intron|C13orf18_uc001vbe.3_Intron|C13orf18_uc001vbh.3_Intron|C13orf18_uc001vbi.3_Intron|C13orf18_uc010aco.1_Intron	NM_025113	NP_079389			hypothetical protein LOC80183												0		Lung NSC(96;2.31e-05)|Breast(56;8.04e-05)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;2.19e-05)														---	---	---	---
C13orf18	80183	broad.mit.edu	37	13	47007548	47007548	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:47007548delA	uc001vbi.3	-							NM_025113	NP_079389			hypothetical protein LOC80183												0		Lung NSC(96;2.31e-05)|Breast(56;8.04e-05)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;2.19e-05)														---	---	---	---
HTR2A	3356	broad.mit.edu	37	13	47426524	47426524	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:47426524delG	uc001vbq.2	-						HTR2A_uc001vbr.2_Intron|HTR2A_uc010acr.2_Intron	NM_000621	NP_000612			5-hydroxytryptamine receptor 2A isoform 1						ERK1 and ERK2 cascade|phosphatidylinositol 3-kinase cascade|phosphatidylinositol biosynthetic process|release of sequestered calcium ion into cytosol|response to drug|synaptic transmission	integral to plasma membrane	1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding|drug binding|phosphatidylinositol phospholipase C activity|serotonin binding|serotonin receptor activity			ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	6		all_lung(13;7.2e-10)|Lung NSC(96;3.77e-07)|Breast(56;2.06e-05)|Prostate(109;0.00116)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)|Myeloproliferative disorder(33;0.0333)		GBM - Glioblastoma multiforme(144;4.67e-05)|COAD - Colon adenocarcinoma(199;0.224)	Aripiprazole(DB01238)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cisapride(DB00604)|Clomipramine(DB01242)|Clozapine(DB00363)|Cyclobenzaprine(DB00924)|Cyproheptadine(DB00434)|Dihydroergotamine(DB00320)|Donepezil(DB00843)|Epinastine(DB00751)|Ergotamine(DB00696)|Fluvoxamine(DB00176)|Mesoridazine(DB00933)|Methysergide(DB00247)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Nefazodone(DB01149)|Olanzapine(DB00334)|Paliperidone(DB01267)|Paroxetine(DB00715)|Prochlorperazine(DB00433)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Risperidone(DB00734)|Sertindole(DB06144)|Thiethylperazine(DB00372)|Thioridazine(DB00679)|Tranylcypromine(DB00752)|Trazodone(DB00656)|Venlafaxine(DB00285)|Ziprasidone(DB00246)													---	---	---	---
HTR2A	3356	broad.mit.edu	37	13	47459186	47459186	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:47459186delT	uc001vbq.2	-						HTR2A_uc001vbr.2_Intron|HTR2A_uc010acr.2_Intron	NM_000621	NP_000612			5-hydroxytryptamine receptor 2A isoform 1						ERK1 and ERK2 cascade|phosphatidylinositol 3-kinase cascade|phosphatidylinositol biosynthetic process|release of sequestered calcium ion into cytosol|response to drug|synaptic transmission	integral to plasma membrane	1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding|drug binding|phosphatidylinositol phospholipase C activity|serotonin binding|serotonin receptor activity			ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	6		all_lung(13;7.2e-10)|Lung NSC(96;3.77e-07)|Breast(56;2.06e-05)|Prostate(109;0.00116)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)|Myeloproliferative disorder(33;0.0333)		GBM - Glioblastoma multiforme(144;4.67e-05)|COAD - Colon adenocarcinoma(199;0.224)	Aripiprazole(DB01238)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cisapride(DB00604)|Clomipramine(DB01242)|Clozapine(DB00363)|Cyclobenzaprine(DB00924)|Cyproheptadine(DB00434)|Dihydroergotamine(DB00320)|Donepezil(DB00843)|Epinastine(DB00751)|Ergotamine(DB00696)|Fluvoxamine(DB00176)|Mesoridazine(DB00933)|Methysergide(DB00247)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Nefazodone(DB01149)|Olanzapine(DB00334)|Paliperidone(DB01267)|Paroxetine(DB00715)|Prochlorperazine(DB00433)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Risperidone(DB00734)|Sertindole(DB06144)|Thiethylperazine(DB00372)|Thioridazine(DB00679)|Tranylcypromine(DB00752)|Trazodone(DB00656)|Venlafaxine(DB00285)|Ziprasidone(DB00246)													---	---	---	---
Unknown	0	broad.mit.edu	37	13	47546351	47546351	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:47546351delC								HTR2A (75301 upstream) : SUCLA2 (970441 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	47726371	47726372	+	IGR	DEL	TC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:47726371_47726372delTC								HTR2A (255321 upstream) : SUCLA2 (790420 downstream)																																			---	---	---	---
SUCLA2	8803	broad.mit.edu	37	13	48570982	48570982	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:48570982delT	uc001vbs.2	-	2	324	c.267delA	c.(265-267)AAAfs	p.K89fs	SUCLA2_uc010tgb.1_Frame_Shift_Del_p.K29fs|SUCLA2_uc010tgc.1_5'UTR|SUCLA2_uc010tgd.1_Frame_Shift_Del_p.K29fs|SUCLA2_uc001vbt.1_RNA|SUCLA2_uc001vbu.1_Frame_Shift_Del_p.K89fs	NM_003850	NP_003841	Q9P2R7	SUCB1_HUMAN	succinate-CoA ligase, ADP-forming, beta subunit	89	ATP-grasp.				succinyl-CoA pathway|tricarboxylic acid cycle	mitochondrial matrix	ATP binding|metal ion binding|protein binding|succinate-CoA ligase (ADP-forming) activity			central_nervous_system(1)	1		all_cancers(8;1.13e-24)|all_epithelial(8;1.78e-13)|all_lung(13;2.85e-06)|Breast(56;0.000141)|Lung NSC(96;0.000226)|all_hematologic(8;0.000885)|Prostate(109;0.00132)|Acute lymphoblastic leukemia(8;0.0167)|Myeloproliferative disorder(33;0.039)|Hepatocellular(98;0.0556)|Lung SC(185;0.102)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(144;2.1e-06)	Succinic acid(DB00139)													---	---	---	---
MED4	29079	broad.mit.edu	37	13	48650323	48650323	+	3'UTR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:48650323delT	uc001vby.1	-	7					MED4_uc010tge.1_Intron|MED4_uc010tgf.1_3'UTR	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)														---	---	---	---
CYSLTR2	57105	broad.mit.edu	37	13	49278653	49278653	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:49278653delT	uc010acx.1	+						CYSLTR2_uc010acy.1_Intron|CYSLTR2_uc010acz.1_Intron|CYSLTR2_uc010ada.1_Intron|CYSLTR2_uc010adb.1_Intron|CYSLTR2_uc010adc.1_Intron|CYSLTR2_uc010add.1_Intron|CYSLTR2_uc010acw.1_Intron|CYSLTR2_uc001vck.2_5'Flank	NM_020377	NP_065110			cysteinyl leukotriene receptor 2						immune response	integral to membrane|plasma membrane				lung(2)	2		all_cancers(8;1.66e-53)|all_epithelial(8;1.96e-19)|all_lung(13;9.94e-09)|all_hematologic(8;7.13e-07)|Lung NSC(96;1.72e-06)|Breast(56;1.53e-05)|Acute lymphoblastic leukemia(8;6.86e-05)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0416)|Lung SC(185;0.0787)		GBM - Glioblastoma multiforme(99;1.19e-09)	Nedocromil(DB00716)													---	---	---	---
Unknown	0	broad.mit.edu	37	13	49787089	49787090	+	IGR	DEL	AA	-	-	rs78522947		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:49787089_49787090delAA								FNDC3A (3175 upstream) : MLNR (7384 downstream)																																			---	---	---	---
SETDB2	83852	broad.mit.edu	37	13	50034542	50034542	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50034542delT	uc001vcz.2	+						SETDB2_uc010adg.2_Intron|SETDB2_uc001vcy.3_Intron|SETDB2_uc010adh.2_Intron|SETDB2_uc001vda.2_Intron	NM_031915	NP_114121			SET domain, bifurcated 2 isoform a						cell division|chromosome segregation|heart looping|left/right axis specification|mitosis|negative regulation of transcription, DNA-dependent	chromosome|nucleus	DNA binding|histone methyltransferase activity (H3-K9 specific)|zinc ion binding			ovary(1)|central_nervous_system(1)	2		Lung NSC(96;0.000408)|Breast(56;0.00131)|Prostate(109;0.00446)|Hepatocellular(98;0.0556)|Glioma(44;0.236)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;3.1e-09)														---	---	---	---
KPNA3	3839	broad.mit.edu	37	13	50359892	50359892	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50359892delA	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)														---	---	---	---
DLEU2	8847	broad.mit.edu	37	13	50599513	50599513	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50599513delT	uc001vdn.1	-						DLEU2_uc001vdo.1_Intron	NR_002612				Homo sapiens BCMS-upstream neighbor (BCMSUN) mRNA, partial sequence.												0																		---	---	---	---
DLEU1	10301	broad.mit.edu	37	13	50734970	50734971	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50734970_50734971delTT	uc010adl.1	+						DLEU1_uc001vee.1_Intron|DLEU1_uc010adm.1_Intron|DLEU1_uc010adn.1_Intron|DLEU1_uc001vef.1_Intron|DLEU1_uc001veg.1_Intron|DLEU1_uc010tgn.1_Intron|DLEU1_uc001vei.1_Intron|DLEU1_uc010ado.1_Intron|DLEU1_uc010adp.1_Intron					Homo sapiens XTP6 (XTP6) mRNA, complete cds.												0																		---	---	---	---
DLEU7	220107	broad.mit.edu	37	13	51323031	51323031	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51323031delT	uc001vex.2	-							NM_198989	NP_945340			deleted in lymphocytic leukemia, 7												0		Acute lymphoblastic leukemia(7;1.03e-07)|Lung NSC(96;0.000818)|Breast(56;0.00122)|Prostate(109;0.0047)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;3.25e-08)														---	---	---	---
RNASEH2B	79621	broad.mit.edu	37	13	51517413	51517413	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51517413delT	uc001vfa.3	+						RNASEH2B_uc001vfb.3_Intron	NM_024570	NP_078846			ribonuclease H2, subunit B isoform 1						RNA catabolic process	nucleus|ribonuclease H2 complex					0		Acute lymphoblastic leukemia(7;1.03e-07)|Breast(56;0.00122)|Lung NSC(96;0.00143)|Prostate(109;0.0047)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;9e-08)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	51767000	51767000	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51767000delA								GUCY1B2 (112002 upstream) : FAM124A (29507 downstream)																																			---	---	---	---
ATP7B	540	broad.mit.edu	37	13	52575933	52575935	+	Intron	DEL	TTT	-	-	rs5803590		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52575933_52575935delTTT	uc001vfw.2	-						ATP7B_uc010adv.2_Intron|ATP7B_uc001vfx.2_Intron|ATP7B_uc001vfy.2_Intron|ATP7B_uc010tgt.1_Intron|ATP7B_uc010tgu.1_Intron|ATP7B_uc010tgv.1_Intron	NM_000053	NP_000044			ATPase, Cu++ transporting, beta polypeptide						ATP biosynthetic process|cellular copper ion homeostasis|copper ion import|response to copper ion|sequestering of calcium ion	Golgi membrane|integral to plasma membrane|late endosome|mitochondrion	ATP binding|copper ion binding|copper-exporting ATPase activity|protein binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Breast(56;0.000207)|Lung NSC(96;0.000845)|Prostate(109;0.0235)|Hepatocellular(98;0.065)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;5.25e-08)										Wilson_disease				---	---	---	---
NEK5	341676	broad.mit.edu	37	13	52680903	52680905	+	Intron	DEL	AAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52680903_52680905delAAA	uc001vge.2	-						NEK5_uc001vgf.2_Intron	NM_199289	NP_954983			NIMA-related kinase 5								ATP binding|metal ion binding|protein serine/threonine kinase activity			upper_aerodigestive_tract(1)	1		Breast(56;0.00173)|Lung NSC(96;0.0168)|Prostate(109;0.0412)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;3.7e-08)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	53708166	53708167	+	IGR	DEL	GT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53708166_53708167delGT								OLFM4 (81980 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	54326551	54326552	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:54326551_54326552delAA								OLFM4 (700365 upstream) : MIR1297 (559555 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	54500448	54500448	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:54500448delT								OLFM4 (874262 upstream) : MIR1297 (385659 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	55144435	55144436	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:55144435_55144436insT								MIR1297 (258252 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	56026883	56026896	+	IGR	DEL	TGTGTGTGTGTGTG	-	-	rs67066745		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:56026883_56026896delTGTGTGTGTGTGTG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	57242936	57242937	+	IGR	DEL	AG	-	-	rs78764946		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:57242936_57242937delAG								None (None upstream) : PRR20C (472115 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	57863952	57863952	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:57863952delT								PRR20B (119600 upstream) : PCDH17 (341837 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	58146605	58146605	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:58146605delT								PRR20B (402253 upstream) : PCDH17 (59184 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	58461023	58461023	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:58461023delA								PCDH17 (157958 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	60124390	60124390	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60124390delA								None (None upstream) : DIAPH3 (115335 downstream)																																			---	---	---	---
DIAPH3	81624	broad.mit.edu	37	13	60547561	60547561	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60547561delA	uc001vht.2	-						DIAPH3_uc001vhu.2_Intron|DIAPH3_uc001vhv.2_Intron	NM_001042517	NP_001035982			diaphanous homolog 3 isoform a						actin cytoskeleton organization		actin binding|Rho GTPase binding			ovary(2)	2		Breast(118;0.052)|Prostate(109;0.103)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;2.77e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	61214856	61214857	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:61214856_61214857insT								TDRD3 (66844 upstream) : PCDH20 (768964 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	61319469	61319469	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:61319469delC								TDRD3 (171457 upstream) : PCDH20 (664352 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	63133950	63133950	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:63133950delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	63713552	63713553	+	IGR	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:63713552_63713553delTG								None (None upstream) : OR7E156P (598015 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	64181700	64181700	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:64181700delA								None (None upstream) : OR7E156P (129868 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	65968649	65968649	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:65968649delA								None (None upstream) : PCDH9 (908318 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	66217060	66217061	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:66217060_66217061delAA								None (None upstream) : PCDH9 (659906 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	66268573	66268573	+	IGR	DEL	T	-	-	rs67784350		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:66268573delT								None (None upstream) : PCDH9 (608394 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	66874027	66874027	+	IGR	DEL	A	-	-	rs115510863	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:66874027delA								None (None upstream) : PCDH9 (2940 downstream)																																			---	---	---	---
PCDH9	5101	broad.mit.edu	37	13	67087969	67087969	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:67087969delT	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	67243561	67243562	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:67243561_67243562delTT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	68576312	68576312	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:68576312delT								PCDH9 (771844 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	69311145	69311145	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:69311145delA								None (None upstream) : KLHL1 (963581 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	69724115	69724115	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:69724115delT								None (None upstream) : KLHL1 (550611 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	71361480	71361480	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:71361480delA								ATXN8OS (647595 upstream) : DACH1 (650618 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	71706151	71706152	+	IGR	DEL	AG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:71706151_71706152delAG								ATXN8OS (992266 upstream) : DACH1 (305946 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	72909706	72909706	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:72909706delG								DACH1 (468376 upstream) : C13orf37 (372789 downstream)																																			---	---	---	---
DIS3	22894	broad.mit.edu	37	13	73347099	73347100	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73347099_73347100insA	uc001vix.3	-						DIS3_uc001viy.3_Intron|DIS3_uc001viz.2_Intron	NM_014953	NP_055768			DIS3 mitotic control isoform a						CUT catabolic process|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|rRNA catabolic process|rRNA processing	cytosol|exosome (RNase complex)|nucleolus|nucleoplasm	3'-5'-exoribonuclease activity|endonuclease activity|guanyl-nucleotide exchange factor activity|protein binding|RNA binding			central_nervous_system(1)	1		Breast(118;0.0074)|Acute lymphoblastic leukemia(28;0.0195)		GBM - Glioblastoma multiforme(99;0.000181)											Multiple Myeloma(4;0.011)			---	---	---	---
Unknown	0	broad.mit.edu	37	13	73687798	73687798	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73687798delA								KLF5 (36123 upstream) : KLF12 (572352 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	73706237	73706238	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73706237_73706238delTT								KLF5 (54562 upstream) : KLF12 (553912 downstream)																																			---	---	---	---
KLF12	11278	broad.mit.edu	37	13	74665843	74665843	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:74665843delA	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)														---	---	---	---
KLF12	11278	broad.mit.edu	37	13	74710044	74710045	+	5'Flank	INS	-	G	G	rs147277894	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:74710044_74710045insG	uc001vjf.2	-						KLF12_uc010aeq.2_5'Flank|KLF12_uc001vjg.3_5'Flank	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	74717341	74717342	+	IGR	DEL	CT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:74717341_74717342delCT								KLF12 (8947 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	75589896	75589896	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:75589896delC								KLF12 (881502 upstream) : LOC647288 (221994 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	75658295	75658296	+	IGR	DEL	GA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:75658295_75658296delGA								KLF12 (949901 upstream) : LOC647288 (153594 downstream)																																			---	---	---	---
TBC1D4	9882	broad.mit.edu	37	13	75863376	75863376	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:75863376delA	uc001vjl.1	-						TBC1D4_uc010tht.1_Intron|TBC1D4_uc010thu.1_Intron|TBC1D4_uc010aer.2_Intron|TBC1D4_uc010aes.2_Intron	NM_014832	NP_055647			TBC1 domain family, member 4							cytoplasm	Rab GTPase activator activity			ovary(4)|central_nervous_system(1)|skin(1)	6		Prostate(6;0.014)|Breast(118;0.0982)		GBM - Glioblastoma multiforme(99;0.0116)														---	---	---	---
TBC1D4	9882	broad.mit.edu	37	13	75912424	75912424	+	Intron	DEL	A	-	-	rs145261843		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:75912424delA	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)														---	---	---	---
LMO7	4008	broad.mit.edu	37	13	76408221	76408221	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76408221delA	uc001vjv.2	+						LMO7_uc010thv.1_Intron|LMO7_uc001vjt.1_Intron|LMO7_uc010thw.1_Intron|LMO7_uc001vjw.1_Intron	NM_015842	NP_056667			LIM domain only 7 isoform 2							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	76957037	76957038	+	IGR	DEL	AA	-	-	rs74477823		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76957037_76957038delAA								LMO7 (523033 upstream) : KCTD12 (497266 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	76997046	76997046	+	IGR	DEL	T	-	-	rs68074422		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76997046delT								LMO7 (563042 upstream) : KCTD12 (457258 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	77007480	77007481	+	IGR	DEL	CA	-	-	rs71711786		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77007480_77007481delCA								LMO7 (573476 upstream) : KCTD12 (446823 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	77082400	77082402	+	IGR	DEL	AGC	-	-	rs146811676		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77082400_77082402delAGC								LMO7 (648396 upstream) : KCTD12 (371902 downstream)																																			---	---	---	---
BTF3L1	690	broad.mit.edu	37	13	77503127	77503127	+	RNA	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77503127delT	uc001vkb.3	+	1		c.543delT				NR_026983				Homo sapiens basic transcription factor 3, like 1, mRNA (cDNA clone IMAGE:40013884).												0																		---	---	---	---
MYCBP2	23077	broad.mit.edu	37	13	77713625	77713625	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77713625delA	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	77834802	77834803	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77834802_77834803delAA	uc001vkf.2	-						MYCBP2_uc010aev.2_Intron	NM_015057	NP_055872			MYC binding protein 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ligase activity|protein binding|zinc ion binding			ovary(4)|breast(4)|skin(3)|lung(2)|pancreas(1)	14		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)														---	---	---	---
MYCBP2	23077	broad.mit.edu	37	13	77891087	77891088	+	Intron	INS	-	T	T	rs148018543	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77891087_77891088insT	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	78588941	78588941	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:78588941delA	uc001vks.2	+											Homo sapiens cDNA FLJ38460 fis, clone FEBRA2020801.																														---	---	---	---
Unknown	0	broad.mit.edu	37	13	80177079	80177079	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:80177079delT								NDFIP2 (46874 upstream) : SPRY2 (733035 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	80721574	80721574	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:80721574delG								NDFIP2 (591369 upstream) : SPRY2 (188540 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	80760052	80760052	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:80760052delC								NDFIP2 (629847 upstream) : SPRY2 (150062 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	80994327	80994327	+	IGR	DEL	C	-	-	rs140110701	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:80994327delC								SPRY2 (79241 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	81264731	81264732	+	IGR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:81264731_81264732insA								SPRY2 (349645 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	81893047	81893048	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:81893047_81893048delTT								SPRY2 (977961 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	82231570	82231570	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:82231570delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	82410304	82410304	+	IGR	DEL	A	-	-	rs35690537		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:82410304delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	82675275	82675275	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:82675275delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	83184006	83184007	+	IGR	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:83184006_83184007delAC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	83251591	83251591	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:83251591delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	83421216	83421217	+	IGR	INS	-	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:83421216_83421217insG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	85295788	85295788	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:85295788delT								SLITRK1 (839260 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	86390647	86390647	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:86390647delT								SLITRK6 (17164 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	87485771	87485771	+	IGR	DEL	A	-	-	rs68035018	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:87485771delA								None (None upstream) : SLITRK5 (839099 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	87863040	87863041	+	IGR	INS	-	TCC	TCC	rs144228386	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:87863040_87863041insTCC								None (None upstream) : SLITRK5 (461829 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	88516843	88516843	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:88516843delA								SLITRK5 (184975 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	88657121	88657121	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:88657121delT								SLITRK5 (325253 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	88675844	88675845	+	IGR	INS	-	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:88675844_88675845insG								SLITRK5 (343976 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	88932383	88932383	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:88932383delA								SLITRK5 (600515 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	89008661	89008662	+	IGR	DEL	CA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:89008661_89008662delCA								SLITRK5 (676793 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	89194106	89194107	+	IGR	INS	-	ATA	ATA	rs146759104	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:89194106_89194107insATA								SLITRK5 (862238 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	89659870	89659871	+	IGR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:89659870_89659871insA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	89705281	89705281	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:89705281delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	89778285	89778285	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:89778285delA								None (None upstream) : None (None downstream)																																			---	---	---	---
GPC5	2262	broad.mit.edu	37	13	92698375	92698375	+	Intron	DEL	A	-	-	rs67323513		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:92698375delA	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	92877100	92877101	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:92877100_92877101insT	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	93194134	93194134	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:93194134delT	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	93250642	93250642	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:93250642delT	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)																---	---	---	---
GPC6	10082	broad.mit.edu	37	13	94157685	94157686	+	Intron	INS	-	AT	AT	rs138313588	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:94157685_94157686insAT	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)																---	---	---	---
Unknown	0	broad.mit.edu	37	13	95648285	95648289	+	IGR	DEL	TAAGA	-	-	rs144122964		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95648285_95648289delTAAGA								SOX21 (283896 upstream) : ABCC4 (23795 downstream)																																			---	---	---	---
DNAJC3	5611	broad.mit.edu	37	13	96340773	96340774	+	Intron	INS	-	T	T	rs113150172		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:96340773_96340774insT	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	97317322	97317322	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:97317322delA	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	97785739	97785740	+	IGR	DEL	AT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:97785739_97785740delAT								OXGR1 (139135 upstream) : MBNL2 (88834 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	98154807	98154808	+	IGR	INS	-	AA	AA	rs144486055		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:98154807_98154808insAA								RAP2A (34556 upstream) : IPO5 (451121 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	98375839	98375840	+	IGR	DEL	GC	-	-	rs67043300		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:98375839_98375840delGC								RAP2A (255588 upstream) : IPO5 (230089 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	98459285	98459286	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:98459285_98459286insT								RAP2A (339034 upstream) : IPO5 (146643 downstream)																																			---	---	---	---
IPO5	3843	broad.mit.edu	37	13	98611426	98611427	+	Intron	DEL	AA	-	-	rs76051453		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:98611426_98611427delAA	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																		---	---	---	---
IPO5	3843	broad.mit.edu	37	13	98666535	98666535	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:98666535delA	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	98734547	98734556	+	IGR	DEL	ACACACACAA	-	-	rs71968292	byFrequency	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:98734547_98734556delACACACACAA								IPO5 (57998 upstream) : FARP1 (60260 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	99265043	99265046	+	IGR	DEL	TCTC	-	-	rs72014127	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99265043_99265046delTCTC								STK24 (35647 upstream) : SLC15A1 (71011 downstream)																																			---	---	---	---
DOCK9	23348	broad.mit.edu	37	13	99450776	99450787	+	Intron	DEL	CCTGAAGACGAC	-	-	rs11275115		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99450776_99450787delCCTGAAGACGAC	uc001vnt.2	-						DOCK9_uc001vnw.2_Intron|DOCK9_uc001vnq.2_Intron|DOCK9_uc001vnr.2_Intron|DOCK9_uc010tin.1_Intron|DOCK9_uc001vns.2_Intron|DOCK9_uc010tio.1_Intron|DOCK9_uc010tip.1_Intron	NM_015296	NP_056111			dedicator of cytokinesis 9 isoform a						blood coagulation	cytosol|endomembrane system|membrane	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			central_nervous_system(1)	1	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)																	---	---	---	---
UBAC2	337867	broad.mit.edu	37	13	99974930	99974930	+	Intron	DEL	A	-	-	rs7333266	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99974930delA	uc001voa.3	+						UBAC2_uc010tiu.1_Intron|UBAC2_uc001vob.3_Intron|UBAC2_uc010tiv.1_Intron|UBAC2_uc001vod.2_Intron|UBAC2_uc001voc.2_Intron|UBAC2_uc010tiw.1_Intron|UBAC2_uc001voh.2_Intron	NM_001144072	NP_001137544			UBA domain containing 2 isoform 1							integral to membrane				ovary(1)	1	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)																	---	---	---	---
Unknown	0	broad.mit.edu	37	13	100048380	100048380	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100048380delT								UBAC2 (9629 upstream) : TM9SF2 (105348 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	100115432	100115467	+	IGR	DEL	TGGATGGGTGGATGGATGGATGGATGGATGGATGGA	-	-	rs71772003		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100115432_100115467delTGGATGGGTGGATGGATGGATGGATGGATGGATGGA								UBAC2 (76681 upstream) : TM9SF2 (38261 downstream)																																			---	---	---	---
CLYBL	171425	broad.mit.edu	37	13	100257423	100257423	+	5'Flank	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100257423delA	uc001vok.2	+						CLYBL_uc010tix.1_5'Flank|CLYBL_uc010tiy.1_5'Flank	NM_206808	NP_996531			citrate lyase beta like precursor						cellular aromatic compound metabolic process	citrate lyase complex|mitochondrion	citrate (pro-3S)-lyase activity|metal ion binding				0	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)																	---	---	---	---
CLYBL	171425	broad.mit.edu	37	13	100322285	100322285	+	Intron	DEL	A	-	-	rs66460427		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100322285delA	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	100388847	100388847	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100388847delA	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	100417738	100417738	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100417738delT	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	100456724	100456724	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100456724delT	uc001vok.2	+						CLYBL_uc010tix.1_Intron|CLYBL_uc010tiy.1_Intron	NM_206808	NP_996531			citrate lyase beta like precursor						cellular aromatic compound metabolic process	citrate lyase complex|mitochondrion	citrate (pro-3S)-lyase activity|metal ion binding				0	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)																	---	---	---	---
PCCA	5095	broad.mit.edu	37	13	100744342	100744342	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100744342delT	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	100832000	100832001	+	Intron	DEL	TG	-	-	rs71800042		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100832000_100832001delTG	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	100912633	100912634	+	Intron	INS	-	TG	TG	rs138371283	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100912633_100912634insTG	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)													---	---	---	---
NALCN	259232	broad.mit.edu	37	13	101952718	101952719	+	Intron	INS	-	TTCC	TTCC	rs560750	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101952718_101952719insTTCC	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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	13	102086288	102086291	+	IGR	DEL	TTTT	-	-	rs34493187		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:102086288_102086291delTTTT								NALCN (17445 upstream) : ITGBL1 (18675 downstream)																																			---	---	---	---
ITGBL1	9358	broad.mit.edu	37	13	102345962	102345963	+	Intron	INS	-	TCTG	TCTG			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:102345962_102345963insTCTG	uc001vpb.2	+						ITGBL1_uc010agb.2_Intron|ITGBL1_uc001vpc.3_Intron	NM_004791	NP_004782			integrin, beta-like 1 (with EGF-like repeat						cell-matrix adhesion|integrin-mediated signaling pathway	extracellular region|integrin complex	binding|receptor activity			ovary(1)|skin(1)	2	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)																	---	---	---	---
Unknown	0	broad.mit.edu	37	13	103184075	103184075	+	IGR	DEL	A	-	-	rs79599030		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103184075delA								FGF14 (129951 upstream) : TPP2 (65211 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	103615172	103615173	+	IGR	DEL	TT	-	-	rs143377549		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103615172_103615173delTT								LOC121952 (66789 upstream) : SLC10A2 (81177 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	103683950	103683951	+	IGR	INS	-	A	A	rs141906938	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103683950_103683951insA								LOC121952 (135567 upstream) : SLC10A2 (12399 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	103797016	103797017	+	IGR	INS	-	T	T	rs34566258		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103797016_103797017insT								SLC10A2 (77820 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	104621315	104621315	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:104621315delT								SLC10A2 (902119 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	104699414	104699414	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:104699414delT								SLC10A2 (980218 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	105654679	105654679	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:105654679delT								None (None upstream) : DAOA (463537 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	106313005	106313005	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:106313005delA								DAOA (169623 upstream) : EFNB2 (829093 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	107054111	107054111	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:107054111delA								DAOA (910729 upstream) : EFNB2 (87987 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	107360362	107360362	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:107360362delT								ARGLU1 (139848 upstream) : FAM155A (460518 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	107808362	107808363	+	IGR	INS	-	TTCC	TTCC	rs71636860		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:107808362_107808363insTTCC								ARGLU1 (587848 upstream) : FAM155A (12517 downstream)																																			---	---	---	---
FAM155A	728215	broad.mit.edu	37	13	108437089	108437089	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:108437089delA	uc001vql.2	-							NM_001080396	NP_001073865			family with sequence similarity 155, member A							integral to membrane	binding			skin(1)	1																		---	---	---	---
MYO16	23026	broad.mit.edu	37	13	109680330	109680331	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:109680330_109680331insA	uc001vqt.1	+						MYO16_uc010agk.1_Intron|MYO16_uc001vqu.1_Intron|MYO16_uc010tjh.1_Intron	NM_015011	NP_055826			myosin heavy chain Myr 8						cerebellum development|negative regulation of cell proliferation|negative regulation of S phase of mitotic cell cycle	myosin complex|nucleoplasm|perinuclear region of cytoplasm|plasma membrane	actin filament binding|ATP binding|motor activity			ovary(6)|large_intestine(1)|kidney(1)|breast(1)|central_nervous_system(1)	10	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)															---	---	---	---
COL4A1	1282	broad.mit.edu	37	13	110888581	110888581	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110888581delA	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)															---	---	---	---
CARS2	79587	broad.mit.edu	37	13	111353420	111353421	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111353420_111353421insT	uc001vrd.2	-						CARS2_uc010tjm.1_Intron	NM_024537	NP_078813			cysteinyl-tRNA synthetase 2, mitochondrial						cysteinyl-tRNA aminoacylation	cytosol|mitochondrial matrix	ATP binding|cysteine-tRNA ligase activity|metal ion binding				0	all_lung(23;3.61e-05)|Lung NSC(43;0.00144)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148)		BRCA - Breast invasive adenocarcinoma(86;0.163)		L-Cysteine(DB00151)													---	---	---	---
Unknown	0	broad.mit.edu	37	13	111472658	111472658	+	5'Flank	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111472658delC	uc001vrj.1	+											full-length cDNA clone CS0DH004YB16 of T cells (Jurkat cell line) of Homo sapiens (human).																														---	---	---	---
ARHGEF7	8874	broad.mit.edu	37	13	111841989	111841989	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111841989delC	uc001vrs.2	+						ARHGEF7_uc001vrr.2_Intron|ARHGEF7_uc001vrt.2_Intron|ARHGEF7_uc010tjn.1_Intron|ARHGEF7_uc001vru.1_Intron|ARHGEF7_uc001vrv.3_Intron|ARHGEF7_uc001vrw.3_Intron|ARHGEF7_uc001vrx.3_Intron	NM_001113511	NP_001106983			PAK-interacting exchange factor beta isoform c						apoptosis|epidermal growth factor receptor signaling pathway|induction of apoptosis by extracellular signals|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	protein binding|Rho guanyl-nucleotide exchange factor activity			ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1)	7	all_lung(23;3.96e-05)|Lung NSC(43;0.00156)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.188)															---	---	---	---
Unknown	0	broad.mit.edu	37	13	112805951	112805951	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:112805951delA								SOX1 (79931 upstream) : C13orf28 (224718 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	113609605	113609605	+	Intron	DEL	C	-	-	rs34071000		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113609605delC	uc001vso.2	+											Homo sapiens cDNA clone IMAGE:5185971, partial cds.																														---	---	---	---
GRTP1	79774	broad.mit.edu	37	13	113986608	113986609	+	Intron	INS	-	CA	CA	rs146797859	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113986608_113986609insCA	uc001vtn.2	-						GRTP1_uc010tkb.1_Intron|GRTP1_uc010tkc.1_Intron	NM_024719	NP_078995			growth hormone regulated TBC protein 1							intracellular	Rab GTPase activator 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;0.0314)|all_epithelial(44;0.011)|all_lung(25;0.0271)|Lung NSC(25;0.0978)|Breast(118;0.188)	all cancers(43;0.025)|GBM - Glioblastoma multiforme(44;0.206)|Epithelial(84;0.246)															---	---	---	---
ADPRHL1	113622	broad.mit.edu	37	13	114097762	114097762	+	Intron	DEL	A	-	-	rs112291276		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114097762delA	uc001vtq.1	-						ADPRHL1_uc001vtp.1_Intron	NM_138430	NP_612439			ADP-ribosylhydrolase like 1 isoform 1						protein de-ADP-ribosylation		ADP-ribosylarginine hydrolase activity|magnesium ion binding				0	Lung NSC(43;0.0161)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0395)|all_epithelial(44;0.011)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	all cancers(43;0.0195)|GBM - Glioblastoma multiforme(44;0.116)															---	---	---	---
TFDP1	7027	broad.mit.edu	37	13	114289228	114289229	+	Intron	DEL	GT	-	-	rs4150800	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114289228_114289229delGT	uc001vtw.2	+						TFDP1_uc010tkd.1_Intron|TFDP1_uc010tke.1_Intron|TFDP1_uc001vty.3_Intron|TFDP1_uc001vtx.2_Intron	NM_007111	NP_009042			transcription factor Dp-1						cell proliferation|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|regulation of transcription from RNA polymerase II promoter	transcription factor complex	DNA binding|protein domain specific binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding			lung(4)|ovary(2)|skin(1)	7	Lung NSC(43;0.0113)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.132)|all_epithelial(44;0.0731)|all_lung(25;0.149)|Breast(118;0.153)	all cancers(43;0.0576)												TSP Lung(29;0.18)			---	---	---	---
Unknown	0	broad.mit.edu	37	14	19024831	19024832	+	IGR	INS	-	G	G	rs149077501	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19024831_19024832insG								None (None upstream) : OR11H12 (352762 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	19075446	19075446	+	IGR	DEL	T	-	-	rs111314972		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19075446delT								None (None upstream) : OR11H12 (302148 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	19098294	19098294	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19098294delA								None (None upstream) : OR11H12 (279300 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	19119596	19119596	+	IGR	DEL	A	-	-	rs78656327		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19119596delA								None (None upstream) : OR11H12 (257998 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	19402783	19402783	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19402783delT								OR11H12 (24211 upstream) : POTEG (150582 downstream)																																			---	---	---	---
POTEG	404785	broad.mit.edu	37	14	19554007	19554008	+	Intron	INS	-	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19554007_19554008insG	uc001vuz.1	+						POTEG_uc001vva.1_Intron|POTEG_uc010ahc.1_Intron	NM_001005356	NP_001005356			POTE ankyrin domain family, member G											ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	19794208	19794208	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19794208delA								POTEG (209266 upstream) : P704P (189746 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	20184761	20184762	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20184761_20184762insT								P704P (164489 upstream) : OR4Q3 (30825 downstream)																																			---	---	---	---
TTC5	91875	broad.mit.edu	37	14	20766131	20766131	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20766131delG	uc001vwt.2	-						TTC5_uc001vwu.2_Intron	NM_138376	NP_612385			tetratricopeptide repeat domain 5						DNA repair	cytoplasm|nucleus	binding			ovary(1)	1	all_cancers(95;0.00092)		Epithelial(56;1.1e-06)|all cancers(55;8.07e-06)	GBM - Glioblastoma multiforme(265;0.0106)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	20952720	20952721	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20952720_20952721delAA								PNP (7474 upstream) : RNASE10 (20975 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	21185124	21185124	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21185124delA								RNASE4 (16367 upstream) : EDDM3A (14736 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	21306637	21306638	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21306637_21306638insT								RNASE1 (35601 upstream) : RNASE3 (52924 downstream)																																			---	---	---	---
METT11D1	64745	broad.mit.edu	37	14	21460882	21460883	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21460882_21460883delTT	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	21755185	21755185	+	5'Flank	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21755185delA	uc001wag.2	+							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)														---	---	---	---
C14orf93	60686	broad.mit.edu	37	14	23457344	23457344	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23457344delT	uc001wib.1	-						C14orf93_uc001wic.1_Intron|C14orf93_uc001wid.1_Intron|C14orf93_uc001wig.2_Intron|C14orf93_uc001wih.2_Intron|C14orf93_uc001wie.2_Intron|C14orf93_uc001wia.3_Intron|C14orf93_uc001wif.2_Intron	NM_021944	NP_068763			hypothetical protein LOC60686 precursor							extracellular region				ovary(1)	1	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.0127)														---	---	---	---
SLC7A8	23428	broad.mit.edu	37	14	23642865	23642865	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23642865delT	uc001wiz.2	-						SLC7A8_uc010akj.2_Intron	NM_012244	NP_036376			solute carrier family 7 (cationic amino acid						blood coagulation|cellular amino acid metabolic process|leukocyte migration|metal ion homeostasis|response to toxin	basolateral plasma membrane|cytoplasm|integral to plasma membrane	neutral amino acid transmembrane transporter activity|organic cation transmembrane transporter activity|peptide antigen binding|protein binding|toxin transporter activity			ovary(1)	1	all_cancers(95;4.6e-05)			GBM - Glioblastoma multiforme(265;0.00809)	L-Alanine(DB00160)|L-Glutamine(DB00130)|L-Phenylalanine(DB00120)													---	---	---	---
Unknown	0	broad.mit.edu	37	14	23695990	23695990	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23695990delT								SLC7A8 (43141 upstream) : HOMEZ (46854 downstream)																																			---	---	---	---
MYH6	4624	broad.mit.edu	37	14	23868776	23868777	+	Intron	DEL	TA	-	-	rs403739	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23868776_23868777delTA	uc001wjv.2	-							NM_002471	NP_002462			myosin heavy chain 6						adult heart development|atrial cardiac muscle tissue morphogenesis|cardiac muscle fiber development|in utero embryonic development|muscle filament sliding|regulation of ATPase activity|regulation of blood pressure|regulation of heart rate|regulation of the force of heart contraction|sarcomere organization|striated muscle contraction|ventricular cardiac muscle tissue morphogenesis|visceral muscle development	cytosol|focal adhesion|muscle myosin complex|myosin filament|nucleus|sarcomere	actin binding|actin-dependent ATPase activity|ATP binding|calmodulin binding|microfilament motor activity|protein kinase binding|structural constituent of muscle			pancreas(2)|ovary(1)|skin(1)	4	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)														---	---	---	---
DHRS2	10202	broad.mit.edu	37	14	24100758	24100758	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24100758delC	uc010aku.1	+											SubName: Full=Dehydrogenase/reductase (SDR family) member 2 isoform 2 variant; Flags: Fragment;						C21-steroid hormone metabolic process|cellular response to oxidative stress|myeloid dendritic cell differentiation|negative regulation of apoptosis|negative regulation of cell proliferation|response to toxin	mitochondrion|nuclear envelope	binding|carbonyl reductase (NADPH) activity			large_intestine(1)|ovary(1)	2				GBM - Glioblastoma multiforme(265;0.00659)														---	---	---	---
DHRS4	10901	broad.mit.edu	37	14	24446438	24446438	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24446438delT	uc001wlc.3	+						DHRS4L2_uc001wld.3_Intron|DHRS4L2_uc001wle.3_Intron|uc001wlf.2_Intron|DHRS4L2_uc001wlg.3_Intron|DHRS4L2_uc001wlh.3_Intron	NM_021004	NP_066284			peroxisomal short-chain alcohol dehydrogenase							mitochondrion|nuclear membrane|peroxisome	binding|carbonyl reductase (NADPH) activity			ovary(1)	1				GBM - Glioblastoma multiforme(265;0.00962)	Vitamin A(DB00162)													---	---	---	---
REC8	9985	broad.mit.edu	37	14	24645280	24645280	+	Intron	DEL	T	-	-	rs112279022		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24645280delT	uc001wmr.2	+						REC8_uc001wms.2_Intron	NM_005132	NP_005123			REC8 homolog						mitotic metaphase/anaphase transition|mitotic prometaphase|reciprocal meiotic recombination|sister chromatid cohesion	nucleoplasm					0				GBM - Glioblastoma multiforme(265;0.00839)														---	---	---	---
ADCY4	196883	broad.mit.edu	37	14	24799926	24799926	+	Intron	DEL	C	-	-	rs76270919		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24799926delC	uc001wov.2	-						ADCY4_uc001wow.2_Intron|ADCY4_uc010toh.1_Intron|ADCY4_uc001wox.2_Intron|ADCY4_uc001woy.2_Intron	NM_139247	NP_640340			adenylate cyclase 4						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	cytoplasm|integral to membrane|plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding|protein binding			ovary(1)|lung(1)|pancreas(1)	3				GBM - Glioblastoma multiforme(265;0.0192)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	25063032	25063033	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:25063032_25063033delTT								CTSG (17566 upstream) : GZMH (12660 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	25771764	25771764	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:25771764delT								STXBP6 (252593 upstream) : None (None downstream)																																			---	---	---	---
NOVA1	4857	broad.mit.edu	37	14	26969710	26969711	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:26969710_26969711insA	uc001wpy.2	-						NOVA1_uc001wpz.2_Intron|NOVA1_uc001wqa.2_Intron|NOVA1_uc001wqb.2_Intron	NM_002515	NP_002506			neuro-oncological ventral antigen 1 isoform 1						locomotory behavior|RNA splicing|synaptic transmission	nucleus	RNA binding			skin(2)|upper_aerodigestive_tract(1)|breast(1)|liver(1)	5				GBM - Glioblastoma multiforme(265;0.0135)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	27936564	27936564	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:27936564delA	uc010amc.1	-											Homo sapiens cDNA clone IMAGE:40107853.																														---	---	---	---
Unknown	0	broad.mit.edu	37	14	29787813	29787813	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:29787813delA								C14orf23 (523814 upstream) : PRKD1 (257876 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	30007213	30007214	+	IGR	DEL	GT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:30007213_30007214delGT								C14orf23 (743214 upstream) : PRKD1 (38475 downstream)																																			---	---	---	---
PRKD1	5587	broad.mit.edu	37	14	30100387	30100387	+	Intron	DEL	A	-	-	rs115860380	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:30100387delA	uc001wqh.2	-							NM_002742	NP_002733			protein kinase D1						cell proliferation|intracellular signal transduction|sphingolipid metabolic process	cytosol|integral to plasma membrane	ATP binding|metal ion binding|protein binding|protein kinase C activity			lung(3)|large_intestine(2)|ovary(2)|skin(1)	8	Hepatocellular(127;0.0604)		LUAD - Lung adenocarcinoma(48;0.00527)|Lung(238;0.0252)	GBM - Glioblastoma multiforme(265;0.00888)														---	---	---	---
PRKD1	5587	broad.mit.edu	37	14	30258592	30258593	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:30258592_30258593insT	uc001wqh.2	-							NM_002742	NP_002733			protein kinase D1						cell proliferation|intracellular signal transduction|sphingolipid metabolic process	cytosol|integral to plasma membrane	ATP binding|metal ion binding|protein binding|protein kinase C activity			lung(3)|large_intestine(2)|ovary(2)|skin(1)	8	Hepatocellular(127;0.0604)		LUAD - Lung adenocarcinoma(48;0.00527)|Lung(238;0.0252)	GBM - Glioblastoma multiforme(265;0.00888)														---	---	---	---
PRKD1	5587	broad.mit.edu	37	14	30375739	30375739	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:30375739delA	uc001wqh.2	-							NM_002742	NP_002733			protein kinase D1						cell proliferation|intracellular signal transduction|sphingolipid metabolic process	cytosol|integral to plasma membrane	ATP binding|metal ion binding|protein binding|protein kinase C activity			lung(3)|large_intestine(2)|ovary(2)|skin(1)	8	Hepatocellular(127;0.0604)		LUAD - Lung adenocarcinoma(48;0.00527)|Lung(238;0.0252)	GBM - Glioblastoma multiforme(265;0.00888)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	31240854	31240854	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31240854delT								SCFD1 (35836 upstream) : COCH (102887 downstream)																																			---	---	---	---
STRN3	29966	broad.mit.edu	37	14	31368948	31368948	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31368948delC	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	31513866	31513867	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31513866_31513867delAA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	31755265	31755266	+	IGR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31755265_31755266insA								HECTD1 (78350 upstream) : HEATR5A (5729 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	31957688	31957689	+	IGR	DEL	AG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31957688_31957689delAG								HEATR5A (31008 upstream) : NUBPL (72902 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	32019217	32019217	+	IGR	DEL	T	-	-	rs112510915		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:32019217delT								HEATR5A (92537 upstream) : NUBPL (11374 downstream)																																			---	---	---	---
NUBPL	80224	broad.mit.edu	37	14	32319999	32319999	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:32319999delT	uc001wrk.3	+						NUBPL_uc010amj.2_Intron|NUBPL_uc010tpl.1_Intron	NM_025152	NP_079428			nucleotide binding protein-like						mitochondrial respiratory chain complex I assembly|mitochondrion morphogenesis	mitochondrion	4 iron, 4 sulfur cluster binding|ATP binding|metal ion binding				0	Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.214)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0677)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.0102)														---	---	---	---
ARHGAP5	394	broad.mit.edu	37	14	32615161	32615162	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:32615161_32615162insT	uc001wrl.2	+						ARHGAP5_uc001wrm.2_Intron|ARHGAP5_uc001wrn.2_Intron|ARHGAP5_uc001wro.2_Intron|ARHGAP5_uc001wrp.2_Intron	NM_001173	NP_001025226			Rho GTPase activating protein 5 isoform b						cell adhesion|Rho protein signal transduction	cytosol|membrane	GTP binding|GTPase activity|Rho GTPase activator activity|SH2 domain binding			ovary(4)|central_nervous_system(1)	5	Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.186)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0952)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00566)														---	---	---	---
AKAP6	9472	broad.mit.edu	37	14	32820769	32820769	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:32820769delA	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	33245501	33245501	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:33245501delT	uc001wrq.2	+						uc001wrr.2_RNA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	33383334	33383336	+	IGR	DEL	ATC	-	-	rs3057232	byFrequency	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:33383334_33383336delATC								AKAP6 (81067 upstream) : NPAS3 (25123 downstream)																																			---	---	---	---
NPAS3	64067	broad.mit.edu	37	14	33446820	33446820	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:33446820delC	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)														---	---	---	---
SNX6	58533	broad.mit.edu	37	14	35039269	35039270	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35039269_35039270delTT	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	35277727	35277727	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35277727delA	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)														---	---	---	---
FAM177A1	283635	broad.mit.edu	37	14	35542289	35542289	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35542289delT	uc001wsp.2	+						FAM177A1_uc001wsq.2_Intron	NM_001079519	NP_001072987			hypothetical protein LOC283635 isoform 2												0																		---	---	---	---
PPP2R3C	55012	broad.mit.edu	37	14	35564881	35564881	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35564881delA	uc001wss.2	-						PPP2R3C_uc001wst.2_Intron|PPP2R3C_uc010tpr.1_Intron|PPP2R3C_uc001wsu.2_Intron	NM_017917	NP_060387			serine/threonine-protein phosphatase 2A							centrosome|nucleus	calcium ion binding			ovary(1)	1	Breast(36;0.0545)|Hepatocellular(127;0.158)|Prostate(35;0.184)		Lung(238;8.62e-06)|LUAD - Lung adenocarcinoma(48;1.42e-05)|Epithelial(34;0.0177)|all cancers(34;0.0491)	GBM - Glioblastoma multiforme(112;0.0803)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	35980962	35980963	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35980962_35980963delTT								NFKBIA (107002 upstream) : INSM2 (22285 downstream)																																			---	---	---	---
RALGAPA1	253959	broad.mit.edu	37	14	36093802	36093804	+	Intron	DEL	AAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:36093802_36093804delAAA	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	36137689	36137689	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:36137689delA	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	36174697	36174697	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:36174697delT	uc001wti.2	-						RALGAPA1_uc001wtj.2_Intron|RALGAPA1_uc010tpv.1_Intron|RALGAPA1_uc010tpw.1_Intron|RALGAPA1_uc001wtk.1_Intron	NM_014990	NP_055805			Ral GTPase activating protein, alpha subunit 1						activation of Ral GTPase activity	cytosol|mitochondrion|nucleus	protein heterodimerization activity|Ral GTPase activator activity			ovary(3)|breast(1)	4																		---	---	---	---
MBIP	51562	broad.mit.edu	37	14	36770037	36770037	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:36770037delA	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)														---	---	---	---
MIPOL1	145282	broad.mit.edu	37	14	37667786	37667786	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:37667786delT	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	39217017	39217018	+	IGR	DEL	CA	-	-	rs79489019	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39217017_39217018delCA								CLEC14A (491443 upstream) : SEC23A (284105 downstream)																																			---	---	---	---
SIP1	8487	broad.mit.edu	37	14	39597689	39597690	+	Intron	INS	-	T	T	rs149334273		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39597689_39597690insT	uc001wuq.2	+						SIP1_uc001wur.2_Intron|SIP1_uc001wus.2_Intron|SIP1_uc010amx.2_Intron	NM_003616	NP_003607			SMN-interacting protein 1 isoform alpha						ncRNA metabolic process|spliceosomal snRNP assembly|spliceosome assembly	Cajal body|cytosol|spliceosomal complex	protein binding				0	Hepatocellular(127;0.213)		Lung(238;0.00047)|LUAD - Lung adenocarcinoma(48;0.000565)	GBM - Glioblastoma multiforme(112;0.0121)														---	---	---	---
CTAGE5	4253	broad.mit.edu	37	14	39737659	39737659	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39737659delA	uc001wvg.3	+						CTAGE5_uc010tqe.1_Intron|CTAGE5_uc001wuz.3_Intron|CTAGE5_uc001wuy.3_Intron|uc001wvd.2_5'Flank|CTAGE5_uc001wvb.3_Intron|CTAGE5_uc001wvc.3_Intron|CTAGE5_uc001wva.3_Intron|CTAGE5_uc001wve.1_Intron|CTAGE5_uc001wvh.3_Intron|CTAGE5_uc001wvf.3_Intron|CTAGE5_uc001wvi.3_Intron|CTAGE5_uc010amz.2_Intron	NM_005930	NP_005921			CTAGE family, member 5 isoform 1								enzyme activator activity|protein binding				0	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0475)														---	---	---	---
CTAGE5	4253	broad.mit.edu	37	14	39784041	39784042	+	Intron	DEL	TA	-	-	rs2415540	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39784041_39784042delTA	uc001wvg.3	+						CTAGE5_uc010tqe.1_Intron|CTAGE5_uc001wuz.3_Intron|CTAGE5_uc001wuy.3_Intron|CTAGE5_uc001wvb.3_Intron|CTAGE5_uc001wvc.3_Intron|CTAGE5_uc001wva.3_Intron|CTAGE5_uc001wvh.3_Intron|CTAGE5_uc001wvf.3_Intron|CTAGE5_uc001wvi.3_Intron|CTAGE5_uc010amz.2_Intron|CTAGE5_uc001wvj.3_Intron	NM_005930	NP_005921			CTAGE family, member 5 isoform 1								enzyme activator activity|protein binding				0	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0475)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	39833569	39833569	+	IGR	DEL	A	-	-	rs79621028		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39833569delA								CTAGE5 (13174 upstream) : FBXO33 (33309 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	41226971	41226971	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:41226971delT								None (None upstream) : LRFN5 (849793 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	41513306	41513306	+	IGR	DEL	G	-	-	rs67382036		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:41513306delG								None (None upstream) : LRFN5 (563458 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	41916103	41916104	+	IGR	DEL	TG	-	-	rs71955969		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:41916103_41916104delTG								None (None upstream) : LRFN5 (160660 downstream)																																			---	---	---	---
LRFN5	145581	broad.mit.edu	37	14	42318646	42318646	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:42318646delA	uc001wvm.2	+						LRFN5_uc010ana.2_Intron	NM_152447	NP_689660			leucine rich repeat and fibronectin type III							integral to membrane				ovary(5)|pancreas(2)|central_nervous_system(1)	8			LUAD - Lung adenocarcinoma(50;0.0223)|Lung(238;0.0728)	GBM - Glioblastoma multiforme(112;0.00847)											HNSCC(30;0.082)			---	---	---	---
Unknown	0	broad.mit.edu	37	14	44161055	44161055	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:44161055delT								None (None upstream) : FSCB (812300 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	44330824	44330824	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:44330824delT								None (None upstream) : FSCB (642531 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	44546597	44546598	+	IGR	DEL	TT	-	-	rs58499747	byFrequency;by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:44546597_44546598delTT								None (None upstream) : FSCB (426757 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	44708915	44708915	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:44708915delT								None (None upstream) : FSCB (264440 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	44710838	44710843	+	IGR	DEL	CGCGCG	-	-	rs113524989		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:44710838_44710843delCGCGCG								None (None upstream) : FSCB (262512 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	45132682	45132682	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45132682delA								FSCB (156183 upstream) : C14orf28 (233825 downstream)																																			---	---	---	---
KLHL28	54813	broad.mit.edu	37	14	45398007	45398007	+	3'UTR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45398007delT	uc001wvq.2	-	5					KLHL28_uc001wvr.2_3'UTR	NM_017658	NP_060128			BTB (POZ) domain containing 5											ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	46549255	46549255	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:46549255delT								C14orf106 (826650 upstream) : RPL10L (570967 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	46653889	46653889	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:46653889delA								C14orf106 (931284 upstream) : RPL10L (466333 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	47139093	47139093	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:47139093delA								RPL10L (18065 upstream) : MDGA2 (169737 downstream)																																			---	---	---	---
SDCCAG1	9147	broad.mit.edu	37	14	50198892	50198892	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50198892delT	uc010anj.1	-						KLHDC1_uc001www.2_Intron|KLHDC1_uc010tqg.1_Intron|KLHDC1_uc010tqh.1_Intron	NM_004713	NP_004704			serologically defined colon cancer antigen 1							cytoplasm|nucleus					0	all_epithelial(31;0.000822)|Breast(41;0.0117)	all_lung(585;1.02e-05)		OV - Ovarian serous cystadenocarcinoma(311;5.99e-34)														---	---	---	---
MAP4K5	11183	broad.mit.edu	37	14	50902053	50902053	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50902053delT	uc001wya.2	-						MAP4K5_uc001wyb.2_Intron	NM_006575	NP_006566			mitogen-activated protein kinase kinase kinase						activation of JUN kinase activity	cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			large_intestine(1)	1	all_epithelial(31;0.000415)|Breast(41;0.0102)																	---	---	---	---
FRMD6	122786	broad.mit.edu	37	14	52111106	52111107	+	Intron	DEL	CT	-	-	rs56168764		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52111106_52111107delCT	uc001wzb.2	+							NM_001042481	NP_001035946			FERM domain containing 6							cytoskeleton|mitochondrion|plasma membrane	binding			ovary(1)|breast(1)|central_nervous_system(1)	3	all_epithelial(31;0.0163)|Breast(41;0.089)																	---	---	---	---
Unknown	0	broad.mit.edu	37	14	52303431	52303431	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52303431delA								FRMD6 (105989 upstream) : GNG2 (10521 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	52699763	52699763	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52699763delT								NID2 (163817 upstream) : PTGDR (34668 downstream)																																			---	---	---	---
ERO1L	30001	broad.mit.edu	37	14	53149927	53149927	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53149927delA	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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	14	53421208	53421209	+	IGR	DEL	TA	-	-	rs72315313		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53421208_53421209delTA								FERMT2 (3393 upstream) : DDHD1 (82250 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	53639061	53639061	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53639061delT								DDHD1 (19015 upstream) : BMP4 (777396 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	53773411	53773412	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53773411_53773412delAA								DDHD1 (153365 upstream) : BMP4 (643045 downstream)																																	OREG0022684	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	53935015	53935017	+	IGR	DEL	TTG	-	-	rs10131065	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53935015_53935017delTTG								DDHD1 (314969 upstream) : BMP4 (481440 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	54731344	54731344	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:54731344delG								BMP4 (307790 upstream) : CDKN3 (132329 downstream)																																			---	---	---	---
SAMD4A	23034	broad.mit.edu	37	14	55210862	55210862	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55210862delG	uc001xbb.2	+						SAMD4A_uc001xbc.2_Intron	NM_015589	NP_056404			sterile alpha motif domain containing 4 isoform						positive regulation of translation	cell junction|cytoplasm|dendrite|synapse|synaptosome	translation repressor activity				0																		---	---	---	---
WDHD1	11169	broad.mit.edu	37	14	55489543	55489545	+	Intron	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55489543_55489545delTTT	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																		---	---	---	---
KTN1	3895	broad.mit.edu	37	14	56080583	56080583	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56080583delA	uc001xcb.2	+						KTN1_uc001xce.2_Intron|KTN1_uc001xcc.2_Intron|KTN1_uc001xcd.2_Intron|KTN1_uc010trb.1_Intron|KTN1_uc001xcf.1_Intron	NM_182926	NP_891556			kinectin 1 isoform a						microtubule-based movement	endoplasmic reticulum membrane|integral to plasma membrane|membrane fraction				breast(3)|ovary(2)|lung(1)|central_nervous_system(1)	7								T	RET	papillary thryoid								---	---	---	---
KTN1	3895	broad.mit.edu	37	14	56104387	56104388	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56104387_56104388delAA	uc001xcb.2	+						KTN1_uc001xce.2_Intron|KTN1_uc001xcc.2_Intron|KTN1_uc001xcd.2_Intron|KTN1_uc010trb.1_Intron|KTN1_uc001xcf.1_Intron	NM_182926	NP_891556			kinectin 1 isoform a						microtubule-based movement	endoplasmic reticulum membrane|integral to plasma membrane|membrane fraction				breast(3)|ovary(2)|lung(1)|central_nervous_system(1)	7								T	RET	papillary thryoid								---	---	---	---
Unknown	0	broad.mit.edu	37	14	56460432	56460432	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56460432delT								C14orf34 (197040 upstream) : PELI2 (124661 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	56521277	56521278	+	IGR	DEL	TC	-	-	rs5808837		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56521277_56521278delTC								C14orf34 (257885 upstream) : PELI2 (63815 downstream)																																			---	---	---	---
PELI2	57161	broad.mit.edu	37	14	56758235	56758235	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56758235delA	uc001xch.2	+							NM_021255	NP_067078			pellino 2						innate immune response|MyD88-dependent toll-like receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of MAPKKK cascade|positive regulation of protein phosphorylation|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	cytosol	protein binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	56801495	56801496	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56801495_56801496delTT								PELI2 (33465 upstream) : C14orf101 (244842 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	56876806	56876806	+	IGR	DEL	T	-	-	rs111574304		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56876806delT								PELI2 (108776 upstream) : C14orf101 (169532 downstream)																																			---	---	---	---
C14orf101	54916	broad.mit.edu	37	14	57091983	57091984	+	Intron	INS	-	TA	TA			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:57091983_57091984insTA	uc001xcm.2	+						C14orf101_uc001xcj.2_Intron|C14orf101_uc001xcl.1_Intron|C14orf101_uc001xcn.2_Intron|C14orf101_uc010trf.1_Intron|C14orf101_uc001xco.2_Intron	NM_017799	NP_060269			hypothetical protein LOC54916							integral to membrane				breast(1)|central_nervous_system(1)	2				OV - Ovarian serous cystadenocarcinoma(311;0.226)														---	---	---	---
C14orf101	54916	broad.mit.edu	37	14	57100289	57100289	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:57100289delT	uc001xcm.2	+						C14orf101_uc001xcj.2_Intron|C14orf101_uc001xcl.1_Intron|C14orf101_uc001xcn.2_Intron|C14orf101_uc010trf.1_Intron|C14orf101_uc001xco.2_Intron	NM_017799	NP_060269			hypothetical protein LOC54916							integral to membrane				breast(1)|central_nervous_system(1)	2				OV - Ovarian serous cystadenocarcinoma(311;0.226)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	57208386	57208387	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:57208386_57208387delTT								C14orf101 (92156 upstream) : OTX2 (59040 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	57337975	57337980	+	Intron	DEL	GCCTTA	-	-	rs113893423		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:57337975_57337980delGCCTTA	uc001xcr.1	+											Homo sapiens cDNA clone IMAGE:5492202, partial cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	14	58200805	58200805	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58200805delG								SLC35F4 (137190 upstream) : C14orf37 (270004 downstream)																																			---	---	---	---
C14orf37	145407	broad.mit.edu	37	14	58604646	58604646	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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																		---	---	---	---
C14orf37	145407	broad.mit.edu	37	14	58727898	58727899	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58727898_58727899delTT	uc010tro.1	-						PSMA3_uc001xdj.1_Intron|PSMA3_uc001xdk.1_Intron	NM_001001872	NP_001001872			hypothetical protein LOC145407 precursor							integral to membrane	binding				0																		---	---	---	---
C14orf37	145407	broad.mit.edu	37	14	58737826	58737826	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58737826delA	uc010tro.1	-						PSMA3_uc001xdj.1_Intron|PSMA3_uc001xdk.1_Intron|uc001xdl.2_Intron	NM_001001872	NP_001001872			hypothetical protein LOC145407 precursor							integral to membrane	binding				0																		---	---	---	---
KIAA0586	9786	broad.mit.edu	37	14	58967514	58967514	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58967514delA	uc001xdv.3	+						KIAA0586_uc010trr.1_Intron|KIAA0586_uc001xdt.3_Intron|KIAA0586_uc001xdu.3_Intron|KIAA0586_uc010trs.1_Intron|KIAA0586_uc010trt.1_Intron	NM_014749	NP_055564			talpid3 protein											ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	59230573	59230573	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:59230573delT								DACT1 (115537 upstream) : DAAM1 (424826 downstream)																																			---	---	---	---
DAAM1	23002	broad.mit.edu	37	14	59667170	59667170	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:59667170delT	uc001xdz.1	+						DAAM1_uc001xea.1_Intron|DAAM1_uc001xeb.1_Intron|DAAM1_uc001xdy.2_Intron	NM_014992	NP_055807			dishevelled-associated activator of						actin cytoskeleton organization	cytoplasm|plasma membrane	actin binding|Rho GTPase binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.165)														---	---	---	---
DAAM1	23002	broad.mit.edu	37	14	59732971	59732971	+	Intron	DEL	A	-	-	rs36021446		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:59732971delA	uc001xdz.1	+						DAAM1_uc001xea.1_Intron|DAAM1_uc001xeb.1_Intron	NM_014992	NP_055807			dishevelled-associated activator of						actin cytoskeleton organization	cytoplasm|plasma membrane	actin binding|Rho GTPase binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.165)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	60830688	60830688	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:60830688delC								PPM1A (64885 upstream) : C14orf39 (71987 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	61124159	61124160	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:61124159_61124160delAA								SIX1 (8004 upstream) : SIX4 (52096 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	61194711	61194712	+	IGR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:61194711_61194712insA								SIX4 (3672 upstream) : MNAT1 (6758 downstream)																																			---	---	---	---
PRKCH	5583	broad.mit.edu	37	14	61880449	61880449	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:61880449delT	uc001xfn.2	+						PRKCH_uc010tsa.1_Intron	NM_006255	NP_006246			protein kinase C, eta						intracellular signal transduction|platelet activation	cytosol|plasma membrane	ATP binding|enzyme binding|metal ion binding|protein kinase C activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|large_intestine(1)|skin(1)	6				OV - Ovarian serous cystadenocarcinoma(108;0.045)|BRCA - Breast invasive adenocarcinoma(234;0.0906)|KIRC - Kidney renal clear cell carcinoma(182;0.182)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	62084443	62084443	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:62084443delA	uc001xfp.2	+											Homo sapiens cDNA: FLJ22447 fis, clone HRC09479.																														---	---	---	---
SNAPC1	6617	broad.mit.edu	37	14	62238816	62238817	+	Intron	INS	-	T	T	rs139183513	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:62238816_62238817insT	uc001xft.2	+							NM_003082	NP_003073			small nuclear RNA activating complex,						regulation of transcription, DNA-dependent|transcription from RNA polymerase III promoter	nucleoplasm	DNA binding				0				OV - Ovarian serous cystadenocarcinoma(108;0.0639)|BRCA - Breast invasive adenocarcinoma(234;0.186)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	62702321	62702321	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:62702321delT								FLJ43390 (105089 upstream) : KCNH5 (471626 downstream)																																			---	---	---	---
KCNH5	27133	broad.mit.edu	37	14	63492573	63492573	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:63492573delA	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)														---	---	---	---
PPP2R5E	5529	broad.mit.edu	37	14	63967586	63967587	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:63967586_63967587delAA	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)														---	---	---	---
MTHFD1	4522	broad.mit.edu	37	14	64886473	64886473	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64886473delT	uc001xhb.2	+						MTHFD1_uc010aqe.2_Intron|MTHFD1_uc010aqf.2_Intron	NM_005956	NP_005947			methylenetetrahydrofolate dehydrogenase 1						folic acid metabolic process|folic acid-containing compound biosynthetic process|histidine biosynthetic process|methionine biosynthetic process|one-carbon metabolic process|purine nucleotide biosynthetic process	cytosol|mitochondrion	ATP binding|formate-tetrahydrofolate ligase activity|methenyltetrahydrofolate cyclohydrolase activity|methylenetetrahydrofolate dehydrogenase (NADP+) activity|methylenetetrahydrofolate dehydrogenase|protein binding			ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(108;8.7e-12)|all cancers(60;3.29e-11)|BRCA - Breast invasive adenocarcinoma(234;0.0488)	NADH(DB00157)|Tetrahydrofolic acid(DB00116)													---	---	---	---
C14orf50	145376	broad.mit.edu	37	14	65036462	65036462	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65036462delT	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	65181623	65181623	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65181623delA	uc001xho.1	+						PLEKHG3_uc001xhn.1_Intron	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)														---	---	---	---
FUT8	2530	broad.mit.edu	37	14	66191207	66191208	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:66191207_66191208insT	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	66383968	66383968	+	IGR	DEL	T	-	-	rs113174416		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:66383968delT								FUT8 (174007 upstream) : C14orf53 (569141 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	66509072	66509072	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:66509072delA								FUT8 (299111 upstream) : C14orf53 (444037 downstream)																																			---	---	---	---
GPHN	10243	broad.mit.edu	37	14	67039370	67039370	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:67039370delT	uc001xiy.2	+						GPHN_uc001xiw.2_Intron|GPHN_uc001xix.2_Intron|GPHN_uc010tss.1_Intron|GPHN_uc010tst.1_Intron	NM_001024218	NP_001019389			gephyrin isoform 2						Mo-molybdopterin cofactor biosynthetic process|water-soluble vitamin metabolic process	cell junction|cytoplasm|cytoskeleton|postsynaptic membrane	ATP binding|metal ion binding|nucleotidyltransferase activity			ovary(2)	2		all_cancers(7;0.0476)|all_hematologic(31;0.0116)		Epithelial(1;1.73e-08)|all cancers(60;3.15e-07)|OV - Ovarian serous cystadenocarcinoma(108;0.000275)|BRCA - Breast invasive adenocarcinoma(234;0.00323)|Colorectal(3;0.0938)|KIRC - Kidney renal clear cell carcinoma(182;0.184)				T	MLL	AL								---	---	---	---
TMEM229B	161145	broad.mit.edu	37	14	67931216	67931218	+	Intron	DEL	CTC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:67931216_67931218delCTC	uc001xjj.1	-											Homo sapiens cDNA FLJ32084 fis, clone OCBBF2000287.							integral to membrane				central_nervous_system(1)	1																		---	---	---	---
RAD51L1	5890	broad.mit.edu	37	14	68315996	68315997	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68315996_68315997delTT	uc001xkf.1	+						RAD51L1_uc010aqq.2_Intron|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	68419320	68419321	+	Intron	DEL	AA	-	-	rs76347795		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68419320_68419321delAA	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	68442818	68442818	+	Intron	DEL	T	-	-	rs11285889		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68442818delT	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	68761649	68761649	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68761649delA	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	68839072	68839073	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68839072_68839073delTT	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					---	---	---	---
Unknown	0	broad.mit.edu	37	14	69277267	69277267	+	IGR	DEL	T	-	-	rs35110169		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69277267delT								C14orf181 (14077 upstream) : ACTN1 (63574 downstream)																																			---	---	---	---
GALNTL1	57452	broad.mit.edu	37	14	69776019	69776022	+	Intron	DEL	TTTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69776019_69776022delTTTT	uc010aqu.1	+						GALNTL1_uc001xla.1_Intron|GALNTL1_uc001xlb.1_Intron	NM_020692	NP_065743			UDP-N-acetyl-alpha-D-galactosamine:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(1)|central_nervous_system(1)	2				all cancers(60;0.00793)|BRCA - Breast invasive adenocarcinoma(234;0.0174)|OV - Ovarian serous cystadenocarcinoma(108;0.0656)														---	---	---	---
GALNTL1	57452	broad.mit.edu	37	14	69786810	69786810	+	Intron	DEL	A	-	-	rs1671532	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69786810delA	uc010aqu.1	+						GALNTL1_uc001xla.1_Intron|GALNTL1_uc001xlb.1_Intron	NM_020692	NP_065743			UDP-N-acetyl-alpha-D-galactosamine:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(1)|central_nervous_system(1)	2				all cancers(60;0.00793)|BRCA - Breast invasive adenocarcinoma(234;0.0174)|OV - Ovarian serous cystadenocarcinoma(108;0.0656)														---	---	---	---
GALNTL1	57452	broad.mit.edu	37	14	69787225	69787234	+	Intron	DEL	AAAAAAAGAA	-	-	rs68043164	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69787225_69787234delAAAAAAAGAA	uc010aqu.1	+						GALNTL1_uc001xla.1_Intron|GALNTL1_uc001xlb.1_Intron	NM_020692	NP_065743			UDP-N-acetyl-alpha-D-galactosamine:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(1)|central_nervous_system(1)	2				all cancers(60;0.00793)|BRCA - Breast invasive adenocarcinoma(234;0.0174)|OV - Ovarian serous cystadenocarcinoma(108;0.0656)														---	---	---	---
SLC39A9	55334	broad.mit.edu	37	14	69916911	69916911	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69916911delA	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	70737543	70737548	+	IGR	DEL	TTTTTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70737543_70737548delTTTTTT								ADAM21P1 (23025 upstream) : COX16 (54251 downstream)																																			---	---	---	---
MED6	10001	broad.mit.edu	37	14	71066183	71066184	+	Intron	INS	-	A	A	rs34442774		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71066183_71066184insA	uc001xmf.2	-						MED6_uc010tth.1_Intron|MED6_uc010tti.1_Intron|MED6_uc001xmg.1_Intron|MED6_uc010ttj.1_Intron	NM_005466	NP_005457			mediator of RNA polymerase II transcription,						positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex	transcription coactivator activity				0				all cancers(60;0.00315)|BRCA - Breast invasive adenocarcinoma(234;0.00685)|OV - Ovarian serous cystadenocarcinoma(108;0.0352)														---	---	---	---
MAP3K9	4293	broad.mit.edu	37	14	71267150	71267150	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71267150delA	uc001xmm.2	-						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)														---	---	---	---
SIPA1L1	26037	broad.mit.edu	37	14	71995830	71995831	+	5'Flank	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71995830_71995831delAA	uc001xms.2	+						SIPA1L1_uc001xmr.1_Intron|SIPA1L1_uc001xmt.2_5'Flank	NM_015556	NP_056371			signal-induced proliferation-associated 1 like						actin cytoskeleton reorganization|activation of Rap GTPase activity|regulation of dendritic spine morphogenesis	cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane|synaptosome	GTPase activator activity			ovary(3)|breast(1)	4				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)														---	---	---	---
RGS6	9628	broad.mit.edu	37	14	72519372	72519373	+	Intron	INS	-	T	T	rs111732049	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:72519372_72519373insT	uc001xna.3	+						RGS6_uc010ttn.1_Intron|RGS6_uc001xmx.3_Intron|RGS6_uc010tto.1_Intron|RGS6_uc001xmy.3_Intron	NM_004296	NP_004287			regulator of G-protein signalling 6						G-protein coupled receptor protein signaling pathway|intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|signal transducer activity			upper_aerodigestive_tract(1)|lung(1)|skin(1)	3				all cancers(60;0.00309)|BRCA - Breast invasive adenocarcinoma(234;0.0281)|STAD - Stomach adenocarcinoma(64;0.0302)|OV - Ovarian serous cystadenocarcinoma(108;0.0476)														---	---	---	---
RGS6	9628	broad.mit.edu	37	14	72769390	72769391	+	Intron	DEL	AC	-	-	rs34627833		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:72769390_72769391delAC	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)														---	---	---	---
DCAF4	26094	broad.mit.edu	37	14	73414036	73414036	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73414036delA	uc001xng.2	+						DCAF4_uc001xnj.2_Intron|DCAF4_uc010ttr.1_Intron|DCAF4_uc001xnh.2_Intron|DCAF4_uc010tts.1_Intron|DCAF4_uc010ttt.1_Intron|DCAF4_uc001xni.2_Intron|DCAF4_uc001xnk.2_Intron	NM_015604	NP_056419			DDB1 and CUL4 associated factor 4 isoform 1							CUL4 RING ubiquitin ligase complex				ovary(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
PAPLN	89932	broad.mit.edu	37	14	73714814	73714815	+	Intron	INS	-	GCGCGC	GCGCGC	rs139626596	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73714814_73714815insGCGCGC	uc010ttx.1	+						PAPLN_uc001xnw.3_Intron|PAPLN_uc010arl.2_Intron|PAPLN_uc010ttw.1_Intron|PAPLN_uc010tty.1_Intron|uc001xnx.2_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)														---	---	---	---
NUMB	8650	broad.mit.edu	37	14	73881897	73881900	+	Intron	DEL	TGCT	-	-	rs142060834		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73881897_73881900delTGCT	uc001xny.1	-						NUMB_uc001xoa.1_Intron|NUMB_uc001xnz.1_Intron|NUMB_uc001xob.1_Intron|NUMB_uc001xod.1_Intron|NUMB_uc001xoc.1_Intron|NUMB_uc010ars.1_Intron|NUMB_uc001xof.1_Intron|NUMB_uc001xog.2_Intron|NUMB_uc001xoh.1_Intron	NM_001005743	NP_001005743			numb homolog isoform 1						axon guidance|lateral ventricle development|neuroblast division in subventricular zone|positive regulation of neurogenesis	integral to plasma membrane				ovary(2)|central_nervous_system(1)|skin(1)	4				BRCA - Breast invasive adenocarcinoma(234;0.00471)|OV - Ovarian serous cystadenocarcinoma(108;0.161)														---	---	---	---
NUMB	8650	broad.mit.edu	37	14	73902714	73902714	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73902714delA	uc001xny.1	-						NUMB_uc001xoa.1_Intron|NUMB_uc001xnz.1_Intron|NUMB_uc001xob.1_Intron|NUMB_uc001xod.1_Intron|NUMB_uc001xoc.1_Intron|NUMB_uc010ars.1_Intron|NUMB_uc001xof.1_Intron|NUMB_uc001xog.2_Intron|NUMB_uc001xoh.1_Intron	NM_001005743	NP_001005743			numb homolog isoform 1						axon guidance|lateral ventricle development|neuroblast division in subventricular zone|positive regulation of neurogenesis	integral to plasma membrane				ovary(2)|central_nervous_system(1)|skin(1)	4				BRCA - Breast invasive adenocarcinoma(234;0.00471)|OV - Ovarian serous cystadenocarcinoma(108;0.161)														---	---	---	---
ACOT4	122970	broad.mit.edu	37	14	74060211	74060213	+	Intron	DEL	AAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74060211_74060213delAAA	uc001xoo.2	+							NM_152331	NP_689544			acyl-CoA thioesterase 4						acyl-CoA metabolic process|dicarboxylic acid metabolic process|long-chain fatty acid metabolic process|saturated monocarboxylic acid metabolic process|short-chain fatty acid metabolic process|succinyl-CoA metabolic process|unsaturated monocarboxylic acid metabolic process|very long-chain fatty acid metabolic process	peroxisome	carboxylesterase activity|palmitoyl-CoA hydrolase activity				0				BRCA - Breast invasive adenocarcinoma(234;0.00331)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	74093494	74093496	+	IGR	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74093494_74093496delTTT								ACOT6 (6904 upstream) : DNAL1 (18082 downstream)																																			---	---	---	---
C14orf45	80127	broad.mit.edu	37	14	74486947	74486947	+	Intron	DEL	T	-	-	rs11287731		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74486947delT	uc010tup.1	+						ENTPD5_uc010tuo.1_5'Flank	NM_025057	NP_079333			hypothetical protein LOC80127												0				BRCA - Breast invasive adenocarcinoma(234;0.00351)														---	---	---	---
ALDH6A1	4329	broad.mit.edu	37	14	74537300	74537300	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74537300delG	uc001xpo.2	-						C14orf45_uc001xpm.1_Intron|ALDH6A1_uc010asa.2_Intron|ALDH6A1_uc010tuq.1_Intron	NM_005589	NP_005580			aldehyde dehydrogenase 6A1 precursor							mitochondrial matrix|nucleus	fatty-acyl-CoA binding|malonate-semialdehyde dehydrogenase (acetylating) activity|methylmalonate-semialdehyde dehydrogenase (acylating) activity				0				BRCA - Breast invasive adenocarcinoma(234;0.00354)	NADH(DB00157)													---	---	---	---
FCF1	51077	broad.mit.edu	37	14	75183724	75183724	+	Intron	DEL	C	-	-	rs34224717		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75183724delC	uc001xqh.2	+						FCF1_uc001xqf.1_Intron|FCF1_uc001xqg.2_Intron|FCF1_uc001xqi.2_Intron	NM_015962	NP_057046			FCF1 small subunit						rRNA processing	nucleolus				ovary(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.0037)														---	---	---	---
YLPM1	56252	broad.mit.edu	37	14	75254279	75254279	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75254279delA	uc001xqj.3	+						YLPM1_uc001xql.3_Intron	NM_019589	NP_062535			YLP motif containing 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear speck				ovary(2)|pancreas(1)	3			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00162)														---	---	---	---
YLPM1	56252	broad.mit.edu	37	14	75260894	75260894	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75260894delT	uc001xqj.3	+						YLPM1_uc001xql.3_Intron	NM_019589	NP_062535			YLP motif containing 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear speck				ovary(2)|pancreas(1)	3			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00162)														---	---	---	---
NEK9	91754	broad.mit.edu	37	14	75581161	75581161	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75581161delA	uc001xrl.2	-						NEK9_uc001xrk.2_Intron	NM_033116	NP_149107			NIMA-related kinase 9						cell division|mitosis	mitochondrion|nucleus	ATP binding|metal ion binding|protein kinase binding|protein serine/threonine kinase activity			lung(2)|stomach(2)|ovary(1)	5				BRCA - Breast invasive adenocarcinoma(234;0.00718)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	75662680	75662683	+	IGR	DEL	TGAG	-	-	rs10593937		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75662680_75662683delTGAG								TMED10 (19331 upstream) : FOS (82798 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	75778836	75778836	+	IGR	DEL	T	-	-	rs72035019		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75778836delT								FOS (29901 upstream) : JDP2 (115673 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	76039887	76039888	+	IGR	INS	-	AT	AT	rs138839373	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76039887_76039888insAT								BATF (26560 upstream) : FLVCR2 (5052 downstream)																																			---	---	---	---
TTLL5	23093	broad.mit.edu	37	14	76183433	76183433	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76183433delT	uc001xrx.2	+						TTLL5_uc010ask.1_Intron|TTLL5_uc001xry.1_Intron	NM_015072	NP_055887			tubulin tyrosine ligase-like family, member 5						protein modification process|transcription, DNA-dependent	centrosome|cilium|microtubule basal body|nucleus	tubulin-tyrosine ligase activity			ovary(2)|central_nervous_system(1)	3				BRCA - Breast invasive adenocarcinoma(234;0.029)														---	---	---	---
C14orf118	55668	broad.mit.edu	37	14	76619283	76619283	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76619283delT	uc001xsh.2	+						C14orf118_uc001xsi.2_Intron|C14orf118_uc001xsj.1_Intron|C14orf118_uc001xsk.1_5'Flank|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	76885362	76885362	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76885362delT	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	77033814	77033814	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77033814delT								ESRRB (65636 upstream) : VASH1 (194421 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	77441984	77441985	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77441984_77441985delTT								C14orf166B (105339 upstream) : C14orf4 (48903 downstream)																																			---	---	---	---
TMED8	283578	broad.mit.edu	37	14	77802683	77802683	+	RNA	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77802683delA	uc010ast.1	-	7		c.2185delT				NM_213601				transmembrane emp24 protein transport domain						transport	integral to membrane					0			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0281)														---	---	---	---
ADCK1	57143	broad.mit.edu	37	14	78308910	78308912	+	Intron	DEL	TTG	-	-	rs28523792	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:78308910_78308912delTTG	uc001xui.2	+						ADCK1_uc010tvo.1_Intron|ADCK1_uc001xuj.2_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)														---	---	---	---
NRXN3	9369	broad.mit.edu	37	14	79694131	79694138	+	Intron	DEL	TCCTCCCT	-	-	rs61995409		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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	80318320	80318321	+	Intron	INS	-	A	A	rs139946946	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:80318320_80318321insA	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	80730107	80730108	+	Intron	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:80730107_80730108delAC	uc001xuw.1	+											Homo sapiens, clone IMAGE:5167652, mRNA.																														---	---	---	---
C14orf145	145508	broad.mit.edu	37	14	81206443	81206443	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81206443delT	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	81307320	81307320	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81307320delT	uc001xux.2	-						C14orf145_uc001xuz.2_Intron|C14orf145_uc001xuy.1_Intron	NM_152446	NP_689659			hypothetical protein LOC145508							centriole|spindle pole					0				BRCA - Breast invasive adenocarcinoma(234;0.0586)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	82051873	82051874	+	IGR	INS	-	AG	AG			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:82051873_82051874insAG								SEL1L (51668 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	82189267	82189267	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:82189267delC								SEL1L (189062 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	83202154	83202154	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:83202154delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	84816612	84816613	+	IGR	DEL	AG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:84816612_84816613delAG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	85281016	85281023	+	IGR	DEL	CCTCCCTC	-	-	rs76839618		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:85281016_85281023delCCTCCCTC								None (None upstream) : FLRT2 (715465 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	85620416	85620416	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:85620416delA								None (None upstream) : FLRT2 (376072 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	86096463	86096463	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:86096463delT								FLRT2 (2194 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	86867572	86867572	+	IGR	DEL	A	-	-	rs34794395		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:86867572delA								FLRT2 (773303 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	87365178	87365178	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:87365178delG								None (None upstream) : GALC (938986 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	88168256	88168256	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88168256delC								None (None upstream) : GALC (135908 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	88513124	88513124	+	Intron	DEL	C	-	-	rs7145963	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88513124delC	uc001xvw.2	+											Homo sapiens cDNA clone IMAGE:4734409.																														---	---	---	---
Unknown	0	broad.mit.edu	37	14	88549266	88549266	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88549266delA	uc001xvw.2	+											Homo sapiens cDNA clone IMAGE:4734409.																														---	---	---	---
PTPN21	11099	broad.mit.edu	37	14	88966984	88966984	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88966984delT	uc001xwv.3	-						PTPN21_uc010twc.1_Intron|PTPN21_uc010atf.1_Intron	NM_007039	NP_008970			protein tyrosine phosphatase, non-receptor type							cytoplasm|cytoskeleton	binding|protein tyrosine phosphatase activity			ovary(3)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	89522197	89522197	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89522197delA								TTC8 (177863 upstream) : FOXN3 (100320 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	90146317	90146318	+	IGR	DEL	AG	-	-	rs113438859	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:90146317_90146318delAG								FOXN3 (60823 upstream) : C14orf143 (117153 downstream)																																			---	---	---	---
TDP1	55775	broad.mit.edu	37	14	90472230	90472230	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:90472230delT	uc001xxy.2	+						TDP1_uc010atm.2_Intron|TDP1_uc001xxz.2_Intron|TDP1_uc010atn.2_Intron|TDP1_uc001xya.2_Intron|TDP1_uc001xyb.2_Intron|TDP1_uc010ato.2_Intron|TDP1_uc001xyd.1_Intron	NM_018319	NP_060789			tyrosyl-DNA phosphodiesterase 1						cell death|double-strand break repair|single strand break repair	cytoplasm|nucleus	3'-tyrosyl-DNA phosphodiesterase activity|double-stranded DNA binding|exonuclease activity|protein binding|single-stranded DNA binding			ovary(2)	2		all_cancers(154;0.185)		COAD - Colon adenocarcinoma(157;0.23)									Repair_of_DNA-protein_crosslinks					---	---	---	---
Unknown	0	broad.mit.edu	37	14	90519127	90519127	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:90519127delT								TDP1 (8021 upstream) : KCNK13 (8981 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	90935483	90935484	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:90935483_90935484insT								CALM1 (60873 upstream) : TTC7B (71449 downstream)																																			---	---	---	---
RPS6KA5	9252	broad.mit.edu	37	14	91380010	91380010	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91380010delT	uc001xys.2	-						RPS6KA5_uc010twi.1_Intron|RPS6KA5_uc001xyt.2_Intron|RPS6KA5_uc010att.1_Intron	NM_004755	NP_004746			ribosomal protein S6 kinase, polypeptide 5						axon guidance|epidermal growth factor receptor signaling pathway|histone phosphorylation|innate immune response|interleukin-1-mediated signaling pathway|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of histone acetylation|positive regulation of histone phosphorylation|positive regulation of transcription from RNA polymerase II promoter|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytoplasm|nucleoplasm	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			ovary(1)	1		all_cancers(154;0.0148)|Melanoma(154;0.099)|all_epithelial(191;0.146)		Epithelial(152;0.182)|BRCA - Breast invasive adenocarcinoma(234;0.201)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	91544095	91544095	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91544095delA								RPS6KA5 (17102 upstream) : C14orf159 (36262 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	91990786	91990791	+	IGR	DEL	TTTTTT	-	-	rs138545139		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91990786_91990791delTTTTTT								SMEK1 (13973 upstream) : C14orf184 (47997 downstream)																																			---	---	---	---
ATXN3	4287	broad.mit.edu	37	14	92534936	92534936	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92534936delT	uc001yac.3	-						ATXN3_uc010aug.2_Intron|ATXN3_uc001yad.3_Intron|ATXN3_uc010auh.2_Intron|ATXN3_uc001yae.3_Intron	NM_004993	NP_004984			ataxin 3 reference isoform						cell death|nervous system development|nucleotide-excision repair|regulation of transcription, DNA-dependent|synaptic transmission|transcription, DNA-dependent	cytoplasm|nuclear matrix|nucleoplasm	cysteine-type peptidase activity|protein binding				0		all_cancers(154;0.0768)		COAD - Colon adenocarcinoma(157;0.224)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	93368699	93368700	+	IGR	INS	-	TCTTCCTTCTCCTCCTCCTCC	TCTTCCTTCTCCTCCTCCTCC	rs146897982	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93368699_93368700insTCTTCCTTCTCCTCCTCCTCC								GOLGA5 (62395 upstream) : CHGA (20745 downstream)																																			---	---	---	---
KIAA1409	57578	broad.mit.edu	37	14	93861801	93861802	+	Intron	INS	-	GA	GA			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93861801_93861802insGA	uc001ybs.1	+							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)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	94307042	94307043	+	IGR	DEL	TC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94307042_94307043delTC								PRIMA1 (52276 upstream) : C14orf86 (64033 downstream)																																			---	---	---	---
PPP4R4	57718	broad.mit.edu	37	14	94650605	94650605	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94650605delT	uc001ycs.1	+						PPP4R4_uc001ycr.2_Intron	NM_058237	NP_478144			HEAT-like repeat-containing protein isoform 1							cytoplasm|protein serine/threonine phosphatase complex	protein binding			skin(3)|upper_aerodigestive_tract(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	95205213	95205213	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95205213delC								SERPINA13 (91883 upstream) : GSC (29348 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	96262129	96262131	+	IGR	DEL	TCT	-	-	rs143074378		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96262129_96262131delTCT								TCL1A (81596 upstream) : C14orf132 (243531 downstream)																																			---	---	---	---
ATG2B	55102	broad.mit.edu	37	14	96777214	96777214	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96777214delA	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)														---	---	---	---
ATG2B	55102	broad.mit.edu	37	14	96822741	96822741	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96822741delA	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)														---	---	---	---
ATG2B	55102	broad.mit.edu	37	14	96823105	96823105	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96823105delA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	96961175	96961175	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96961175delT								AK7 (6063 upstream) : PAPOLA (7545 downstream)																																			---	---	---	---
PAPOLA	10914	broad.mit.edu	37	14	96998599	96998599	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96998599delT	uc001yfq.2	+						PAPOLA_uc001yfp.2_Intron|PAPOLA_uc001yfr.2_Intron|PAPOLA_uc010twv.1_Intron|PAPOLA_uc010avp.2_Intron	NM_032632	NP_116021			poly(A) polymerase alpha						mRNA polyadenylation|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	cytoplasm|nucleoplasm	ATP binding|magnesium ion binding|manganese ion binding|polynucleotide adenylyltransferase activity|RNA binding				0		all_cancers(154;0.0555)|all_epithelial(191;0.149)|Melanoma(154;0.155)		COAD - Colon adenocarcinoma(157;0.213)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	97137128	97137128	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:97137128delT								PAPOLA (103682 upstream) : VRK1 (126556 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	97891388	97891388	+	IGR	DEL	A	-	-	rs72108730		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:97891388delA								VRK1 (543438 upstream) : C14orf64 (500559 downstream)																																			---	---	---	---
C14orf64	388011	broad.mit.edu	37	14	98427601	98427601	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:98427601delC	uc001yfw.2	-						C14orf64_uc001yfx.2_Intron|C14orf64_uc001yfy.2_Intron|C14orf64_uc010avq.2_Intron	NR_015430				Homo sapiens cDNA FLJ34349 fis, clone FEBRA2011063.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	98480461	98480462	+	IGR	INS	-	CTTT	CTTT	rs149441117	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:98480461_98480462insCTTT								C14orf64 (36000 upstream) : C14orf177 (697488 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	98664391	98664394	+	IGR	DEL	GTGT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:98664391_98664394delGTGT								C14orf64 (219930 upstream) : C14orf177 (513556 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	98811287	98811287	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:98811287delA								C14orf64 (366826 upstream) : C14orf177 (366663 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	99370171	99370180	+	IGR	DEL	ACACACATAC	-	-	rs66571520	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:99370171_99370180delACACACATAC								C14orf177 (186074 upstream) : BCL11B (265447 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	99437111	99437111	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:99437111delT								C14orf177 (253014 upstream) : BCL11B (198516 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	99504647	99504648	+	IGR	DEL	CA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:99504647_99504648delCA								C14orf177 (320550 upstream) : BCL11B (130979 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	100087445	100087445	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100087445delT								CCDC85C (16718 upstream) : HHIPL1 (24035 downstream)																																			---	---	---	---
HHIPL1	84439	broad.mit.edu	37	14	100123124	100123124	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100123124delA	uc010avs.2	+						HHIPL1_uc001ygl.1_Intron	NM_001127258	NP_001120730			HHIP-like protein 1 isoform a						carbohydrate metabolic process	extracellular region|membrane	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor|quinone binding|scavenger receptor activity			skin(2)	2		Melanoma(154;0.128)																---	---	---	---
EML1	2009	broad.mit.edu	37	14	100213835	100213835	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100213835delG	uc010avt.1	+							NM_004434	NP_004425			echinoderm microtubule associated protein like 1							cytoplasm|microtubule|microtubule associated complex	calcium ion binding|protein binding			large_intestine(2)|pancreas(1)|ovary(1)|skin(1)	5		Melanoma(154;0.0879)|all_epithelial(191;0.216)																---	---	---	---
EML1	2009	broad.mit.edu	37	14	100326605	100326605	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100326605delT	uc001ygs.2	+						EML1_uc010avt.1_Intron|EML1_uc010tww.1_Intron|EML1_uc001ygq.2_Intron|EML1_uc001ygr.2_Intron	NM_004434	NP_004425			echinoderm microtubule associated protein like 1							cytoplasm|microtubule|microtubule associated complex	calcium ion binding|protein binding			large_intestine(2)|pancreas(1)|ovary(1)|skin(1)	5		Melanoma(154;0.0879)|all_epithelial(191;0.216)																---	---	---	---
Unknown	0	broad.mit.edu	37	14	101483695	101483695	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101483695delA								SNORD114-31 (24050 upstream) : MIR379 (4708 downstream)																																			---	---	---	---
PPP2R5C	5527	broad.mit.edu	37	14	102274618	102274618	+	5'Flank	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102274618delA	uc001yko.2	+						PPP2R5C_uc001ykj.3_Intron|PPP2R5C_uc010txr.1_Intron|PPP2R5C_uc001ykk.2_Intron|PPP2R5C_uc010txt.1_5'Flank|PPP2R5C_uc001ykn.2_5'Flank|PPP2R5C_uc001ykp.2_5'Flank|PPP2R5C_uc010txs.1_5'Flank	NM_002719	NP_002710			gamma isoform of regulatory subunit B56, protein						DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|negative regulation of cell proliferation|proteasomal ubiquitin-dependent protein catabolic process|signal transduction	chromosome, centromeric region|nucleus|protein phosphatase type 2A complex	protein binding|protein binding|protein phosphatase type 2A regulator activity|protein phosphatase type 2A regulator activity			ovary(1)|breast(1)	2																		---	---	---	---
RAGE	5891	broad.mit.edu	37	14	102724816	102724817	+	Intron	INS	-	TTC	TTC	rs148767114	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102724816_102724817insTTC	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																		---	---	---	---
CINP	51550	broad.mit.edu	37	14	102811837	102811839	+	Intron	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102811837_102811839delTTT	uc001ylu.1	-											Homo sapiens from HeLa cyclin-dependent kinase 2 interacting protein (CINP) mRNA, complete cds.						cell cycle|cell division|DNA repair|DNA replication	nucleus	protein binding			large_intestine(1)	1																		---	---	---	---
CINP	51550	broad.mit.edu	37	14	102813756	102813756	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102813756delA	uc001ylu.1	-											Homo sapiens from HeLa cyclin-dependent kinase 2 interacting protein (CINP) mRNA, complete cds.						cell cycle|cell division|DNA repair|DNA replication	nucleus	protein binding			large_intestine(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	103029038	103029038	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103029038delA								ANKRD9 (52910 upstream) : RCOR1 (30195 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	103210854	103210854	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103210854delT								RCOR1 (13942 upstream) : TRAF3 (32962 downstream)																																			---	---	---	---
TRAF3	7187	broad.mit.edu	37	14	103248581	103248581	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103248581delT	uc001ymc.1	+						TRAF3_uc001yme.1_Intron|TRAF3_uc001ymd.1_Intron|TRAF3_uc010txy.1_Intron	NM_145725	NP_663777			TNF receptor-associated factor 3 isoform 1						apoptosis|induction of apoptosis|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production|regulation of defense response to virus|regulation of interferon-beta production|regulation of proteolysis|toll-like receptor signaling pathway|tumor necrosis factor-mediated signaling pathway	CD40 receptor complex|cytosol|endosome|internal side of plasma membrane|mitochondrion	signal transducer activity|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|lung(1)|breast(1)	3		all_cancers(154;7.87e-06)|all_epithelial(191;0.0024)		Epithelial(152;9.92e-24)|all cancers(159;2.23e-21)|OV - Ovarian serous cystadenocarcinoma(161;7.85e-12)|Colorectal(3;0.0971)														---	---	---	---
CDC42BPB	9578	broad.mit.edu	37	14	103461515	103461517	+	Intron	DEL	TCT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103461515_103461517delTCT	uc001ymi.1	-							NM_006035	NP_006026			CDC42-binding protein kinase beta						actin cytoskeleton reorganization|establishment or maintenance of cell polarity|intracellular signal transduction	cell leading edge|cell-cell junction|cytoplasm|cytoskeleton	ATP binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity			large_intestine(3)|skin(3)|lung(2)|stomach(1)|breast(1)|ovary(1)	11		Melanoma(154;0.155)		Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(2;0.0419)|Epithelial(152;0.0474)|all cancers(159;0.199)														---	---	---	---
MARK3	4140	broad.mit.edu	37	14	103905330	103905331	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103905330_103905331delAA	uc001ymz.3	+						MARK3_uc001ymx.3_Intron|MARK3_uc001ymw.3_Intron|MARK3_uc001yna.3_Intron|MARK3_uc001ymy.3_Intron|MARK3_uc010awp.2_Intron	NM_001128918	NP_001122390			MAP/microtubule affinity-regulating kinase 3								ATP binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(2)|ovary(1)|stomach(1)	4		Melanoma(154;0.155)	Epithelial(46;0.241)															---	---	---	---
MARK3	4140	broad.mit.edu	37	14	103948856	103948858	+	Intron	DEL	AAA	-	-	rs35079029		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103948856_103948858delAAA	uc001ymz.3	+						MARK3_uc001ymx.3_Intron|MARK3_uc001ymw.3_Intron|MARK3_uc001yna.3_Intron|MARK3_uc001ymy.3_Intron|MARK3_uc010awp.2_Intron|MARK3_uc010tyb.1_Intron|MARK3_uc010awq.2_Intron	NM_001128918	NP_001122390			MAP/microtubule affinity-regulating kinase 3								ATP binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(2)|ovary(1)|stomach(1)	4		Melanoma(154;0.155)	Epithelial(46;0.241)															---	---	---	---
KLC1	3831	broad.mit.edu	37	14	104139336	104139337	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104139336_104139337insT	uc001yno.2	+						KLC1_uc010tyd.1_Intron|KLC1_uc010tye.1_Intron|KLC1_uc001ynm.1_Intron|KLC1_uc001ynn.1_Intron|KLC1_uc010tyf.1_Intron|KLC1_uc001ynp.1_5'Flank|KLC1_uc001ynr.1_5'Flank|KLC1_uc010awu.1_5'Flank|KLC1_uc001ynq.1_5'Flank|KLC1_uc001yns.2_5'Flank	NM_182923	NP_891553			kinesin light chain 1 isoform 2						blood coagulation|microtubule-based movement|stress granule disassembly	cytosol|kinesin complex|microtubule	microtubule motor activity|protein binding				0		Melanoma(154;0.155)|all_epithelial(191;0.19)																---	---	---	---
PPP1R13B	23368	broad.mit.edu	37	14	104235598	104235598	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104235598delT	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)																---	---	---	---
ASPG	374569	broad.mit.edu	37	14	104575935	104575936	+	Intron	DEL	AT	-	-	rs151058850		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104575935_104575936delAT	uc001yoq.1	+						ASPG_uc001yop.1_Intron|ASPG_uc001yor.1_Intron	NM_001080464	NP_001073933			60 kDa lysophospholipase						lipid catabolic process		1-alkyl-2-acetylglycerophosphocholine esterase activity|asparaginase activity|lysophospholipase activity				0																		---	---	---	---
INF2	64423	broad.mit.edu	37	14	105327062	105327062	+	Intron	DEL	C	-	-	rs141864729		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105327062delC	uc010tyi.1	+							NM_022489	NP_071934			inverted formin 2 isoform 1						actin cytoskeleton organization	endoplasmic reticulum|nucleus|perinuclear region of cytoplasm	actin binding|Rho GTPase binding				0		all_cancers(154;0.0896)|Melanoma(154;0.155)|all_epithelial(191;0.172)	all cancers(16;0.00188)|OV - Ovarian serous cystadenocarcinoma(23;0.0191)|Epithelial(46;0.047)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.176)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	105386095	105386096	+	IGR	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105386095_105386096delTG								KIAA0284 (23009 upstream) : PLD4 (5091 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	105548288	105548288	+	IGR	DEL	A	-	-	rs111603731		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105548288delA								GPR132 (16534 upstream) : JAG2 (59789 downstream)																																			---	---	---	---
BRF1	2972	broad.mit.edu	37	14	105682190	105682191	+	Intron	DEL	CA	-	-	rs62639549		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105682190_105682191delCA	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	105733802	105733803	+	Intron	INS	-	T	T	rs113422074		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105733802_105733803insT	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)														---	---	---	---
ADAM6	8755	broad.mit.edu	37	14	106088481	106088481	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106088481delC	uc010tyt.1	-						uc001yrs.2_Intron|uc001yrt.2_Intron|uc001yrw.1_Intron|uc001yrx.1_Intron					Parts of antibodies, mostly variable regions.												0																		---	---	---	---
ADAM6	8755	broad.mit.edu	37	14	106960149	106960149	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106960149delA	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0																		---	---	---	---
ADAM6	8755	broad.mit.edu	37	14	106993545	106993545	+	Intron	DEL	A	-	-	rs34821324		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106993545delA	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0																		---	---	---	---
ADAM6	8755	broad.mit.edu	37	14	106993571	106993572	+	Intron	INS	-	A	A	rs141641352	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106993571_106993572insA	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0																		---	---	---	---
ADAM6	8755	broad.mit.edu	37	14	107242564	107242565	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:107242564_107242565insA	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0																		---	---	---	---
ADAM6	8755	broad.mit.edu	37	14	107281367	107281367	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:107281367delG	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	20006983	20006983	+	IGR	DEL	T	-	-	rs147398640		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20006983delT								None (None upstream) : GOLGA6L6 (730111 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	20035752	20035754	+	IGR	DEL	AAT	-	-	rs73385219	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20035752_20035754delAAT								None (None upstream) : GOLGA6L6 (701340 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	20453741	20453741	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20453741delG								None (None upstream) : GOLGA6L6 (283353 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	20514327	20514329	+	IGR	DEL	ATG	-	-	rs146838837		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20514327_20514329delATG								None (None upstream) : GOLGA6L6 (222765 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	20558488	20558489	+	IGR	INS	-	A	A	rs147955745		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20558488_20558489insA								None (None upstream) : GOLGA6L6 (178605 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	20607082	20607082	+	Intron	DEL	A	-	-	rs28755877		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20607082delA	uc001ytg.2	-						uc010tyx.1_Intron					RecName: Full=Putative HERC2-like protein 3;																														---	---	---	---
Unknown	0	broad.mit.edu	37	15	20854148	20854148	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20854148delA								GOLGA8C (73122 upstream) : BCL8 (15908 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	21914454	21914455	+	IGR	DEL	GG	-	-	rs140240894		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21914454_21914455delGG								NF1P1 (779829 upstream) : LOC646214 (18059 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	22412840	22412841	+	IGR	INS	-	A	A	rs144900878	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22412840_22412841insA								OR4N4 (29025 upstream) : OR4N3P (861 downstream)																																			---	---	---	---
NIPA1	123606	broad.mit.edu	37	15	23065264	23065265	+	Intron	DEL	CA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23065264_23065265delCA	uc001yvc.2	-						NIPA1_uc001yvd.2_Intron|NIPA1_uc001yve.2_Intron	NM_144599	NP_653200			non-imprinted in Prader-Willi/Angelman syndrome						cell death	early endosome|integral to membrane|plasma membrane					0		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;4.18e-06)|Epithelial(43;3.97e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00165)														---	---	---	---
HERC2P2	400322	broad.mit.edu	37	15	23348963	23348964	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23348963_23348964delAA	uc001yvr.2	-						HERC2P2_uc010ayf.1_Intron					RecName: Full=Putative HERC2-like protein 3;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	23478356	23478356	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23478356delT								GOLGA8E (29933 upstream) : MKRN3 (332098 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	23690751	23690751	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23690751delA	uc001ywg.1	-						uc010ayh.1_Intron					RecName: Full=Golgin subfamily A member 6-like protein 2;																														---	---	---	---
Unknown	0	broad.mit.edu	37	15	23770487	23770487	+	IGR	DEL	T	-	-	rs35477679		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23770487delT								GOLGA8E (322064 upstream) : MKRN3 (39967 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	24198229	24198229	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:24198229delT								NDN (265779 upstream) : PWRN2 (211697 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	24617460	24617460	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:24617460delA								PWRN2 (202365 upstream) : PWRN1 (161379 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	24706645	24706646	+	IGR	DEL	GT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:24706645_24706646delGT								PWRN2 (291550 upstream) : PWRN1 (72193 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	24979731	24979732	+	IGR	DEL	TC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:24979731_24979732delTC								C15orf2 (51139 upstream) : SNRPN (89062 downstream)																																			---	---	---	---
SNRPN	6638	broad.mit.edu	37	15	25153844	25153844	+	Intron	DEL	T	-	-	rs71412612		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25153844delT	uc001ywp.1	+						SNRPN_uc001ywq.1_Intron|SNRPN_uc001ywr.1_Intron|SNRPN_uc001yws.1_Intron|SNRPN_uc001ywt.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				---	---	---	---
Unknown	0	broad.mit.edu	37	15	25499163	25499163	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25499163delT	uc001zae.2	+											Homo sapiens clone Rt-16 SNURF-SNRPN mRNA, downstream untranslated exons, alternatively spliced.																														---	---	---	---
Unknown	0	broad.mit.edu	37	15	25521566	25521566	+	Intron	DEL	C	-	-	rs76786491		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25521566delC	uc001zae.2	+						uc001zan.1_Intron|SNORD109B_uc001zap.1_5'Flank					Homo sapiens clone Rt-16 SNURF-SNRPN mRNA, downstream untranslated exons, alternatively spliced.																														---	---	---	---
Unknown	0	broad.mit.edu	37	15	25734907	25734907	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25734907delA								UBE3A (50779 upstream) : ATP10A (188955 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	26120898	26120899	+	IGR	INS	-	TCTCTCTC	TCTCTCTC	rs150055745	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:26120898_26120899insTCTCTCTC								ATP10A (10581 upstream) : GABRB3 (667796 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	26217911	26217912	+	IGR	INS	-	C	C	rs142206804	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:26217911_26217912insC								ATP10A (107594 upstream) : GABRB3 (570783 downstream)																																			---	---	---	---
GABRB3	2562	broad.mit.edu	37	15	26819033	26819034	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:26819033_26819034insA	uc001zaz.2	-						GABRB3_uc010uae.1_Intron|GABRB3_uc001zba.2_Intron|GABRB3_uc001zbb.2_Intron	NM_000814	NP_000805			gamma-aminobutyric acid (GABA) A receptor, beta						synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			upper_aerodigestive_tract(1)|ovary(1)|lung(1)|liver(1)|central_nervous_system(1)	5		all_cancers(20;1.89e-22)|all_lung(180;6.35e-15)|Breast(32;0.000279)|Colorectal(260;0.232)		all cancers(64;1.46e-07)|Epithelial(43;2.89e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0251)|COAD - Colon adenocarcinoma(236;0.235)|Lung(196;0.243)	Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)													---	---	---	---
GABRB3	2562	broad.mit.edu	37	15	26888770	26888771	+	Intron	DEL	TG	-	-	rs72114279		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:26888770_26888771delTG	uc001zaz.2	-						GABRB3_uc001zba.2_Intron|GABRB3_uc001zbb.2_Intron	NM_000814	NP_000805			gamma-aminobutyric acid (GABA) A receptor, beta						synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			upper_aerodigestive_tract(1)|ovary(1)|lung(1)|liver(1)|central_nervous_system(1)	5		all_cancers(20;1.89e-22)|all_lung(180;6.35e-15)|Breast(32;0.000279)|Colorectal(260;0.232)		all cancers(64;1.46e-07)|Epithelial(43;2.89e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0251)|COAD - Colon adenocarcinoma(236;0.235)|Lung(196;0.243)	Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)													---	---	---	---
GABRB3	2562	broad.mit.edu	37	15	26914752	26914753	+	Intron	DEL	TC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:26914752_26914753delTC	uc001zaz.2	-						GABRB3_uc001zba.2_Intron|GABRB3_uc001zbb.2_Intron	NM_000814	NP_000805			gamma-aminobutyric acid (GABA) A receptor, beta						synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			upper_aerodigestive_tract(1)|ovary(1)|lung(1)|liver(1)|central_nervous_system(1)	5		all_cancers(20;1.89e-22)|all_lung(180;6.35e-15)|Breast(32;0.000279)|Colorectal(260;0.232)		all cancers(64;1.46e-07)|Epithelial(43;2.89e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0251)|COAD - Colon adenocarcinoma(236;0.235)|Lung(196;0.243)	Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)													---	---	---	---
GABRB3	2562	broad.mit.edu	37	15	27138141	27138142	+	Intron	DEL	GT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:27138141_27138142delGT	uc001zbb.2	-						GABRA5_uc001zbd.1_Intron	NM_021912	NP_068712			gamma-aminobutyric acid (GABA) A receptor, beta						synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			upper_aerodigestive_tract(1)|ovary(1)|lung(1)|liver(1)|central_nervous_system(1)	5		all_cancers(20;1.89e-22)|all_lung(180;6.35e-15)|Breast(32;0.000279)|Colorectal(260;0.232)		all cancers(64;1.46e-07)|Epithelial(43;2.89e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0251)|COAD - Colon adenocarcinoma(236;0.235)|Lung(196;0.243)	Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)													---	---	---	---
OCA2	4948	broad.mit.edu	37	15	28262217	28262217	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28262217delG	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				---	---	---	---
WHAMML2	440253	broad.mit.edu	37	15	29009478	29009479	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29009478_29009479delAA	uc001zci.1	+											Homo sapiens cDNA FLJ33935 fis, clone CTONG2017910.												0																		---	---	---	---
FAM189A1	23359	broad.mit.edu	37	15	29548114	29548114	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29548114delA	uc010azk.1	-							NM_015307	NP_056122			hypothetical protein LOC23359							integral to membrane					0																		---	---	---	---
FAM189A1	23359	broad.mit.edu	37	15	29683207	29683207	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29683207delA	uc010azk.1	-							NM_015307	NP_056122			hypothetical protein LOC23359							integral to membrane					0																		---	---	---	---
FAM189A1	23359	broad.mit.edu	37	15	29736329	29736329	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29736329delA	uc010azk.1	-							NM_015307	NP_056122			hypothetical protein LOC23359							integral to membrane					0																		---	---	---	---
FAM189A1	23359	broad.mit.edu	37	15	29827727	29827727	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29827727delA	uc010azk.1	-							NM_015307	NP_056122			hypothetical protein LOC23359							integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	30205393	30205394	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:30205393_30205394delAA								TJP1 (90687 upstream) : FAM7A3 (190541 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	30365680	30365681	+	IGR	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:30365680_30365681delTG								TJP1 (250974 upstream) : FAM7A3 (30254 downstream)																																			---	---	---	---
TRPM1	4308	broad.mit.edu	37	15	31370014	31370015	+	Intron	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31370014_31370015delTG	uc001zfm.2	-						TRPM1_uc001zfn.3_Intron	NM_002420	NP_002411			transient receptor potential cation channel,						cellular response to light stimulus|visual perception	integral to plasma membrane	calcium channel activity|receptor activity			ovary(2)|pancreas(1)|skin(1)	4		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	33578669	33578669	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33578669delA								FMN1 (218584 upstream) : RYR3 (24508 downstream)																																			---	---	---	---
RYR3	6263	broad.mit.edu	37	15	33600965	33600966	+	5'Flank	DEL	CC	-	-	rs3082611	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33600965_33600966delCC	uc001zhi.2	+						RYR3_uc010bar.2_5'Flank	NM_001036	NP_001027			ryanodine receptor 3						cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)														---	---	---	---
RYR3	6263	broad.mit.edu	37	15	33853923	33853925	+	Intron	DEL	AAC	-	-	rs113317372		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33853923_33853925delAAC	uc001zhi.2	+						RYR3_uc010bar.2_Intron	NM_001036	NP_001027			ryanodine receptor 3						cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)														---	---	---	---
RYR3	6263	broad.mit.edu	37	15	33873557	33873557	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33873557delA	uc001zhi.2	+						RYR3_uc010bar.2_Intron	NM_001036	NP_001027			ryanodine receptor 3						cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)														---	---	---	---
RYR3	6263	broad.mit.edu	37	15	33923503	33923503	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33923503delT	uc001zhi.2	+						RYR3_uc010bar.2_Intron	NM_001036	NP_001027			ryanodine receptor 3						cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)														---	---	---	---
CHRM5	1133	broad.mit.edu	37	15	34309335	34309336	+	Intron	DEL	GA	-	-	rs66703947		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34309335_34309336delGA	uc001zhk.1	+						AVEN_uc001zhj.2_Intron|CHRM5_uc001zhl.1_5'Flank	NM_012125	NP_036257			cholinergic receptor, muscarinic 5						cell proliferation|inhibition of adenylate cyclase activity by muscarinic acetylcholine receptor signaling pathway	cell junction|integral to plasma membrane|postsynaptic membrane	muscarinic acetylcholine receptor activity|phosphatidylinositol phospholipase C activity			ovary(1)|central_nervous_system(1)	2		all_lung(180;1.76e-08)		all cancers(64;4.82e-17)|GBM - Glioblastoma multiforme(113;2.58e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0262)	Atropine(DB00572)|Benzquinamide(DB00767)|Cryptenamine(DB00785)|Homatropine Methylbromide(DB00725)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Olanzapine(DB00334)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Thiethylperazine(DB00372)													---	---	---	---
CHRM5	1133	broad.mit.edu	37	15	34315382	34315383	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34315382_34315383insA	uc001zhk.1	+						AVEN_uc001zhj.2_Intron|CHRM5_uc001zhl.1_Intron	NM_012125	NP_036257			cholinergic receptor, muscarinic 5						cell proliferation|inhibition of adenylate cyclase activity by muscarinic acetylcholine receptor signaling pathway	cell junction|integral to plasma membrane|postsynaptic membrane	muscarinic acetylcholine receptor activity|phosphatidylinositol phospholipase C activity			ovary(1)|central_nervous_system(1)	2		all_lung(180;1.76e-08)		all cancers(64;4.82e-17)|GBM - Glioblastoma multiforme(113;2.58e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0262)	Atropine(DB00572)|Benzquinamide(DB00767)|Cryptenamine(DB00785)|Homatropine Methylbromide(DB00725)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Olanzapine(DB00334)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Thiethylperazine(DB00372)													---	---	---	---
Unknown	0	broad.mit.edu	37	15	34883743	34883743	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34883743delC								GOLGA8B (55521 upstream) : GJD2 (160936 downstream)																																			---	---	---	---
ZNF770	54989	broad.mit.edu	37	15	35277676	35277676	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:35277676delA	uc001ziw.2	-							NM_014106	NP_054825			zinc finger protein 770						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Lung NSC(122;4.59e-10)|all_lung(180;8.78e-09)		all cancers(64;1.97e-18)|GBM - Glioblastoma multiforme(113;2.11e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0643)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	36847120	36847120	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:36847120delA								None (None upstream) : C15orf41 (24692 downstream)																																			---	---	---	---
MEIS2	4212	broad.mit.edu	37	15	37392947	37392948	+	5'Flank	DEL	GC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:37392947_37392948delGC	uc001zjr.2	-						MEIS2_uc001zjl.2_5'Flank|MEIS2_uc010ucj.1_5'Flank|MEIS2_uc001zjm.2_5'Flank|MEIS2_uc001zjn.2_5'Flank|MEIS2_uc001zjo.2_5'Flank|MEIS2_uc001zjp.2_5'Flank|MEIS2_uc001zjs.2_5'Flank|MEIS2_uc001zju.2_Intron|MEIS2_uc001zjt.2_Intron	NM_170675	NP_733775			Meis homeobox 2 isoform c						negative regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(2)	2		all_epithelial(112;9.77e-14)|Lung NSC(122;1.42e-09)|all_lung(180;2.2e-08)|Ovarian(310;0.134)|Melanoma(134;0.155)		all cancers(64;9.33e-21)|GBM - Glioblastoma multiforme(113;1.71e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0288)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	37447330	37447330	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:37447330delA								MEIS2 (53830 upstream) : TMCO5A (779497 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	37474381	37474382	+	IGR	INS	-	TTCCTTCCTTCCTTCCTTCCTTCCTTCC	TTCCTTCCTTCCTTCCTTCCTTCCTTCC	rs67966909		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:37474381_37474382insTTCCTTCCTTCCTTCCTTCCTTCCTTCC								MEIS2 (80881 upstream) : TMCO5A (752445 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	37558063	37558063	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:37558063delA								MEIS2 (164563 upstream) : TMCO5A (668764 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	37894881	37894884	+	IGR	DEL	GAGA	-	-	rs113993445		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:37894881_37894884delGAGA								MEIS2 (501381 upstream) : TMCO5A (331943 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	38654580	38654583	+	IGR	DEL	GACT	-	-	rs34382163		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38654580_38654583delGACT								SPRED1 (5131 upstream) : FAM98B (91745 downstream)																																			---	---	---	---
RASGRP1	10125	broad.mit.edu	37	15	38806001	38806001	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38806001delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	39436023	39436023	+	IGR	DEL	T	-	-	rs10709839		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:39436023delT								C15orf53 (443784 upstream) : C15orf54 (106862 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	39652411	39652414	+	IGR	DEL	TCTG	-	-	rs111374895		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:39652411_39652414delTCTG								C15orf54 (105363 upstream) : THBS1 (220866 downstream)																																			---	---	---	---
BUB1B	701	broad.mit.edu	37	15	40469994	40469994	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40469994delT	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				---	---	---	---
IVD	3712	broad.mit.edu	37	15	40704367	40704367	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40704367delA	uc001zls.3	+						IVD_uc001zlq.2_Intron|IVD_uc001zlr.2_5'Flank	NM_002225	NP_002216			isovaleryl Coenzyme A dehydrogenase isoform 1						leucine catabolic process	mitochondrial matrix	flavin adenine dinucleotide binding|isovaleryl-CoA dehydrogenase activity			ovary(1)	1		all_cancers(109;1.19e-18)|all_epithelial(112;1.52e-15)|Lung NSC(122;5.14e-11)|all_lung(180;1.27e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;3.65e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0808)														---	---	---	---
CASC5	57082	broad.mit.edu	37	15	40931970	40931970	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40931970delA	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	40990382	40990382	+	Intron	DEL	T	-	-	rs34665687		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40990382delT	uc001zmi.3	+						RAD51_uc010bbw.2_Intron|RAD51_uc010bbx.2_Intron|RAD51_uc001zmk.3_Intron|RAD51_uc001zml.3_Intron|RAD51_uc001zmm.1_5'Flank|RAD51_uc001zmn.1_5'Flank	NM_002875	NP_002866			RAD51 homolog protein isoform 1						DNA recombinase assembly|DNA unwinding involved in replication|mitotic recombination|positive regulation of DNA ligation|protein homooligomerization|reciprocal meiotic recombination	mitochondrial matrix|nucleus|perinuclear region of cytoplasm|PML body	ATP binding|damaged DNA binding|double-stranded DNA binding|identical protein binding|protein C-terminus binding|single-stranded DNA binding|single-stranded DNA-dependent ATPase activity				0		all_cancers(109;1.19e-18)|all_epithelial(112;2.33e-15)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;1.45e-05)|BRCA - Breast invasive adenocarcinoma(123;0.000421)|COAD - Colon adenocarcinoma(120;0.163)									Homologous_recombination					---	---	---	---
INO80	54617	broad.mit.edu	37	15	41361532	41361532	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41361532delT	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																		---	---	---	---
EXD1	161829	broad.mit.edu	37	15	41480376	41480376	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41480376delT	uc001znk.2	-						EXD1_uc001znj.2_Intron|EXD1_uc010ucv.1_Intron	NM_152596	NP_689809			exonuclease 3'-5' domain containing 1						nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	intracellular	3'-5' exonuclease activity|nucleic acid binding			ovary(1)	1																		---	---	---	---
MAPKBP1	23005	broad.mit.edu	37	15	42102916	42102918	+	Intron	DEL	AAA	-	-	rs113122683		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42102916_42102918delAAA	uc001zok.3	+						MAPKBP1_uc001zoj.3_Intron|MAPKBP1_uc010bcj.2_Intron|MAPKBP1_uc010bci.2_Intron|MAPKBP1_uc010udb.1_Intron|MAPKBP1_uc010bck.2_Intron|MAPKBP1_uc010bcl.2_5'Flank	NM_001128608	NP_001122080			mitogen-activated protein kinase binding protein											central_nervous_system(5)|breast(2)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	10		all_cancers(109;7.71e-14)|all_epithelial(112;5.15e-12)|Lung NSC(122;3.74e-08)|all_lung(180;1.81e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.95e-17)|GBM - Glioblastoma multiforme(94;5.71e-07)|Lung(196;0.0436)|BRCA - Breast invasive adenocarcinoma(123;0.203)|LUSC - Lung squamous cell carcinoma(244;0.225)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	42306008	42306008	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42306008delT								PLA2G4E (3563 upstream) : PLA2G4D (53874 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	42318344	42318344	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42318344delA								PLA2G4E (15899 upstream) : PLA2G4D (41538 downstream)																																			---	---	---	---
TMEM87A	25963	broad.mit.edu	37	15	42547340	42547340	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42547340delT	uc010udd.1	-						TMEM87A_uc001zpf.3_Intron|TMEM87A_uc010bcu.1_Intron	NM_015497	NP_056312			transmembrane protein 87A isoform 1							integral to membrane				ovary(1)	1		all_cancers(109;4.28e-16)|all_epithelial(112;1.04e-14)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;1.03e-06)														---	---	---	---
SNAP23	8773	broad.mit.edu	37	15	42803921	42803921	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42803921delT	uc001zpz.1	+						SNAP23_uc001zqa.1_Intron	NM_003825	NP_003816			synaptosomal-associated protein 23 isoform						cellular membrane fusion|post-Golgi vesicle-mediated transport|protein transport|vesicle targeting	azurophil granule|cell junction|Golgi apparatus|nucleus|plasma membrane enriched fraction|specific granule|synapse|synaptosome	protein binding				0		all_cancers(109;7.14e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;1.18e-08)|all_lung(180;4.2e-08)|Melanoma(134;0.0179)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;2.62e-06)														---	---	---	---
TTBK2	146057	broad.mit.edu	37	15	43180139	43180140	+	Intron	INS	-	T	T	rs142851151	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43180139_43180140insT	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)														---	---	---	---
TMEM62	80021	broad.mit.edu	37	15	43423947	43423948	+	5'Flank	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43423947_43423948insA	uc001zqr.2	+						TMEM62_uc010bda.2_5'Flank	NM_024956	NP_079232			transmembrane protein 62							integral to membrane				ovary(1)|breast(1)	2		all_cancers(109;1.16e-10)|all_epithelial(112;2.01e-09)|Lung NSC(122;8.91e-07)|all_lung(180;8.8e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;4.23e-07)														---	---	---	---
EPB42	2038	broad.mit.edu	37	15	43512848	43512850	+	Intron	DEL	CCC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43512848_43512850delCCC	uc001zra.3	-						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)														---	---	---	---
CATSPER2	117155	broad.mit.edu	37	15	43927354	43927355	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43927354_43927355delTT	uc001zsh.2	-						STRC_uc010udz.1_5'Flank|CATSPER2_uc010bdm.2_Intron|CATSPER2_uc001zsi.2_Intron|CATSPER2_uc001zsj.2_Intron	NM_172095	NP_742093			sperm-associated cation channel 2 isoform 2						cell differentiation|multicellular organismal development|spermatogenesis	cilium|flagellar membrane|integral to membrane	calcium channel activity|protein binding|voltage-gated ion channel activity			ovary(1)	1		all_cancers(109;3.26e-15)|all_epithelial(112;1.48e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.56e-07)												OREG0003957	type=REGULATORY REGION|Gene=AK093318|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	---	---	---	---
ELL3	80237	broad.mit.edu	37	15	44065726	44065727	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44065726_44065727insA	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)														---	---	---	---
WDR76	79968	broad.mit.edu	37	15	44156799	44156800	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44156799_44156800delTT	uc001zti.1	+							NM_024908	NP_079184			WD repeat domain 76												0		all_cancers(109;3.26e-11)|all_epithelial(112;4.82e-09)|Lung NSC(122;1.61e-06)|all_lung(180;1.5e-05)|Melanoma(134;0.0417)		all cancers(107;3.78e-21)|GBM - Glioblastoma multiforme(94;5.04e-07)														---	---	---	---
CASC4	113201	broad.mit.edu	37	15	44660735	44660735	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44660735delT	uc001zto.1	+						CASC4_uc001ztp.2_Intron|CASC4_uc001ztq.2_Intron	NM_138423	NP_612432			cancer susceptibility candidate 4 isoform a							integral to membrane				ovary(1)	1		all_cancers(109;1.69e-13)|all_epithelial(112;3.94e-11)|Lung NSC(122;1.66e-07)|all_lung(180;1.47e-06)|Melanoma(134;0.027)		all cancers(107;2.91e-20)|GBM - Glioblastoma multiforme(94;1.57e-06)|COAD - Colon adenocarcinoma(120;0.217)|Colorectal(105;0.237)														---	---	---	---
CTDSPL2	51496	broad.mit.edu	37	15	44808072	44808072	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44808072delA	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)														---	---	---	---
DUOX1	53905	broad.mit.edu	37	15	45434984	45434987	+	Intron	DEL	AGGG	-	-	rs67057268		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45434984_45434987delAGGG	uc001zus.1	+						DUOX1_uc001zut.1_Intron|DUOX1_uc010bee.1_Intron	NM_017434	NP_059130			dual oxidase 1 precursor						cuticle development|cytokine-mediated signaling pathway|hormone biosynthetic process|hydrogen peroxide biosynthetic process|hydrogen peroxide catabolic process|response to cAMP|superoxide anion generation	apical plasma membrane|integral to membrane	calcium ion binding|electron carrier activity|flavin adenine dinucleotide binding|heme binding|NAD(P)H oxidase activity|NADP binding|peroxidase activity			ovary(5)|skin(2)|breast(1)	8		all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;5.77e-18)|GBM - Glioblastoma multiforme(94;5.11e-07)|COAD - Colon adenocarcinoma(120;0.071)|Colorectal(133;0.0717)														---	---	---	---
SLC28A2	9153	broad.mit.edu	37	15	45555013	45555013	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45555013delT	uc001zva.2	+							NM_004212	NP_004203			solute carrier family 28 (sodium-coupled						nucleobase, nucleoside and nucleotide metabolic process	integral to plasma membrane|membrane fraction	nucleoside binding|nucleoside:sodium symporter activity|purine nucleoside transmembrane transporter activity			ovary(4)	4		all_cancers(109;8.53e-07)|all_epithelial(112;1.39e-05)|Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;3.77e-16)|GBM - Glioblastoma multiforme(94;2.71e-06)														---	---	---	---
PLDN	26258	broad.mit.edu	37	15	45898316	45898316	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45898316delT	uc001zvq.2	+						PLDN_uc001zvr.2_Intron|PLDN_uc001zvs.2_Intron	NM_012388	NP_036520			pallidin						post-Golgi vesicle-mediated transport|synaptic vesicle docking involved in exocytosis	BLOC-1 complex|endomembrane system|membrane	identical protein binding|syntaxin-13 binding			skin(1)	1		Lung NSC(122;1.6e-06)|all_lung(180;1.13e-05)|Melanoma(134;0.027)		all cancers(107;6.58e-18)|GBM - Glioblastoma multiforme(94;5.91e-07)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	45994710	45994710	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45994710delT								SQRDL (11232 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	46245097	46245097	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:46245097delT								SQRDL (261619 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	47344080	47344081	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:47344080_47344081insT								None (None upstream) : SEMA6D (132322 downstream)																																			---	---	---	---
SEMA6D	80031	broad.mit.edu	37	15	47908362	47908362	+	Intron	DEL	T	-	-	rs113189802		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:47908362delT	uc001zvw.2	+							NM_020858	NP_065909			semaphorin 6D isoform 1 precursor						axon guidance	cytoplasm|integral to membrane|plasma membrane	receptor activity			skin(3)|breast(1)	4		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)														---	---	---	---
SEMA6D	80031	broad.mit.edu	37	15	47957188	47957188	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:47957188delG	uc001zvw.2	+							NM_020858	NP_065909			semaphorin 6D isoform 1 precursor						axon guidance	cytoplasm|integral to membrane|plasma membrane	receptor activity			skin(3)|breast(1)	4		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	48205053	48205053	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48205053delT								SEMA6D (138634 upstream) : SLC24A5 (208116 downstream)																																			---	---	---	---
CEP152	22995	broad.mit.edu	37	15	49082769	49082769	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49082769delT	uc001zwy.2	-						CEP152_uc001zwz.2_Intron|CEP152_uc001zxa.1_Intron	NM_014985	NP_055800			centrosomal protein 152kDa						centrosome duplication|G2/M transition of mitotic cell cycle	centrosome|cytosol	protein kinase binding			lung(2)	2		all_lung(180;0.0428)		all cancers(107;1.08e-07)|GBM - Glioblastoma multiforme(94;2.32e-06)														---	---	---	---
SHC4	399694	broad.mit.edu	37	15	49149503	49149503	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49149503delT	uc001zxb.1	-						SHC4_uc010uey.1_Intron|SHC4_uc010uez.1_Intron	NM_203349	NP_976224			rai-like protein						intracellular signal transduction	cell junction|postsynaptic membrane				ovary(3)|pancreas(2)	5		all_lung(180;0.00466)		all cancers(107;9.4e-08)|GBM - Glioblastoma multiforme(94;5.94e-07)														---	---	---	---
SHC4	399694	broad.mit.edu	37	15	49223709	49223709	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49223709delT	uc001zxb.1	-							NM_203349	NP_976224			rai-like protein						intracellular signal transduction	cell junction|postsynaptic membrane				ovary(3)|pancreas(2)	5		all_lung(180;0.00466)		all cancers(107;9.4e-08)|GBM - Glioblastoma multiforme(94;5.94e-07)														---	---	---	---
SECISBP2L	9728	broad.mit.edu	37	15	49302694	49302694	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49302694delT	uc001zxe.1	-						SECISBP2L_uc001zxd.1_Intron|SECISBP2L_uc010bep.1_Intron	NM_014701	NP_055516			SECIS binding protein 2-like											breast(1)|skin(1)	2																		---	---	---	---
GALK2	2585	broad.mit.edu	37	15	49534220	49534220	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49534220delT	uc001zxj.1	+						GALK2_uc001zxi.1_Intron|GALK2_uc010ufb.1_Intron|GALK2_uc001zxk.2_Intron|GALK2_uc010ufc.1_Intron	NM_002044	NP_002035			galactokinase 2 isoform 1						galactose metabolic process	cytoplasm	ATP binding|galactokinase activity|N-acetylgalactosamine kinase activity			breast(1)	1		all_lung(180;0.000325)		all cancers(107;3.71e-08)|GBM - Glioblastoma multiforme(94;7e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	49955188	49955188	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49955188delT								DTWD1 (17856 upstream) : ATP8B4 (195248 downstream)																																			---	---	---	---
GABPB1	2553	broad.mit.edu	37	15	50581976	50581977	+	Intron	INS	-	TTTTTT	TTTTTT	rs140176493	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50581976_50581977insTTTTTT	uc001zyb.2	-						GABPB1_uc001zya.2_Intron|GABPB1_uc010ufg.1_Intron|GABPB1_uc001zyc.2_Intron|GABPB1_uc001zyd.2_Intron|GABPB1_uc001zye.2_Intron|GABPB1_uc001zyf.2_Intron	NM_005254	NP_005245			GA binding protein transcription factor, beta						positive regulation of transcription from RNA polymerase II promoter	nucleus	protein binding|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			large_intestine(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	50703209	50703209	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50703209delA								LOC100129387 (52708 upstream) : USP8 (13370 downstream)																																			---	---	---	---
SPPL2A	84888	broad.mit.edu	37	15	51009443	51009443	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51009443delC	uc001zyv.2	-							NM_032802	NP_116191			signal peptide peptidase-like 2A							integral to membrane	aspartic-type endopeptidase activity				0				all cancers(107;0.000712)|GBM - Glioblastoma multiforme(94;0.00314)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	51134119	51134119	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51134119delA	uc001zyw.1	-											Homo sapiens cDNA FLJ34587 fis, clone KIDNE2008795.																														---	---	---	---
TNFAIP8L3	388121	broad.mit.edu	37	15	51372610	51372610	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51372610delT	uc001zyy.2	-							NM_207381	NP_997264			tumor necrosis factor, alpha-induced protein												0				all cancers(107;0.000389)|GBM - Glioblastoma multiforme(94;0.00338)														---	---	---	---
DMXL2	23312	broad.mit.edu	37	15	51783640	51783640	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51783640delA	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)														---	---	---	---
TMOD2	29767	broad.mit.edu	37	15	52045744	52045744	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52045744delA	uc002abk.2	+						LYSMD2_uc002abj.2_5'Flank|TMOD2_uc002abl.3_Intron|TMOD2_uc010bfb.2_Intron	NM_014548	NP_055363			neuronal tropomodulin isoform a						nervous system development	cytoplasm|cytoskeleton	actin binding|tropomyosin binding			ovary(2)	2				all cancers(107;0.00435)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	53493134	53493135	+	IGR	DEL	AA	-	-	rs71889566		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:53493134_53493135delAA								ONECUT1 (410925 upstream) : WDR72 (312803 downstream)																																			---	---	---	---
UNC13C	440279	broad.mit.edu	37	15	54444379	54444380	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:54444379_54444380insT	uc002ack.2	+							NM_001080534	NP_001074003			unc-13 homolog C						exocytosis|intracellular signal transduction	cell junction|cytoplasm|presynaptic membrane	metal ion binding			ovary(5)|pancreas(2)	7				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)														---	---	---	---
UNC13C	440279	broad.mit.edu	37	15	54782857	54782858	+	Intron	DEL	TT	-	-	rs112020160		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:54782857_54782858delTT	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	54935847	54935847	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:54935847delA								UNC13C (15042 upstream) : RSL24D1 (537674 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	55133253	55133255	+	IGR	DEL	AAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55133253_55133255delAAA								UNC13C (212448 upstream) : RSL24D1 (340266 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	55405780	55405780	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55405780delC								UNC13C (484975 upstream) : RSL24D1 (67741 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	56595809	56595809	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:56595809delA								RFX7 (60326 upstream) : TEX9 (61835 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	56597465	56597465	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:56597465delA								RFX7 (61982 upstream) : TEX9 (60179 downstream)																																			---	---	---	---
TCF12	6938	broad.mit.edu	37	15	57457333	57457334	+	Intron	DEL	TG	-	-	rs71824898		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57457333_57457334delTG	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	57529334	57529335	+	Intron	DEL	AG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57529334_57529335delAG	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|TCF12_uc002aee.2_Intron|TCF12_uc010bft.2_Intron|TCF12_uc010ugo.1_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	57530405	57530405	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57530405delT	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|TCF12_uc002aee.2_Intron|TCF12_uc010bft.2_Intron|TCF12_uc010ugo.1_Intron	NM_207038	NP_996921			transcription factor 12 isoform b						immune response|muscle organ development|regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(5)|ovary(2)|lung(1)	8		Colorectal(260;0.0907)		all cancers(107;0.000313)|GBM - Glioblastoma multiforme(80;0.00878)|STAD - Stomach adenocarcinoma(283;0.239)				T	TEC	extraskeletal myxoid chondrosarcoma								---	---	---	---
CGNL1	84952	broad.mit.edu	37	15	57821758	57821769	+	Intron	DEL	ACACACACACAC	-	-	rs10652758		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57821758_57821769delACACACACACAC	uc002aeg.2	+						CGNL1_uc010bfw.2_Intron	NM_032866	NP_116255			cingulin-like 1							myosin complex|tight junction	motor activity			skin(6)|ovary(4)|central_nervous_system(1)	11				all cancers(107;0.121)|GBM - Glioblastoma multiforme(80;0.186)														---	---	---	---
FAM63B	54629	broad.mit.edu	37	15	59101990	59101991	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59101990_59101991insT	uc002afj.2	+						FAM63B_uc002afi.2_Intron|FAM63B_uc002afk.2_Intron|FAM63B_uc002afl.2_Intron	NM_001040450	NP_001035540			hypothetical protein LOC54629 isoform a											central_nervous_system(1)	1																		---	---	---	---
SLTM	79811	broad.mit.edu	37	15	59178467	59178473	+	Intron	DEL	TTTTTTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59178467_59178473delTTTTTTT	uc002afp.2	-						SLTM_uc002afn.2_Intron|SLTM_uc002afo.2_Intron|SLTM_uc002afq.2_Intron|SLTM_uc010bgd.2_Intron	NM_024755	NP_079031			modulator of estrogen induced transcription						apoptosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleotide binding|RNA binding			ovary(1)	1																		---	---	---	---
RNF111	54778	broad.mit.edu	37	15	59324144	59324144	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59324144delT	uc002afv.2	+						RNF111_uc002afs.2_Intron|RNF111_uc002aft.2_Intron|RNF111_uc002afu.2_Intron|RNF111_uc002afw.2_Intron	NM_017610	NP_060080			ring finger protein 111						multicellular organismal development|positive regulation of transcription, DNA-dependent	cytoplasm|nucleus	protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2				all cancers(107;0.194)														---	---	---	---
MYO1E	4643	broad.mit.edu	37	15	59439995	59439996	+	Intron	DEL	GT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59439995_59439996delGT	uc002aga.2	-							NM_004998	NP_004989			myosin IE						actin filament-based movement	myosin complex	actin binding|ATP binding|ATPase activity, coupled|calmodulin binding|microfilament motor activity			central_nervous_system(3)	3				all cancers(107;0.207)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	59816801	59816802	+	IGR	DEL	CA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59816801_59816802delCA								FAM81A (1050 upstream) : GCNT3 (87180 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	60050690	60050690	+	IGR	DEL	C	-	-	rs72753124		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:60050690delC								BNIP2 (69048 upstream) : FOXB1 (245731 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	60121616	60121616	+	IGR	DEL	A	-	-	rs112937512		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:60121616delA								BNIP2 (139974 upstream) : FOXB1 (174805 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	60200885	60200885	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:60200885delT								BNIP2 (219243 upstream) : FOXB1 (95536 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	60337512	60337512	+	IGR	DEL	T	-	-	rs67490421		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:60337512delT								FOXB1 (9104 upstream) : ANXA2 (301839 downstream)																																			---	---	---	---
RORA	6095	broad.mit.edu	37	15	61111946	61111955	+	Intron	DEL	ACACACACAC	-	-	rs72029004		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:61111946_61111955delACACACACAC	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	61345902	61345902	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:61345902delT	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	61374219	61374219	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:61374219delG	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	62242755	62242756	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62242755_62242756delAA	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	63702973	63702973	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63702973delC								CA12 (28898 upstream) : USP3 (93837 downstream)																																			---	---	---	---
USP3	9960	broad.mit.edu	37	15	63852271	63852271	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63852271delA	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)														---	---	---	---
ZNF609	23060	broad.mit.edu	37	15	64822234	64822234	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64822234delT	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																		---	---	---	---
PDCD7	10081	broad.mit.edu	37	15	65412483	65412483	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65412483delT	uc002aol.2	-							NM_005707	NP_005698			programmed cell death 7						apoptosis|induction of apoptosis|response to glucocorticoid stimulus	U12-type spliceosomal complex					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	65530629	65530629	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65530629delA								CILP (26789 upstream) : PARP16 (19805 downstream)																																			---	---	---	---
C15orf44	81556	broad.mit.edu	37	15	65874807	65874807	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65874807delA	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	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-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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																		---	---	---	---
DENND4A	10260	broad.mit.edu	37	15	66051817	66051817	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66051817delA	uc002aph.2	-						DENND4A_uc002api.2_Intron|DENND4A_uc002apj.3_Intron|DENND4A_uc010ujj.1_Intron	NM_005848	NP_005839			DENN/MADD domain containing 4A isoform 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	66135127	66135128	+	IGR	DEL	TT	-	-	rs111938753		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66135127_66135128delTT								DENND4A (50496 upstream) : RAB11A (26668 downstream)																																			---	---	---	---
MEGF11	84465	broad.mit.edu	37	15	66240653	66240653	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66240653delT	uc002apm.2	-						MEGF11_uc002apl.2_Intron|MEGF11_uc002apn.1_Intron	NM_032445	NP_115821			multiple EGF-like-domains 11 precursor							basolateral plasma membrane|integral to membrane				pancreas(1)	1																		---	---	---	---
MEGF11	84465	broad.mit.edu	37	15	66257236	66257237	+	Intron	INS	-	A	A	rs138144863	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66257236_66257237insA	uc002apm.2	-						MEGF11_uc002apl.2_Intron|MEGF11_uc002apn.1_Intron	NM_032445	NP_115821			multiple EGF-like-domains 11 precursor							basolateral plasma membrane|integral to membrane				pancreas(1)	1																		---	---	---	---
MEGF11	84465	broad.mit.edu	37	15	66311014	66311015	+	Intron	INS	-	GTGTGCAA	GTGTGCAA	rs138757760	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66311014_66311015insGTGTGCAA	uc002apm.2	-						MEGF11_uc002apl.2_Intron|MEGF11_uc002apn.1_Intron	NM_032445	NP_115821			multiple EGF-like-domains 11 precursor							basolateral plasma membrane|integral to membrane				pancreas(1)	1																		---	---	---	---
ZWILCH	55055	broad.mit.edu	37	15	66802738	66802738	+	Intron	DEL	T	-	-	rs67789554		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66802738delT	uc002aqb.2	+						RPL4_uc002apx.2_Intron|ZWILCH_uc010bhu.1_Intron|ZWILCH_uc002aqa.2_Intron|ZWILCH_uc010bhv.2_Intron	NM_017975	NP_060445			Zwilch						cell division|mitotic cell cycle checkpoint|mitotic prometaphase	condensed chromosome kinetochore|cytosol	protein binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	67207489	67207489	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:67207489delT								SMAD6 (133154 upstream) : SMAD3 (150706 downstream)																																			---	---	---	---
PIAS1	8554	broad.mit.edu	37	15	68474452	68474452	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:68474452delA	uc002aqz.2	+						PIAS1_uc002ara.2_Intron	NM_016166	NP_057250			protein inhibitor of activated STAT, 1						androgen receptor signaling pathway|interferon-gamma-mediated signaling pathway|JAK-STAT cascade|positive regulation of protein sumoylation|positive regulation of transcription, DNA-dependent|regulation of interferon-gamma-mediated signaling pathway|transcription, DNA-dependent	nuclear speck	androgen receptor binding|DNA binding|enzyme binding|SUMO ligase activity|transcription coactivator activity|transcription corepressor activity|zinc ion binding			ovary(1)|lung(1)	2																		---	---	---	---
CORO2B	10391	broad.mit.edu	37	15	69020047	69020047	+	3'UTR	DEL	T	-	-	rs71747415		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69020047delT	uc002arj.3	+	12					CORO2B_uc010bic.2_3'UTR|CORO2B_uc002ark.2_3'UTR	NM_006091	NP_006082			coronin, actin binding protein, 2B						actin cytoskeleton organization	actin cytoskeleton|cytoplasm|membrane	actin filament binding			ovary(3)|skin(2)|large_intestine(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	69126634	69126634	+	IGR	DEL	C	-	-	rs59781278		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69126634delC								ANP32A (13373 upstream) : NOX5 (96230 downstream)																																			---	---	---	---
NOX5	79400	broad.mit.edu	37	15	69315022	69315022	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69315022delA	uc002ars.1	+						NOX5_uc002arp.1_Intron|NOX5_uc002arq.1_Intron|NOX5_uc010bid.1_Intron|NOX5_uc002arr.1_Intron|NOX5_uc010bie.1_Intron|NOX5_uc002aro.2_RNA	NM_024505	NP_078781			NADPH oxidase, EF-hand calcium binding domain 5						angiogenesis|angiogenesis|cytokine secretion|cytokinesis|electron transport chain|endothelial cell proliferation|induction of apoptosis|positive regulation of reactive oxygen species metabolic process|regulation of fusion of sperm to egg plasma membrane|regulation of proton transport|superoxide anion generation	endoplasmic reticulum|endoplasmic reticulum|integral to membrane	calcium ion binding|electron carrier activity|flavin adenine dinucleotide binding|heme binding|hydrogen ion channel activity|NADP binding|superoxide-generating NADPH oxidase activity			breast(1)|pancreas(1)	2																		---	---	---	---
GLCE	26035	broad.mit.edu	37	15	69555767	69555767	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69555767delT	uc002ary.1	+							NM_015554	NP_056369			D-glucuronyl C5-epimerase						heparan sulfate proteoglycan biosynthetic process|heparin biosynthetic process	Golgi membrane|integral to membrane	UDP-glucuronate 5'-epimerase activity			ovary(2)	2																		---	---	---	---
TLE3	7090	broad.mit.edu	37	15	70369061	70369061	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70369061delT	uc002asm.2	-						TLE3_uc002ask.2_Intron|TLE3_uc002asl.2_Intron|TLE3_uc010ukd.1_Intron|TLE3_uc010bik.1_Intron|TLE3_uc010bil.1_Intron|TLE3_uc002asn.2_Intron|TLE3_uc002asp.2_Intron|TLE3_uc002aso.2_Intron|TLE3_uc010bim.1_5'Flank	NM_005078	NP_005069			transducin-like enhancer protein 3 isoform a						organ morphogenesis|regulation of transcription, DNA-dependent|transcription, DNA-dependent|Wnt receptor signaling pathway	nucleus	protein binding|protein binding			lung(2)	2																		---	---	---	---
THSD4	79875	broad.mit.edu	37	15	71545752	71545754	+	Intron	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:71545752_71545754delTTT	uc002atb.1	+						THSD4_uc002atd.1_Intron	NM_024817	NP_079093			thrombospondin, type I, domain containing 4							proteinaceous extracellular matrix	metalloendopeptidase activity			ovary(2)	2																		---	---	---	---
THSD4	79875	broad.mit.edu	37	15	72034024	72034039	+	Intron	DEL	ACACACACACACACAC	-	-	rs72404204		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72034024_72034039delACACACACACACACAC	uc002atb.1	+						THSD4_uc002ate.2_Intron	NM_024817	NP_079093			thrombospondin, type I, domain containing 4							proteinaceous extracellular matrix	metalloendopeptidase activity			ovary(2)	2																		---	---	---	---
MYO9A	4649	broad.mit.edu	37	15	72347241	72347241	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72347241delA	uc002atl.3	-						MYO9A_uc010biq.2_Intron|MYO9A_uc002ato.2_Intron	NM_006901	NP_008832			myosin IXA						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction|visual perception	cytosol|integral to membrane|unconventional myosin complex	actin binding|ATP binding|GTPase activator activity|metal ion binding|motor activity			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
MYO9A	4649	broad.mit.edu	37	15	72382133	72382133	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72382133delA	uc002atl.3	-						MYO9A_uc010biq.2_Intron|MYO9A_uc002ato.2_Intron	NM_006901	NP_008832			myosin IXA						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction|visual perception	cytosol|integral to membrane|unconventional myosin complex	actin binding|ATP binding|GTPase activator activity|metal ion binding|motor activity			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
PKM2	5315	broad.mit.edu	37	15	72526431	72526432	+	5'Flank	DEL	AC	-	-	rs143530719		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72526431_72526432delAC	uc002atx.1	-						PKM2_uc010uki.1_5'Flank|PKM2_uc002atv.1_5'Flank|PKM2_uc002atw.1_5'Flank|PKM2_uc002aty.1_5'Flank|PKM2_uc010ukj.1_5'Flank|PKM2_uc010ukk.1_5'Flank|PKM2_uc002atz.1_5'Flank	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)													---	---	---	---
CELF6	60677	broad.mit.edu	37	15	72613008	72613008	+	5'Flank	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72613008delC	uc002auh.2	-						uc002aug.2_Intron|CELF6_uc002auk.3_RNA|CELF6_uc010biv.1_RNA|CELF6_uc010ukm.1_5'UTR|CELF6_uc002aui.2_5'UTR|CELF6_uc002auj.2_5'UTR	NM_052840	NP_443072			bruno-like 6, RNA binding protein						mRNA processing|regulation of alternative nuclear mRNA splicing, via spliceosome	cytoplasm|nucleus	nucleotide binding|RNA binding			large_intestine(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	73252841	73252844	+	IGR	DEL	TTTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73252841_73252844delTTTT								ADPGK (176174 upstream) : NEO1 (92031 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	73295422	73295423	+	IGR	INS	-	CA	CA	rs150995541	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73295422_73295423insCA								ADPGK (218755 upstream) : NEO1 (49452 downstream)																																			---	---	---	---
NEO1	4756	broad.mit.edu	37	15	73508276	73508276	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73508276delT	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-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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																		---	---	---	---
C15orf39	56905	broad.mit.edu	37	15	75490419	75490421	+	5'Flank	DEL	TTG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75490419_75490421delTTG	uc002azp.3	+							NM_015492	NP_056307			hypothetical protein LOC56905												0																		---	---	---	---
MAN2C1	4123	broad.mit.edu	37	15	75656148	75656149	+	Intron	DEL	AA	-	-	rs35339457		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75656148_75656149delAA	uc002baf.2	-						MAN2C1_uc002bag.2_Intron|MAN2C1_uc002bah.2_Intron|MAN2C1_uc010bkk.2_Intron|MAN2C1_uc010umi.1_Intron|MAN2C1_uc010umj.1_Intron	NM_006715	NP_006706			mannosidase, alpha, class 2C, member 1						mannose metabolic process		alpha-mannosidase activity|carbohydrate binding|protein binding|zinc ion binding				0																		---	---	---	---
SIN3A	25942	broad.mit.edu	37	15	75706706	75706707	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75706706_75706707delAA	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																		---	---	---	---
FBXO22	26263	broad.mit.edu	37	15	76202129	76202130	+	Intron	DEL	TA	-	-	rs58447748		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76202129_76202130delTA	uc002bbk.2	+						FBXO22_uc002bbj.1_Intron|FBXO22_uc002bbl.2_Intron	NM_147188	NP_671717			F-box only protein 22 isoform a						ubiquitin-dependent protein catabolic process		ubiquitin-protein ligase activity				0																		---	---	---	---
SCAPER	49855	broad.mit.edu	37	15	76788333	76788340	+	Intron	DEL	AGACACAC	-	-	rs113529598		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76788333_76788340delAGACACAC	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	77019395	77019395	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77019395delA	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																		---	---	---	---
LINGO1	84894	broad.mit.edu	37	15	77916232	77916232	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77916232delA	uc002bct.1	-						LINGO1_uc002bcu.1_Intron	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	78061724	78061725	+	IGR	INS	-	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78061724_78061725insC								LINGO1 (73249 upstream) : LOC645752 (144834 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	78533133	78533133	+	IGR	DEL	G	-	-	rs66632602		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78533133delG								ACSBG1 (6234 upstream) : DNAJA4 (23354 downstream)																																			---	---	---	---
WDR61	80349	broad.mit.edu	37	15	78587083	78587083	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78587083delT	uc002bdn.2	-						WDR61_uc002bdo.2_Intron|WDR61_uc010umz.1_Intron|WDR61_uc010una.1_Intron|WDR61_uc010blc.1_3'UTR	NM_025234	NP_079510			WD repeat domain 61								protein binding			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	78988380	78988382	+	IGR	DEL	CTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78988380_78988382delCTT								CHRNB4 (35506 upstream) : ADAMTS7 (63164 downstream)																																			---	---	---	---
ADAMTS7	11173	broad.mit.edu	37	15	79083579	79083579	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79083579delG	uc002bej.3	-						ADAMTS7_uc010und.1_Intron|ADAMTS7_uc002bek.1_Intron	NM_014272	NP_055087			ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	79126096	79126097	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79126096_79126097delTT								ADAMTS7 (22323 upstream) : MORF4L1 (39075 downstream)																																			---	---	---	---
MORF4L1	10933	broad.mit.edu	37	15	79175061	79175061	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79175061delA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	79465266	79465266	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79465266delC								RASGRF1 (82051 upstream) : MIR184 (36864 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	79477728	79477731	+	IGR	DEL	CTTG	-	-	rs146430112		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79477728_79477731delCTTG								RASGRF1 (94513 upstream) : MIR184 (24399 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	79835254	79835254	+	IGR	DEL	T	-	-	rs11307168		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79835254delT								KIAA1024 (70612 upstream) : MTHFS (302066 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	79854087	79854087	+	IGR	DEL	A	-	-	rs77091701		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79854087delA								KIAA1024 (89445 upstream) : MTHFS (283233 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	79882252	79882252	+	IGR	DEL	A	-	-	rs58452206	byFrequency;by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79882252delA								KIAA1024 (117610 upstream) : MTHFS (255068 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	80106860	80106869	+	IGR	DEL	GTGTGTGTGT	-	-	rs138040625		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:80106860_80106869delGTGTGTGTGT								KIAA1024 (342218 upstream) : MTHFS (30451 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	80331442	80331442	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:80331442delT								BCL2A1 (67799 upstream) : ZFAND6 (20579 downstream)																																			---	---	---	---
FAM108C1	58489	broad.mit.edu	37	15	80989436	80989436	+	Intron	DEL	T	-	-	rs76567558		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:80989436delT	uc002bfu.2	+						FAM108C1_uc002bft.2_Intron	NM_021214	NP_067037			hypothetical protein LOC58489								hydrolase activity				0																		---	---	---	---
IL16	3603	broad.mit.edu	37	15	81485640	81485640	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81485640delT	uc010unp.1	+						IL16_uc002bgc.2_Intron|IL16_uc010blq.1_Intron|IL16_uc002bge.3_Intron	NM_172217	NP_757366			interleukin 16 isoform 2						immune response|interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|extracellular space|nucleus|plasma membrane	cytokine activity			ovary(2)|lung(1)|skin(1)	4																		---	---	---	---
STARD5	80765	broad.mit.edu	37	15	81611436	81611436	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81611436delA	uc002bgm.2	-						STARD5_uc002bgn.2_Intron	NM_181900	NP_871629			StAR-related lipid transfer protein 5						C21-steroid hormone biosynthetic process|lipid transport	cytosol	lipid binding			ovary(1)	1																		---	---	---	---
TMC3	342125	broad.mit.edu	37	15	81629957	81629959	+	Intron	DEL	GAG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81629957_81629959delGAG	uc002bgo.1	-						TMC3_uc010blr.1_Intron	NM_001080532	NP_001074001			transmembrane channel-like 3							integral to membrane				ovary(1)|liver(1)	2																		---	---	---	---
CPEB1	64506	broad.mit.edu	37	15	83236227	83236228	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83236227_83236228delAA	uc002bit.2	-						CPEB1_uc002biq.2_Intron|CPEB1_uc002bir.2_Intron|CPEB1_uc002bis.2_Intron|CPEB1_uc010uod.1_Intron|CPEB1_uc010uoe.1_Intron|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)															---	---	---	---
Unknown	0	broad.mit.edu	37	15	83412613	83412613	+	IGR	DEL	A	-	-	rs77579321		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83412613delA								AP3B2 (33978 upstream) : SCARNA15 (12084 downstream)																																			---	---	---	---
FSD2	123722	broad.mit.edu	37	15	83464584	83464585	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83464584_83464585delAA	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																		---	---	---	---
HOMER2	9455	broad.mit.edu	37	15	83607931	83607932	+	Intron	INS	-	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83607931_83607932insC	uc002bjg.2	-						HOMER2_uc002bjh.2_Intron|HOMER2_uc002bjj.2_Intron|HOMER2_uc002bji.2_Intron	NM_199330	NP_955362			homer 2 isoform 2						metabotropic glutamate receptor signaling pathway	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane					0																		---	---	---	---
C15orf40	123207	broad.mit.edu	37	15	83671553	83671553	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83671553delT	uc010uoo.1	-						C15orf40_uc010uon.1_Intron	NM_001160115	NP_001153587			hypothetical protein LOC123207 isoform d											skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	84012335	84012335	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84012335delT								BNC1 (58867 upstream) : SH3GL3 (103756 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	84063040	84063041	+	IGR	INS	-	AGGG	AGGG			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84063040_84063041insAGGG								BNC1 (109572 upstream) : SH3GL3 (53050 downstream)																																			---	---	---	---
ADAMTSL3	57188	broad.mit.edu	37	15	84582289	84582289	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84582289delT	uc002bjz.3	+						ADAMTSL3_uc010bmt.1_Intron|ADAMTSL3_uc010bmu.1_Intron	NM_207517	NP_997400			ADAMTS-like 3 precursor							proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			ovary(6)|central_nervous_system(5)|lung(5)|large_intestine(4)|breast(3)|skin(2)|kidney(1)|pancreas(1)	27			BRCA - Breast invasive adenocarcinoma(143;0.211)															---	---	---	---
Unknown	0	broad.mit.edu	37	15	85070267	85070267	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85070267delA								GOLGA6L5 (10189 upstream) : UBE2Q2P1 (160 downstream)																																			---	---	---	---
SCAND2	54581	broad.mit.edu	37	15	85184705	85184705	+	RNA	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85184705delA	uc002bku.2	+	5		c.3520delA			SCAND2_uc002bkt.2_RNA|uc002bky.1_5'Flank	NR_004859				Homo sapiens SCAND2 mRNA, complete cds.												0																		---	---	---	---
ALPK3	57538	broad.mit.edu	37	15	85405086	85405086	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85405086delT	uc002ble.2	+						ALPK3_uc010upc.1_5'Flank	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)															---	---	---	---
PDE8A	5151	broad.mit.edu	37	15	85624601	85624601	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85624601delG	uc002blh.2	+						PDE8A_uc002bli.2_Intron|PDE8A_uc010bnc.2_Intron|PDE8A_uc010bnd.2_Intron|PDE8A_uc002blj.2_Intron|PDE8A_uc002blk.2_Intron	NM_002605	NP_002596			phosphodiesterase 8A isoform 1						cyclic nucleotide metabolic process|regulation of transcription, DNA-dependent	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding|two-component response regulator activity			ovary(2)|pancreas(1)|skin(1)	4	Colorectal(223;0.227)		BRCA - Breast invasive adenocarcinoma(143;0.0608)															---	---	---	---
PDE8A	5151	broad.mit.edu	37	15	85669755	85669755	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85669755delT	uc002blh.2	+						PDE8A_uc002bli.2_Intron|PDE8A_uc010bnc.2_Intron|PDE8A_uc010bnd.2_Intron|PDE8A_uc002blj.2_Intron|PDE8A_uc002blk.2_Intron|PDE8A_uc002bll.2_Intron	NM_002605	NP_002596			phosphodiesterase 8A isoform 1						cyclic nucleotide metabolic process|regulation of transcription, DNA-dependent	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding|two-component response regulator activity			ovary(2)|pancreas(1)|skin(1)	4	Colorectal(223;0.227)		BRCA - Breast invasive adenocarcinoma(143;0.0608)															---	---	---	---
Unknown	0	broad.mit.edu	37	15	85731012	85731013	+	IGR	DEL	CA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85731012_85731013delCA								PDE8A (48642 upstream) : AKAP13 (192858 downstream)																																			---	---	---	---
AKAP13	11214	broad.mit.edu	37	15	86060581	86060582	+	Intron	INS	-	T	T	rs144012758	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86060581_86060582insT	uc002blv.1	+						AKAP13_uc002bls.2_Intron|AKAP13_uc002blt.1_Intron|AKAP13_uc002blu.1_Intron	NM_007200	NP_009131			A-kinase anchor protein 13 isoform 2						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|membrane|membrane fraction|nucleus	cAMP-dependent protein kinase activity|metal ion binding|protein binding|Rho guanyl-nucleotide exchange factor activity|signal transducer activity			central_nervous_system(3)|kidney(2)|urinary_tract(1)|liver(1)|skin(1)|ovary(1)	9																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	86398268	86398268	+	IGR	DEL	T	-	-	rs34828137		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86398268delT								KLHL25 (60079 upstream) : AGBL1 (286974 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	86660547	86660547	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86660547delT								KLHL25 (322358 upstream) : AGBL1 (24695 downstream)																																			---	---	---	---
AGBL1	123624	broad.mit.edu	37	15	86822483	86822483	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86822483delG	uc002blz.1	+						AGBL1_uc002bma.1_Intron|AGBL1_uc002bmb.1_Intron	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	86885378	86885378	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86885378delT	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	88372356	88372361	+	IGR	DEL	AGAGAG	-	-	rs111691160		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:88372356_88372361delAGAGAG								NCRNA00052 (249439 upstream) : NTRK3 (47627 downstream)																																			---	---	---	---
NTRK3	4916	broad.mit.edu	37	15	88423337	88423338	+	Intron	DEL	TT	-	-	rs71851481		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:88423337_88423338delTT	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)			---	---	---	---
NTRK3	4916	broad.mit.edu	37	15	88568279	88568280	+	Intron	DEL	CA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:88568279_88568280delCA	uc002bme.1	-						NTRK3_uc002bmh.2_Intron|NTRK3_uc002bmf.1_Intron|NTRK3_uc010upl.1_Intron|NTRK3_uc010bnh.1_Intron|NTRK3_uc002bmg.2_Intron|NTRK3_uc010bni.2_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	88916420	88916421	+	IGR	INS	-	AGA	AGA	rs148831649	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:88916420_88916421insAGA								NTRK3 (116759 upstream) : MRPL46 (86287 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	88916532	88916532	+	IGR	DEL	G	-	-	rs34160917		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:88916532delG								NTRK3 (116871 upstream) : MRPL46 (86176 downstream)																																			---	---	---	---
MRPL46	26589	broad.mit.edu	37	15	89009057	89009057	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89009057delA	uc002bmj.2	-						MRPL46_uc002bmi.1_5'Flank|MRPL46_uc002bmk.2_Intron|MRPS11_uc002bmm.2_5'Flank|MRPS11_uc002bml.2_5'Flank|MRPS11_uc002bmn.2_5'Flank|MRPS11_uc010bnj.2_5'Flank	NM_022163	NP_071446			mitochondrial ribosomal protein L46 precursor							mitochondrion|ribosome	hydrolase activity			central_nervous_system(1)	1	Lung NSC(78;0.203)		BRCA - Breast invasive adenocarcinoma(143;0.188)															---	---	---	---
Unknown	0	broad.mit.edu	37	15	89301895	89301895	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89301895delA								ISG20 (103016 upstream) : ACAN (44779 downstream)																																			---	---	---	---
AP3S2	10239	broad.mit.edu	37	15	90402493	90402493	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90402493delT	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)															---	---	---	---
TTLL13	440307	broad.mit.edu	37	15	90791783	90791784	+	5'Flank	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90791783_90791784insA	uc002bpd.1	+						TTLL13_uc002bpe.1_5'Flank	NM_001029964	NP_001025135			tubulin tyrosine ligase-like family, member 13						protein modification process		ATP binding|tubulin-tyrosine ligase activity				0	Melanoma(11;0.00551)|Lung NSC(78;0.0178)|all_lung(78;0.0378)		KIRC - Kidney renal clear cell carcinoma(17;0.0286)|BRCA - Breast invasive adenocarcinoma(143;0.0323)|Kidney(142;0.0514)															---	---	---	---
CRTC3	64784	broad.mit.edu	37	15	91186961	91186961	+	3'UTR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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								---	---	---	---
RCCD1	91433	broad.mit.edu	37	15	91503905	91503905	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91503905delC	uc002bqj.2	+						RCCD1_uc002bqk.2_Intron|RCCD1_uc002bql.2_Intron|RCCD1_uc010bob.2_Intron	NM_033544	NP_291022			RCC1 domain containing 1												0	Lung NSC(78;0.0987)|all_lung(78;0.175)		Lung(145;0.189)															---	---	---	---
VPS33B	26276	broad.mit.edu	37	15	91552953	91552953	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91552953delG	uc002bqp.1	-						VPS33B_uc002bqq.1_Intron|VPS33B_uc010uqu.1_Intron	NM_018668	NP_061138			vacuolar protein sorting 33B (yeast homolog))						cellular membrane fusion|lysosome localization|melanosome localization|platelet alpha granule organization|protein transport|vesicle docking involved in exocytosis	late endosome membrane|lysosomal membrane|perinuclear region of cytoplasm|platelet alpha granule	protein binding			ovary(2)	2	Lung NSC(78;0.0987)|all_lung(78;0.175)																	---	---	---	---
SV2B	9899	broad.mit.edu	37	15	91740435	91740436	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91740435_91740436insT	uc010uqv.1	+						SV2B_uc002bqt.2_Intron|SV2B_uc002bqu.3_Intron	NM_014848	NP_055663			synaptic vesicle protein 2B homolog						neurotransmitter transport	acrosomal vesicle|cell junction|integral to membrane|synaptic vesicle membrane	transmembrane transporter activity			ovary(3)|central_nervous_system(2)|skin(2)|upper_aerodigestive_tract(1)	8	Lung NSC(78;0.0987)|all_lung(78;0.172)		BRCA - Breast invasive adenocarcinoma(143;0.0895)															---	---	---	---
Unknown	0	broad.mit.edu	37	15	91963358	91963359	+	IGR	INS	-	TCTCTCTGTCTC	TCTCTCTGTCTC	rs139715662	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91963358_91963359insTCTCTCTGTCTC								SV2B (124710 upstream) : SLCO3A1 (433579 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	92233247	92233247	+	IGR	DEL	T	-	-	rs34224468		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:92233247delT								SV2B (394599 upstream) : SLCO3A1 (163691 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	92320549	92320549	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:92320549delA								SV2B (481901 upstream) : SLCO3A1 (76389 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	92334669	92334669	+	IGR	DEL	A	-	-	rs35853094		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:92334669delA								SV2B (496021 upstream) : SLCO3A1 (62269 downstream)																																			---	---	---	---
SLCO3A1	28232	broad.mit.edu	37	15	92629257	92629257	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:92629257delC	uc002bqx.2	+						SLCO3A1_uc002bqy.2_Intron|SLCO3A1_uc010boc.1_Intron|SLCO3A1_uc002bqz.1_Intron	NM_013272	NP_037404			solute carrier organic anion transporter family,						sodium-independent organic anion transport	integral to membrane|plasma membrane	sodium-independent organic anion transmembrane transporter activity			skin(1)	1	Lung NSC(78;0.0158)|all_lung(78;0.0255)		BRCA - Breast invasive adenocarcinoma(143;0.0841)															---	---	---	---
Unknown	0	broad.mit.edu	37	15	93327370	93327370	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:93327370delT								FAM174B (50066 upstream) : CHD2 (102063 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	93873153	93873154	+	Intron	DEL	TG	-	-	rs112844170	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:93873153_93873154delTG	uc002bsu.1	+											Homo sapiens cDNA FLJ37033 fis, clone BRACE2011389.																														---	---	---	---
Unknown	0	broad.mit.edu	37	15	94166258	94166258	+	IGR	DEL	G	-	-	rs34879777		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:94166258delG								RGMA (533825 upstream) : MCTP2 (608543 downstream)																																			---	---	---	---
MCTP2	55784	broad.mit.edu	37	15	95001209	95001209	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:95001209delG	uc002btj.2	+						MCTP2_uc010boj.2_Intron|MCTP2_uc010bok.2_Intron|MCTP2_uc002btl.2_Intron	NM_018349	NP_060819			multiple C2 domains, transmembrane 2 isoform 1						calcium-mediated signaling	integral to membrane|membrane fraction	calcium ion binding			ovary(1)|pancreas(1)|skin(1)	3	Lung NSC(78;0.0821)|all_lung(78;0.148)		BRCA - Breast invasive adenocarcinoma(143;0.0323)|OV - Ovarian serous cystadenocarcinoma(32;0.0593)															---	---	---	---
Unknown	0	broad.mit.edu	37	15	95091257	95091258	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:95091257_95091258delTT								MCTP2 (64077 upstream) : LOC145820 (885064 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	95400887	95400888	+	IGR	DEL	GC	-	-	rs34580686	byFrequency;by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:95400887_95400888delGC								MCTP2 (373707 upstream) : LOC145820 (575434 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	96790528	96790528	+	IGR	DEL	T	-	-	rs35733131		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:96790528delT								LOC145820 (739454 upstream) : NR2F2 (78629 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	98140597	98140597	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98140597delA								SPATA8 (811753 upstream) : LOC91948 (145249 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	98158500	98158501	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98158500_98158501insT								SPATA8 (829656 upstream) : LOC91948 (127345 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	98924859	98924859	+	IGR	DEL	A	-	-	rs67371320		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98924859delA								ARRDC4 (407792 upstream) : FAM169B (55532 downstream)																																			---	---	---	---
FAM169B	283777	broad.mit.edu	37	15	99022966	99022966	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99022966delA	uc002buk.1	-							NM_182562	NP_872368			hypothetical protein LOC283777												0																		---	---	---	---
FAM169B	283777	broad.mit.edu	37	15	99052675	99052675	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99052675delA	uc002buk.1	-							NM_182562	NP_872368			hypothetical protein LOC283777												0																		---	---	---	---
IGF1R	3480	broad.mit.edu	37	15	99473685	99473686	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99473685_99473686insT	uc002bul.2	+						IGF1R_uc010bon.2_Intron|IGF1R_uc010boo.1_Intron	NM_000875	NP_000866			insulin-like growth factor 1 receptor precursor						anti-apoptosis|immune response|insulin receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of DNA replication|protein autophosphorylation|protein tetramerization	microsome	ATP binding|identical protein binding|insulin binding|insulin receptor binding|insulin receptor substrate binding|insulin-like growth factor I binding|insulin-like growth factor receptor activity|metal ion binding|phosphatidylinositol 3-kinase binding			lung(3)|kidney(3)|ovary(1)|central_nervous_system(1)	8	all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261)		Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Mecasermin(DB01277)													---	---	---	---
PGPEP1L	145814	broad.mit.edu	37	15	99514424	99514432	+	Intron	DEL	GGGGGGGGG	-	-	rs74852431		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99514424_99514432delGGGGGGGGG	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	99556161	99556162	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99556161_99556162delTT								PGPEP1L (5137 upstream) : SYNM (89124 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	100456098	100456099	+	IGR	DEL	AA	-	-	rs71993572		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:100456098_100456099delAA								C15orf51 (108966 upstream) : ADAMTS17 (55544 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	100480914	100480916	+	IGR	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:100480914_100480916delTTT								C15orf51 (133782 upstream) : ADAMTS17 (30727 downstream)																																			---	---	---	---
ADAMTS17	170691	broad.mit.edu	37	15	100516084	100516085	+	Intron	INS	-	T	T	rs146057782	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:100516084_100516085insT	uc002bvv.1	-						ADAMTS17_uc002bvw.1_Intron	NM_139057	NP_620688			ADAM metallopeptidase with thrombospondin type 1						proteolysis	intracellular|proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(2)|central_nervous_system(1)	3	Lung NSC(78;0.00299)|all_lung(78;0.00457)|Melanoma(26;0.00571)		OV - Ovarian serous cystadenocarcinoma(32;0.0013)|LUSC - Lung squamous cell carcinoma(107;0.132)|Lung(145;0.161)	COAD - Colon adenocarcinoma(1;0.111)|all cancers(203;0.219)														---	---	---	---
LRRK1	79705	broad.mit.edu	37	15	101538209	101538209	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101538209delC	uc002bwr.2	+						LRRK1_uc010usb.1_Intron|LRRK1_uc010usc.1_Intron	NM_024652	NP_078928			leucine-rich repeat kinase 1						small GTPase mediated signal transduction	mitochondrion	ATP binding|GTP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			ovary(4)|lung(4)|central_nervous_system(3)|large_intestine(1)	12	Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)															---	---	---	---
Unknown	0	broad.mit.edu	37	15	101803388	101803388	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101803388delT								CHSY1 (11262 upstream) : SELS (7826 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	102438881	102438881	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102438881delA								OR4F15 (79555 upstream) : OR4F4 (23464 downstream)																																			---	---	---	---
NPRL3	8131	broad.mit.edu	37	16	183529	183532	+	Intron	DEL	TTGT	-	-	rs140186394		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:183529_183532delTTGT	uc002cfr.2	-						NPRL3_uc010uua.1_Intron|NPRL3_uc002cfp.1_Intron|NPRL3_uc002cfq.2_Intron|NPRL3_uc010uub.1_Intron|NPRL3_uc002cfs.1_Intron	NM_001077350	NP_001070818			conserved gene telomeric to alpha globin cluster								protein binding			ovary(1)	1																		---	---	---	---
AXIN1	8312	broad.mit.edu	37	16	353385	353386	+	Intron	DEL	TT	-	-	rs111734984		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:353385_353386delTT	uc002cgp.1	-						AXIN1_uc002cgq.1_Intron	NM_003502	NP_003493			axin 1 isoform a						activation of JUN kinase activity|activation of protein kinase activity|apoptosis|axial mesoderm formation|canonical Wnt receptor signaling pathway involved in neural plate anterior/posterior pattern formation|cellular protein complex assembly|cellular response to organic cyclic compound|cytoplasmic microtubule organization|determination of left/right symmetry|dorsal/ventral axis specification|embryonic eye morphogenesis|embryonic skeletal joint morphogenesis|forebrain anterior/posterior pattern formation|muscle cell development|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of fat cell differentiation|olfactory placode formation|optic placode formation|positive regulation of JNK cascade|positive regulation of peptidyl-serine phosphorylation|positive regulation of peptidyl-threonine phosphorylation|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of transcription, DNA-dependent|positive regulation of ubiquitin-protein ligase activity|regulation of catenin import into nucleus|tail morphogenesis|Wnt receptor signaling pathway involved in forebrain neuron fate commitment|Wnt receptor signaling pathway involved in somitogenesis	APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|cell cortex|cytoplasmic membrane-bounded vesicle|cytoplasmic microtubule|cytosol|lateral plasma membrane|nucleus|perinuclear region of cytoplasm|postsynaptic density	armadillo repeat domain binding|beta-catenin binding|GTPase activator activity|I-SMAD binding|p53 binding|protein complex scaffold|protein homodimerization activity|protein kinase binding|signal transducer activity|ubiquitin protein ligase binding			breast(1)|liver(1)	2		all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187)																---	---	---	---
Unknown	0	broad.mit.edu	37	16	443601	443601	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:443601delT								LOC100134368 (641 upstream) : NME4 (3124 downstream)																																			---	---	---	---
DECR2	26063	broad.mit.edu	37	16	460579	460579	+	Intron	DEL	T	-	-	rs11315123		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:460579delT	uc002chb.2	+						DECR2_uc002chc.2_Intron|DECR2_uc010bqv.2_Intron|DECR2_uc002chd.2_Intron|DECR2_uc002che.1_Intron	NM_020664	NP_065715			2,4-dienoyl CoA reductase 2							peroxisome	2,4-dienoyl-CoA reductase (NADPH) activity|binding				0		Hepatocellular(16;0.00015)																---	---	---	---
METRN	79006	broad.mit.edu	37	16	767426	767427	+	3'UTR	INS	-	G	G	rs147270224	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:767426_767427insG	uc002cjd.2	+	4					uc010bra.1_5'Flank	NM_024042	NP_076947			meteorin, glial cell differentiation regulator												0		Hepatocellular(780;0.00335)																---	---	---	---
LMF1	64788	broad.mit.edu	37	16	963828	963829	+	Intron	INS	-	AG	AG	rs151186514	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:963828_963829insAG	uc002ckj.2	-						LMF1_uc010brh.2_Intron|LMF1_uc010bri.2_Intron|LMF1_uc002ckk.2_Intron|LMF1_uc010uuu.1_Intron|LMF1_uc010uuv.1_Intron	NM_022773	NP_073610			lipase maturation factor 1							endoplasmic reticulum membrane|integral to membrane					0		Hepatocellular(780;0.00308)																---	---	---	---
IFT140	9742	broad.mit.edu	37	16	1567842	1567842	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1567842delT	uc002cmb.2	-						IFT140_uc002clz.2_Intron	NM_014714	NP_055529			intraflagellar transport 140											ovary(3)|pancreas(1)|skin(1)	5		Hepatocellular(780;0.219)																---	---	---	---
IFT140	9742	broad.mit.edu	37	16	1650895	1650897	+	Intron	DEL	AAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1650895_1650897delAAA	uc002cmb.2	-							NM_014714	NP_055529			intraflagellar transport 140											ovary(3)|pancreas(1)|skin(1)	5		Hepatocellular(780;0.219)																---	---	---	---
MAPK8IP3	23162	broad.mit.edu	37	16	1809115	1809115	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1809115delG	uc002cmk.2	+						MAPK8IP3_uc002cml.2_Intron|MAPK8IP3_uc010uvl.1_Intron	NM_015133	NP_055948			mitogen-activated protein kinase 8 interacting						vesicle-mediated transport	Golgi membrane	kinesin binding|MAP-kinase scaffold activity|protein kinase binding			breast(2)|central_nervous_system(1)	3																		---	---	---	---
C16orf73	254528	broad.mit.edu	37	16	1925559	1925559	+	Intron	DEL	T	-	-	rs111720551		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1925559delT	uc010uvr.1	-							NM_001163560	NP_001157032			hypothetical protein LOC254528 isoform 1						meiosis	cytoplasm					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	1978193	1978194	+	IGR	INS	-	TA	TA	rs4027416		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1978193_1978194insTA								HS3ST6 (9962 upstream) : SEPX1 (10041 downstream)																																			---	---	---	---
PKD1	5310	broad.mit.edu	37	16	2180674	2180674	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2180674delA	uc002cos.1	-						PKD1_uc002cot.1_Intron	NM_001009944	NP_001009944			polycystin 1 isoform 1 precursor						calcium-independent cell-matrix adhesion|homophilic cell adhesion|neuropeptide signaling pathway	basolateral plasma membrane|integral to plasma membrane	protein domain specific binding|sugar binding			central_nervous_system(2)|skin(1)	3																		---	---	---	---
PDPK1	5170	broad.mit.edu	37	16	2640130	2640130	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2640130delT	uc002cqs.2	+						PDPK1_uc002cqt.2_Intron|PDPK1_uc010bsn.2_Intron|PDPK1_uc002cqu.2_Intron|uc002cqw.1_5'Flank	NM_002613	NP_002604			3-phosphoinositide dependent protein kinase-1						actin cytoskeleton organization|activation of protein kinase B activity|insulin receptor signaling pathway|negative regulation of protein kinase activity|nerve growth factor receptor signaling pathway|peptidyl-threonine phosphorylation|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of establishment of protein localization in plasma membrane|synaptic transmission|T cell costimulation|T cell receptor signaling pathway	cytosol|nucleoplasm|plasma membrane	3-phosphoinositide-dependent protein kinase activity|ATP binding			central_nervous_system(2)|ovary(1)	3		Ovarian(90;0.17)			Celecoxib(DB00482)													---	---	---	---
TCEB2	6923	broad.mit.edu	37	16	2822706	2822706	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2822706delA	uc002crn.2	-						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																		---	---	---	---
IL32	9235	broad.mit.edu	37	16	3114266	3114268	+	5'Flank	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3114266_3114268delTTT	uc002cto.2	+						IL32_uc002ctk.2_5'Flank|IL32_uc010uwp.1_5'Flank|IL32_uc010btb.2_5'Flank|IL32_uc002ctl.2_5'Flank|IL32_uc002ctm.2_5'Flank|IL32_uc002ctn.2_5'Flank|IL32_uc010btc.1_5'Flank|IL32_uc002cts.3_5'Flank|IL32_uc002ctp.2_5'Flank|IL32_uc010uwq.1_5'Flank|IL32_uc002ctq.2_5'Flank|IL32_uc002ctr.2_5'Flank|IL32_uc002ctt.2_5'Flank|IL32_uc010uwr.1_5'Flank|IL32_uc002ctu.2_5'Flank	NM_004221	NP_004212			interleukin 32 isoform B						cell adhesion|defense response|immune response	extracellular space	cytokine activity			pancreas(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	3154796	3154796	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3154796delT								ZSCAN10 (5503 upstream) : MGC3771 (5665 downstream)																																			---	---	---	---
ZNF263	10127	broad.mit.edu	37	16	3326825	3326826	+	Intron	INS	-	T	T	rs150999333	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3326825_3326826insT	uc010uww.1	+							NM_005741	NP_005732			zinc finger protein 263						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(3)|ovary(1)	4																		---	---	---	---
ZNF75A	7627	broad.mit.edu	37	16	3364624	3364624	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3364624delT	uc002cut.3	+						ZNF75A_uc002cuv.3_Intron	NM_153028	NP_694573			zinc finger protein 75a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	3473168	3473168	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3473168delT								ZNF174 (13806 upstream) : ZNF597 (12943 downstream)																																			---	---	---	---
CREBBP	1387	broad.mit.edu	37	16	3885979	3885979	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3885979delC	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	3994946	3994946	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3994946delT								CREBBP (64825 upstream) : ADCY9 (17707 downstream)																																			---	---	---	---
SRL	6345	broad.mit.edu	37	16	4274148	4274149	+	Intron	DEL	GA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4274148_4274149delGA	uc002cvz.3	-						SRL_uc002cvy.3_Intron	NM_001098814	NP_001092284			sarcalumenin							sarcoplasmic reticulum lumen	GTP binding|GTPase activity			ovary(3)|skin(2)	5																		---	---	---	---
CORO7	79585	broad.mit.edu	37	16	4407353	4407357	+	Intron	DEL	TTTCT	-	-	rs150167261		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4407353_4407357delTTTCT	uc002cwh.3	-						CORO7_uc002cwe.2_Intron|CORO7_uc002cwf.2_Intron|CORO7_uc002cwg.3_Intron|CORO7_uc010uxh.1_Intron|CORO7_uc010uxi.1_Intron	NM_024535	NP_078811			coronin 7							cytoplasmic membrane-bounded vesicle|cytosol|Golgi membrane|integral to membrane of membrane fraction|soluble fraction					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	4597687	4597706	+	IGR	DEL	TTCCTTCTTTCTTTCTTTCT	-	-	rs144983706		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4597687_4597706delTTCCTTCTTTCTTTCTTTCT								C16orf5 (8871 upstream) : LOC342346 (8785 downstream)																																			---	---	---	---
SEPT12	124404	broad.mit.edu	37	16	4838179	4838180	+	Intron	DEL	AG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4838179_4838180delAG	uc002cxq.2	-						SEPT12_uc002cxr.2_Intron|SEPT12_uc010bty.2_Intron|uc002cxt.2_5'Flank	NM_144605	NP_653206			septin 12 isoform 2						cell cycle|cell division	cleavage furrow|midbody|perinuclear region of cytoplasm|septin complex|spindle|stress fiber	GDP binding|GTP binding|phosphatidylinositol binding|protein homodimerization activity			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	4997132	4997135	+	IGR	DEL	TCCA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4997132_4997135delTCCA								PPL (9996 upstream) : SEC14L5 (11183 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	5152567	5152570	+	IGR	DEL	TTTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5152567_5152570delTTTT								FAM86A (4778 upstream) : A2BP1 (916562 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	5432394	5432395	+	Intron	DEL	TT	-	-	rs34198517		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5432394_5432395delTT	uc002cyq.1	+											Homo sapiens cDNA clone IMAGE:5244947, **** WARNING: chimeric clone ****.																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	5677420	5677421	+	IGR	DEL	GT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5677420_5677421delGT								FAM86A (529631 upstream) : A2BP1 (391711 downstream)																																			---	---	---	---
A2BP1	54715	broad.mit.edu	37	16	6681409	6681410	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:6681409_6681410insT	uc002cys.2	+						A2BP1_uc010buf.1_Intron|A2BP1_uc002cyr.1_Intron|A2BP1_uc002cyt.2_Intron|A2BP1_uc010uxz.1_Intron|A2BP1_uc010uya.1_Intron|A2BP1_uc002cyv.1_Intron	NM_018723	NP_061193			ataxin 2-binding protein 1 isoform 4						mRNA processing|RNA splicing|RNA transport	nucleus|trans-Golgi network	nucleotide binding|protein C-terminus binding|RNA binding				0		all_cancers(2;4.54e-52)|Colorectal(2;6.95e-44)|all_epithelial(2;1.15e-37)|Lung NSC(2;0.000289)|all_lung(2;0.00148)|Myeloproliferative disorder(2;0.0122)|Medulloblastoma(2;0.0354)|all_neural(2;0.0381)|all_hematologic(2;0.0749)|Renal(2;0.0758)|Melanoma(2;0.211)		Colorectal(1;3.55e-51)|COAD - Colon adenocarcinoma(2;1.92e-46)|all cancers(1;5.36e-16)|Epithelial(1;3.98e-15)|READ - Rectum adenocarcinoma(2;3.71e-05)|GBM - Glioblastoma multiforme(1;0.0499)														---	---	---	---
A2BP1	54715	broad.mit.edu	37	16	6702455	6702455	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:6702455delA	uc002cys.2	+						A2BP1_uc010buf.1_Intron|A2BP1_uc002cyr.1_Intron|A2BP1_uc002cyt.2_Intron|A2BP1_uc010uxz.1_Intron|A2BP1_uc010uya.1_Intron|A2BP1_uc002cyv.1_Intron	NM_018723	NP_061193			ataxin 2-binding protein 1 isoform 4						mRNA processing|RNA splicing|RNA transport	nucleus|trans-Golgi network	nucleotide binding|protein C-terminus binding|RNA binding				0		all_cancers(2;4.54e-52)|Colorectal(2;6.95e-44)|all_epithelial(2;1.15e-37)|Lung NSC(2;0.000289)|all_lung(2;0.00148)|Myeloproliferative disorder(2;0.0122)|Medulloblastoma(2;0.0354)|all_neural(2;0.0381)|all_hematologic(2;0.0749)|Renal(2;0.0758)|Melanoma(2;0.211)		Colorectal(1;3.55e-51)|COAD - Colon adenocarcinoma(2;1.92e-46)|all cancers(1;5.36e-16)|Epithelial(1;3.98e-15)|READ - Rectum adenocarcinoma(2;3.71e-05)|GBM - Glioblastoma multiforme(1;0.0499)														---	---	---	---
A2BP1	54715	broad.mit.edu	37	16	6840914	6840914	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:6840914delT	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	7095654	7095654	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7095654delT	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	7108574	7108575	+	Intron	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7108574_7108575delTG	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	7380510	7380511	+	Intron	DEL	TT	-	-	rs59025287		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7380510_7380511delTT	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_5'Flank|A2BP1_uc002cyy.2_5'Flank|A2BP1_uc002cyx.2_5'Flank|A2BP1_uc010uyc.1_5'Flank	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	7407724	7407724	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7407724delC	uc002cys.2	+						A2BP1_uc010buf.1_Intron|A2BP1_uc002cyr.1_Intron|A2BP1_uc002cyt.2_Intron|A2BP1_uc010uxz.1_Intron|A2BP1_uc010uya.1_Intron|A2BP1_uc002cyv.1_Intron|A2BP1_uc010uyb.1_Intron|A2BP1_uc002cyw.2_Intron|A2BP1_uc002cyy.2_Intron|A2BP1_uc002cyx.2_Intron|A2BP1_uc010uyc.1_Intron	NM_018723	NP_061193			ataxin 2-binding protein 1 isoform 4						mRNA processing|RNA splicing|RNA transport	nucleus|trans-Golgi network	nucleotide binding|protein C-terminus binding|RNA binding				0		all_cancers(2;4.54e-52)|Colorectal(2;6.95e-44)|all_epithelial(2;1.15e-37)|Lung NSC(2;0.000289)|all_lung(2;0.00148)|Myeloproliferative disorder(2;0.0122)|Medulloblastoma(2;0.0354)|all_neural(2;0.0381)|all_hematologic(2;0.0749)|Renal(2;0.0758)|Melanoma(2;0.211)		Colorectal(1;3.55e-51)|COAD - Colon adenocarcinoma(2;1.92e-46)|all cancers(1;5.36e-16)|Epithelial(1;3.98e-15)|READ - Rectum adenocarcinoma(2;3.71e-05)|GBM - Glioblastoma multiforme(1;0.0499)														---	---	---	---
A2BP1	54715	broad.mit.edu	37	16	7436561	7436561	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7436561delT	uc002cys.2	+						A2BP1_uc010buf.1_Intron|A2BP1_uc002cyr.1_Intron|A2BP1_uc002cyt.2_Intron|A2BP1_uc010uxz.1_Intron|A2BP1_uc010uya.1_Intron|A2BP1_uc002cyv.1_Intron|A2BP1_uc010uyb.1_Intron|A2BP1_uc002cyw.2_Intron|A2BP1_uc002cyy.2_Intron|A2BP1_uc002cyx.2_Intron|A2BP1_uc010uyc.1_Intron	NM_018723	NP_061193			ataxin 2-binding protein 1 isoform 4						mRNA processing|RNA splicing|RNA transport	nucleus|trans-Golgi network	nucleotide binding|protein C-terminus binding|RNA binding				0		all_cancers(2;4.54e-52)|Colorectal(2;6.95e-44)|all_epithelial(2;1.15e-37)|Lung NSC(2;0.000289)|all_lung(2;0.00148)|Myeloproliferative disorder(2;0.0122)|Medulloblastoma(2;0.0354)|all_neural(2;0.0381)|all_hematologic(2;0.0749)|Renal(2;0.0758)|Melanoma(2;0.211)		Colorectal(1;3.55e-51)|COAD - Colon adenocarcinoma(2;1.92e-46)|all cancers(1;5.36e-16)|Epithelial(1;3.98e-15)|READ - Rectum adenocarcinoma(2;3.71e-05)|GBM - Glioblastoma multiforme(1;0.0499)														---	---	---	---
A2BP1	54715	broad.mit.edu	37	16	7507821	7507821	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7507821delA	uc002cys.2	+						A2BP1_uc010buf.1_Intron|A2BP1_uc002cyr.1_Intron|A2BP1_uc002cyt.2_Intron|A2BP1_uc010uxz.1_Intron|A2BP1_uc010uya.1_Intron|A2BP1_uc002cyv.1_Intron|A2BP1_uc010uyb.1_Intron|A2BP1_uc002cyw.2_Intron|A2BP1_uc002cyy.2_Intron|A2BP1_uc002cyx.2_Intron|A2BP1_uc010uyc.1_Intron	NM_018723	NP_061193			ataxin 2-binding protein 1 isoform 4						mRNA processing|RNA splicing|RNA transport	nucleus|trans-Golgi network	nucleotide binding|protein C-terminus binding|RNA binding				0		all_cancers(2;4.54e-52)|Colorectal(2;6.95e-44)|all_epithelial(2;1.15e-37)|Lung NSC(2;0.000289)|all_lung(2;0.00148)|Myeloproliferative disorder(2;0.0122)|Medulloblastoma(2;0.0354)|all_neural(2;0.0381)|all_hematologic(2;0.0749)|Renal(2;0.0758)|Melanoma(2;0.211)		Colorectal(1;3.55e-51)|COAD - Colon adenocarcinoma(2;1.92e-46)|all cancers(1;5.36e-16)|Epithelial(1;3.98e-15)|READ - Rectum adenocarcinoma(2;3.71e-05)|GBM - Glioblastoma multiforme(1;0.0499)														---	---	---	---
A2BP1	54715	broad.mit.edu	37	16	7550086	7550086	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7550086delA	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	8461166	8461166	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8461166delC								A2BP1 (697826 upstream) : TMEM114 (158337 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	8593443	8593464	+	IGR	DEL	CTTGCGTCATGCAATGGTGCAC	-	-	rs58465368		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8593443_8593464delCTTGCGTCATGCAATGGTGCAC								A2BP1 (830103 upstream) : TMEM114 (26039 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	9262253	9262253	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9262253delA								C16orf72 (48708 upstream) : GRIN2A (585014 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	9402628	9402629	+	IGR	INS	-	G	G	rs146762815	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9402628_9402629insG								C16orf72 (189083 upstream) : GRIN2A (444638 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	9844004	9844004	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9844004delA								C16orf72 (630459 upstream) : GRIN2A (3263 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	10415844	10415844	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10415844delC								GRIN2A (139233 upstream) : ATF7IP2 (64068 downstream)																																			---	---	---	---
CIITA	4261	broad.mit.edu	37	16	11005980	11005980	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11005980delT	uc002dai.3	+						CIITA_uc002daj.3_Intron|CIITA_uc002dak.3_Intron	NM_000246	NP_000237			class II transactivator						interferon-gamma-mediated signaling pathway|negative regulation of transcription from RNA polymerase II promoter|positive regulation of MHC class I biosynthetic process|positive regulation of transcription from RNA polymerase II promoter|response to antibiotic|transcription, DNA-dependent	nucleus	activating transcription factor binding|ATP binding|protein C-terminus binding|protein complex binding|transcription coactivator activity|transcription regulatory region DNA binding			central_nervous_system(1)	1								T	FLJ27352|CD274|CD273|RALGDS|RUNDC2A|C16orf75	PMBL|Hodgkin Lymphona|								---	---	---	---
Unknown	0	broad.mit.edu	37	16	11510970	11510970	+	IGR	DEL	C	-	-	rs111473327		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11510970delC								C16orf75 (65353 upstream) : LITAF (130612 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	11720703	11720703	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11720703delT								LITAF (39381 upstream) : SNN (41598 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	12031882	12031883	+	IGR	DEL	TG	-	-	rs116770375		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12031882_12031883delTG								GSPT1 (21363 upstream) : TNFRSF17 (27081 downstream)																																			---	---	---	---
SNX29	92017	broad.mit.edu	37	16	12480641	12480641	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12480641delA	uc002dby.3	+							NM_001080530	NP_001073999			sorting nexin 29						cell communication		phosphatidylinositol binding			ovary(1)	1																		---	---	---	---
CPPED1	55313	broad.mit.edu	37	16	12825582	12825582	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12825582delT	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	12938408	12938410	+	IGR	DEL	AAA	-	-	rs111601551		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12938408_12938410delAAA								CPPED1 (40664 upstream) : SHISA9 (57067 downstream)																																			---	---	---	---
SHISA9	729993	broad.mit.edu	37	16	13167814	13167815	+	Intron	INS	-	T	T	rs11442270		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:13167814_13167815insT	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																		---	---	---	---
SHISA9	729993	broad.mit.edu	37	16	13175396	13175398	+	Intron	DEL	TTT	-	-	rs79142091		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:13175396_13175398delTTT	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	14110178	14110178	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14110178delA								ERCC4 (63973 upstream) : MKL2 (55018 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	14155012	14155013	+	IGR	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14155012_14155013delAC								ERCC4 (108807 upstream) : MKL2 (10183 downstream)																																			---	---	---	---
MKL2	57496	broad.mit.edu	37	16	14297002	14297002	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14297002delT	uc010uza.1	+						MKL2_uc002dcg.2_Intron|MKL2_uc002dch.2_Intron|MKL2_uc010uzb.1_Intron	NM_014048	NP_054767			megakaryoblastic leukemia 2 protein						cell differentiation|muscle organ development|positive regulation of striated muscle tissue development|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent		identical protein binding|nucleic acid binding|transcription coactivator activity			ovary(3)|kidney(1)|pancreas(1)	5																		---	---	---	---
MKL2	57496	broad.mit.edu	37	16	14312561	14312561	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14312561delT	uc010uza.1	+						MKL2_uc002dcg.2_Intron|MKL2_uc002dch.2_Intron|MKL2_uc010uzb.1_Intron	NM_014048	NP_054767			megakaryoblastic leukemia 2 protein						cell differentiation|muscle organ development|positive regulation of striated muscle tissue development|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent		identical protein binding|nucleic acid binding|transcription coactivator activity			ovary(3)|kidney(1)|pancreas(1)	5																		---	---	---	---
PARN	5073	broad.mit.edu	37	16	14556507	14556508	+	Intron	INS	-	AGA	AGA	rs146679843	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14556507_14556508insAGA	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																		---	---	---	---
BFAR	51283	broad.mit.edu	37	16	14731688	14731689	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14731688_14731689delAA	uc002dco.2	+						BFAR_uc002dcm.2_Intron|BFAR_uc002dcn.2_Intron|BFAR_uc002dcp.2_Intron	NM_016561	NP_057645			bifunctional apoptosis regulator						anti-apoptosis|apoptosis	endoplasmic reticulum membrane|integral to plasma membrane|membrane fraction	structural molecule activity|zinc ion binding			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	15060861	15060862	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15060861_15060862delAA								NPIP (14931 upstream) : PDXDC1 (7737 downstream)																																			---	---	---	---
PDXDC1	23042	broad.mit.edu	37	16	15080954	15080954	+	Intron	DEL	A	-	-	rs74816966		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15080954delA	uc002dda.3	+						PDXDC1_uc010uzl.1_Intron|PDXDC1_uc010uzm.1_Intron|PDXDC1_uc010bvc.1_Intron|PDXDC1_uc002dcz.2_Intron|PDXDC1_uc002ddb.3_Intron|PDXDC1_uc010uzn.1_Intron|PDXDC1_uc002ddc.2_Intron	NM_015027	NP_055842			pyridoxal-dependent decarboxylase domain						carboxylic acid metabolic process		carboxy-lyase activity|protein binding|pyridoxal phosphate binding			skin(1)	1					Pyridoxal Phosphate(DB00114)													---	---	---	---
PDXDC1	23042	broad.mit.edu	37	16	15111650	15111652	+	Intron	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15111650_15111652delTTT	uc002dda.3	+						PDXDC1_uc010uzl.1_Intron|PDXDC1_uc010uzm.1_Intron|PDXDC1_uc002dcz.2_Intron|PDXDC1_uc002ddb.3_Intron|PDXDC1_uc010uzn.1_Intron|PDXDC1_uc002ddc.2_Intron	NM_015027	NP_055842			pyridoxal-dependent decarboxylase domain						carboxylic acid metabolic process		carboxy-lyase activity|protein binding|pyridoxal phosphate binding			skin(1)	1					Pyridoxal Phosphate(DB00114)													---	---	---	---
Unknown	0	broad.mit.edu	37	16	15385956	15385957	+	IGR	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15385956_15385957delAC								PDXDC1 (152761 upstream) : MPV17L (103654 downstream)																																			---	---	---	---
C16orf45	89927	broad.mit.edu	37	16	15606736	15606736	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15606736delA	uc002ddo.2	+						C16orf45_uc002ddp.2_Intron	NM_033201	NP_149978			hypothetical protein LOC89927 isoform 1											ovary(1)	1																		---	---	---	---
C16orf45	89927	broad.mit.edu	37	16	15613568	15613568	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15613568delG	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	15870962	15870963	+	Intron	DEL	AC	-	-	rs1569299		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15870962_15870963delAC	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	15928384	15928386	+	Intron	DEL	AAA	-	-	rs75140765		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15928384_15928386delAAA	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								---	---	---	---
ABCC6	368	broad.mit.edu	37	16	16266914	16266915	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:16266914_16266915insA	uc002den.3	-						ABCC6_uc010bvo.2_Intron	NM_001171	NP_001162			ATP-binding cassette, sub-family C, member 6						response to drug|visual perception	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			skin(2)|ovary(1)	3				UCEC - Uterine corpus endometrioid carcinoma (3;0.123)														---	---	---	---
XYLT1	64131	broad.mit.edu	37	16	17202273	17202274	+	3'UTR	INS	-	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:17202273_17202274insG	uc002dfa.2	-	12						NM_022166	NP_071449			xylosyltransferase I						glycosaminoglycan biosynthetic process	endoplasmic reticulum membrane|extracellular region|Golgi membrane|integral to membrane	acetylglucosaminyltransferase activity|protein xylosyltransferase activity			ovary(4)	4																		---	---	---	---
XYLT1	64131	broad.mit.edu	37	16	17436579	17436579	+	Intron	DEL	A	-	-	rs78391175		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:17436579delA	uc002dfa.2	-							NM_022166	NP_071449			xylosyltransferase I						glycosaminoglycan biosynthetic process	endoplasmic reticulum membrane|extracellular region|Golgi membrane|integral to membrane	acetylglucosaminyltransferase activity|protein xylosyltransferase activity			ovary(4)	4																		---	---	---	---
XYLT1	64131	broad.mit.edu	37	16	17515849	17515849	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:17515849delT	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	17641681	17641684	+	IGR	DEL	ATCT	-	-	rs66504203		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:17641681_17641684delATCT								XYLT1 (76943 upstream) : NOMO2 (869499 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	17934257	17934257	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:17934257delA								XYLT1 (369519 upstream) : NOMO2 (576926 downstream)																																			---	---	---	---
ARL6IP1	23204	broad.mit.edu	37	16	18814382	18814396	+	5'Flank	DEL	TTTTTTTTTTTTTTT	-	-	rs143428863		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18814382_18814396delTTTTTTTTTTTTTTT	uc002dfl.1	-						ARL6IP1_uc010van.1_5'Flank|ARL6IP1_uc010bvz.1_5'Flank	NM_015161	NP_055976			ADP-ribosylation factor-like 6 interacting							integral to membrane	protein binding				0																		---	---	---	---
SMG1	23049	broad.mit.edu	37	16	18883764	18883764	+	Intron	DEL	A	-	-	rs117332168	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18883764delA	uc002dfm.2	-						SMG1_uc010bwb.2_Intron	NM_015092	NP_055907			PI-3-kinase-related kinase SMG-1						DNA repair|mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|peptidyl-serine phosphorylation|phosphatidylinositol phosphorylation|protein autophosphorylation	cytoplasm|nucleus	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			breast(5)|stomach(4)|lung(4)|kidney(2)|ovary(1)	16																		---	---	---	---
TMC7	79905	broad.mit.edu	37	16	19020932	19020932	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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	19115599	19115600	+	IGR	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19115599_19115600delTG								COQ7 (24249 upstream) : ITPRIPL2 (9654 downstream)																																			---	---	---	---
TMC5	79838	broad.mit.edu	37	16	19502034	19502053	+	Intron	DEL	TTCCTTCCTTCCTTCCTTCC	-	-	rs71887982		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19502034_19502053delTTCCTTCCTTCCTTCCTTCC	uc002dgc.3	+						TMC5_uc010vaq.1_Intron|TMC5_uc002dgb.3_Intron|TMC5_uc010var.1_Intron|TMC5_uc002dgd.1_Intron|TMC5_uc002dge.3_Intron|TMC5_uc002dgf.3_Intron|TMC5_uc002dgg.3_Intron	NM_001105248	NP_001098718			transmembrane channel-like 5 isoform a							integral to membrane				skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	19966223	19966224	+	IGR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19966223_19966224insA								GPRC5B (69391 upstream) : GPR139 (76819 downstream)																																			---	---	---	---
ERI2	112479	broad.mit.edu	37	16	20902322	20902322	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20902322delT	uc002dht.3	-						DCUN1D3_uc002dhz.2_Intron	NM_001142725	NP_001136197			exoribonuclease 2 isoform 1							intracellular	exonuclease activity|nucleic acid binding|zinc ion binding			large_intestine(1)	1																		---	---	---	---
DNAH3	55567	broad.mit.edu	37	16	21118102	21118103	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21118102_21118103insA	uc010vbe.1	-						DNAH3_uc002die.2_Intron	NM_017539	NP_060009			dynein, axonemal, heavy chain 3						ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(10)|skin(3)|large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	18				GBM - Glioblastoma multiforme(48;0.207)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	21371807	21371808	+	IGR	DEL	TG	-	-	rs10541508		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21371807_21371808delTG								NCRNA00169 (41895 upstream) : NPIPL3 (41643 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	21469830	21469830	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21469830delC	uc002diq.3	+						LOC100271836_uc002diu.1_Intron|LOC100271836_uc002diz.1_5'Flank					Homo sapiens cDNA FLJ59829 complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	21890632	21890632	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21890632delA	uc002djr.3	-						uc002djs.3_Intron|uc010vbo.1_RNA	NM_130464	NP_569731			nuclear pore complex interacting protein-like 3																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	21948326	21948326	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21948326delA								RRN3P1 (116595 upstream) : UQCRC2 (16283 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	22665185	22665185	+	IGR	DEL	A	-	-	rs71213770		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22665185delA								LOC653786 (76999 upstream) : HS3ST2 (160675 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	22805805	22805806	+	IGR	INS	-	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22805805_22805806insG								LOC653786 (217619 upstream) : HS3ST2 (20054 downstream)																																			---	---	---	---
HS3ST2	9956	broad.mit.edu	37	16	22896655	22896655	+	Intron	DEL	A	-	-	rs66534821		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22896655delA	uc002dli.2	+						HS3ST2_uc002dlj.2_Intron	NM_006043	NP_006034			heparan sulfate D-glucosaminyl							Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine 3-sulfotransferase 2 activity			ovary(1)|pancreas(1)	2				GBM - Glioblastoma multiforme(48;0.0299)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	23185353	23185353	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23185353delA								USP31 (24762 upstream) : SCNN1G (8687 downstream)																																			---	---	---	---
SCNN1B	6338	broad.mit.edu	37	16	23315653	23315656	+	Intron	DEL	ACAC	-	-	rs146184597		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23315653_23315656delACAC	uc002dln.2	+							NM_000336	NP_000327			sodium channel, nonvoltage-gated 1, beta						excretion|sensory perception of taste	apical plasma membrane	ligand-gated sodium channel activity|WW domain binding			ovary(3)|breast(2)|large_intestine(1)|pancreas(1)	7				GBM - Glioblastoma multiforme(48;0.0465)	Amiloride(DB00594)|Triamterene(DB00384)													---	---	---	---
SCNN1B	6338	broad.mit.edu	37	16	23354797	23354800	+	Intron	DEL	AAGG	-	-	rs149808226	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23354797_23354800delAAGG	uc002dln.2	+							NM_000336	NP_000327			sodium channel, nonvoltage-gated 1, beta						excretion|sensory perception of taste	apical plasma membrane	ligand-gated sodium channel activity|WW domain binding			ovary(3)|breast(2)|large_intestine(1)|pancreas(1)	7				GBM - Glioblastoma multiforme(48;0.0465)	Amiloride(DB00594)|Triamterene(DB00384)													---	---	---	---
COG7	91949	broad.mit.edu	37	16	23420386	23420387	+	Intron	DEL	GT	-	-	rs28587587		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23420386_23420387delGT	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)														---	---	---	---
PALB2	79728	broad.mit.edu	37	16	23619548	23619549	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23619548_23619549delTT	uc002dlx.1	-							NM_024675	NP_078951			partner and localizer of BRCA2						double-strand break repair via homologous recombination	nucleoplasm	DNA binding|protein binding			lung(3)|breast(3)|ovary(2)|skin(1)|kidney(1)|pancreas(1)	11				GBM - Glioblastoma multiforme(48;0.0167)				F|N|Mis			Wilms tumor|medulloblastoma|AML ,breast		Direct_reversal_of_damage|Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia_type_N|Fanconi_Anemia|PALB2-associated_Familial_Breast_and_Pancreatic_Cancer|Pancreatic_Cancer_Familial_Clustering_of				---	---	---	---
PRKCB	5579	broad.mit.edu	37	16	24167604	24167605	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24167604_24167605delTT	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	24680809	24680809	+	Intron	DEL	A	-	-	rs112501966		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24680809delA	uc002dml.1	-											Homo sapiens cDNA FLJ45256 fis, clone BRHIP2016125.																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	24695619	24695619	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24695619delG								RBBP6 (111438 upstream) : TNRC6A (45430 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	24737029	24737029	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24737029delA								RBBP6 (152848 upstream) : TNRC6A (4020 downstream)																																			---	---	---	---
SLC5A11	115584	broad.mit.edu	37	16	24856546	24856546	+	5'Flank	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24856546delA	uc002dmu.2	+						SLC5A11_uc002dms.2_5'Flank|SLC5A11_uc010vcd.1_5'Flank|SLC5A11_uc002dmt.2_5'Flank|SLC5A11_uc010vce.1_5'Flank|SLC5A11_uc010bxt.2_5'Flank	NM_052944	NP_443176			solute carrier family 5 (sodium/glucose						apoptosis|carbohydrate transport|sodium ion transport	integral to membrane|plasma membrane	polyol transmembrane transporter activity|symporter activity			ovary(2)	2				GBM - Glioblastoma multiforme(48;0.0365)														---	---	---	---
LCMT1	51451	broad.mit.edu	37	16	25141967	25141967	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25141967delA	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	25300771	25300774	+	IGR	DEL	TTCT	-	-	rs8044599		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25300771_25300774delTTCT								ZKSCAN2 (31916 upstream) : HS3ST4 (402573 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	25452363	25452364	+	IGR	INS	-	TG	TG	rs141496461	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25452363_25452364insTG								ZKSCAN2 (183508 upstream) : HS3ST4 (250983 downstream)																																			---	---	---	---
HS3ST4	9951	broad.mit.edu	37	16	25775773	25775774	+	Intron	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25775773_25775774delTG	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	25865441	25865441	+	Intron	DEL	C	-	-	rs75525216		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25865441delC	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	25952854	25952854	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25952854delT	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	25974585	25974585	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25974585delT	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	26192747	26192748	+	IGR	INS	-	C	C	rs145440798	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26192747_26192748insC								HS3ST4 (43739 upstream) : C16orf82 (885471 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	26268893	26268893	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26268893delA								HS3ST4 (119885 upstream) : C16orf82 (809326 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	26282537	26282537	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26282537delT								HS3ST4 (133529 upstream) : C16orf82 (795682 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	27088704	27088705	+	IGR	INS	-	CTTT	CTTT	rs143025532	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27088704_27088705insCTTT								C16orf82 (8218 upstream) : JMJD5 (126102 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	27127149	27127149	+	IGR	DEL	A	-	-	rs10715949		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27127149delA								C16orf82 (46663 upstream) : JMJD5 (87658 downstream)																																			---	---	---	---
GSG1L	146395	broad.mit.edu	37	16	28001060	28001062	+	Intron	DEL	AAA	-	-	rs151290281		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28001060_28001062delAAA	uc002doz.2	-						GSG1L_uc010bya.1_Intron	NM_001109763	NP_001103233			GSG1-like isoform 1							integral to membrane				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	28564195	28564195	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28564195delA	uc010vct.1	-						CCDC101_uc002dqf.2_5'Flank					RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	28821875	28821875	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28821875delA	uc010vct.1	-						uc002dqx.1_Intron					RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																														---	---	---	---
ATXN2L	11273	broad.mit.edu	37	16	28844038	28844038	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28844038delT	uc002drc.2	+						uc010vct.1_Intron|ATXN2L_uc010byl.1_Intron|ATXN2L_uc002drb.2_Intron|ATXN2L_uc002dqy.2_Intron|ATXN2L_uc002dra.2_Intron|ATXN2L_uc002dqz.2_Intron|ATXN2L_uc010vdb.1_Intron|ATXN2L_uc002dre.2_Intron|ATXN2L_uc002drf.2_Intron|ATXN2L_uc002drg.2_5'Flank	NM_007245	NP_009176			ataxin 2 related protein isoform A							membrane				upper_aerodigestive_tract(1)|ovary(1)	2																		---	---	---	---
CD19	930	broad.mit.edu	37	16	28944128	28944129	+	Intron	DEL	TC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28944128_28944129delTC	uc002drs.2	+						uc010vct.1_Intron|CD19_uc010byo.1_Intron	NM_001770	NP_001761			CD19 antigen precursor						cellular defense response	external side of plasma membrane|integral to plasma membrane	protein binding|receptor signaling protein activity			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	29351684	29351684	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29351684delT	uc010vct.1	-						RUNDC2C_uc010bys.1_Intron					RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																														---	---	---	---
MAZ	4150	broad.mit.edu	37	16	29821984	29821987	+	3'UTR	DEL	TTTT	-	-	rs112142128		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29821984_29821987delTTTT	uc002dty.2	+	5					uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|MAZ_uc002dtv.1_3'UTR|MAZ_uc010vdx.1_3'UTR|MAZ_uc002dtw.2_3'UTR|MAZ_uc002dtx.2_3'UTR|MAZ_uc010bzg.2_3'UTR|MAZ_uc002dtz.1_3'UTR|MAZ_uc002dua.2_3'UTR|MAZ_uc010vdy.1_3'UTR|uc002duc.1_RNA|PRRT2_uc002dud.2_5'Flank|PRRT2_uc002due.3_5'Flank|PRRT2_uc002duf.1_5'Flank	NM_002383	NP_002374			MYC-associated zinc finger protein isoform 1						regulation of transcription, DNA-dependent|termination of RNA polymerase II transcription|transcription initiation from RNA polymerase II promoter	nucleus	DNA binding|protein binding|RNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
PRRT2	112476	broad.mit.edu	37	16	29826362	29826364	+	3'UTR	DEL	GCC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29826362_29826364delGCC	uc002due.3	+	4					uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|PRRT2_uc002duf.1_3'UTR|C16orf53_uc002dug.3_5'Flank	NM_145239	NP_660282			proline-rich transmembrane protein 2						response to biotic stimulus	integral to membrane					0																		---	---	---	---
BOLA2	552900	broad.mit.edu	37	16	30029284	30029286	+	Intron	DEL	AAA	-	-	rs113271952		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30029284_30029286delAAA	uc010bzb.1	-						uc002dtf.2_Intron					SubName: Full=Putative uncharacterized protein ENSP00000369970; Flags: Fragment;												0																		---	---	---	---
LOC595101	595101	broad.mit.edu	37	16	30301097	30301097	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30301097delA	uc002dxp.1	-							NR_002453				Homo sapiens cDNA FLJ39663 fis, clone SMINT2007187.												0																		---	---	---	---
STX4	6810	broad.mit.edu	37	16	31050769	31050769	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31050769delT	uc002eal.2	+						STX4_uc002eak.2_Intron|STX4_uc002eam.2_Intron|uc002ean.1_5'Flank	NM_004604	NP_004595			syntaxin 4						intracellular protein transport|platelet activation|post-Golgi vesicle-mediated transport	basolateral plasma membrane|cell surface|cytosol|integral to membrane|plasma membrane enriched fraction|specific granule|vacuole	SNAP receptor activity				0																		---	---	---	---
ZNF668	79759	broad.mit.edu	37	16	31074788	31074788	+	Intron	DEL	A	-	-	rs78977889		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31074788delA	uc010caf.2	-						ZNF668_uc002eao.2_Intron	NM_024706	NP_078982			zinc finger protein 668						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(4)	4																		---	---	---	---
ITGAX	3687	broad.mit.edu	37	16	31370135	31370137	+	Intron	DEL	TTT	-	-	rs142979565		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31370135_31370137delTTT	uc002ebu.1	+						ITGAX_uc002ebt.2_Intron|ITGAX_uc010vfk.1_5'Flank	NM_000887	NP_000878			integrin alpha X precursor						blood coagulation|cell adhesion|integrin-mediated signaling pathway|leukocyte migration|organ morphogenesis	integrin complex	protein binding|receptor activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	32083409	32083410	+	IGR	DEL	GT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32083409_32083410delGT								ZNF267 (154783 upstream) : HERC2P4 (79200 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32371012	32371012	+	IGR	DEL	A	-	-	rs76763000		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32371012delA								HERC2P4 (207138 upstream) : TP53TG3B (313829 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32387422	32387422	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32387422delG								HERC2P4 (223548 upstream) : TP53TG3B (297419 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32400646	32400646	+	IGR	DEL	T	-	-	rs143885987		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32400646delT								HERC2P4 (236772 upstream) : TP53TG3B (284195 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32423001	32423001	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32423001delT								HERC2P4 (259127 upstream) : TP53TG3B (261840 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32428788	32428789	+	IGR	INS	-	C	C	rs150978089	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32428788_32428789insC								HERC2P4 (264914 upstream) : TP53TG3B (256052 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32446696	32446696	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32446696delC								HERC2P4 (282822 upstream) : TP53TG3B (238145 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32518493	32518493	+	IGR	DEL	G	-	-	rs76677034		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32518493delG								HERC2P4 (354619 upstream) : TP53TG3B (166348 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32522596	32522596	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32522596delA								HERC2P4 (358722 upstream) : TP53TG3B (162245 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32532115	32532116	+	IGR	INS	-	A	A	rs141107018		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32532115_32532116insA								HERC2P4 (368241 upstream) : TP53TG3B (152725 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32534235	32534235	+	IGR	DEL	A	-	-	rs113189996		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32534235delA								HERC2P4 (370361 upstream) : TP53TG3B (150606 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32542450	32542450	+	IGR	DEL	A	-	-	rs113216239		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32542450delA								HERC2P4 (378576 upstream) : TP53TG3B (142391 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32574917	32574918	+	IGR	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32574917_32574918delTG								HERC2P4 (411043 upstream) : TP53TG3B (109923 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32618573	32618574	+	IGR	DEL	AA	-	-	rs113288475		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32618573_32618574delAA								HERC2P4 (454699 upstream) : TP53TG3B (66267 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32632412	32632412	+	IGR	DEL	G	-	-	rs76118947		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32632412delG								HERC2P4 (468538 upstream) : TP53TG3B (52429 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32841066	32841066	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32841066delC								TP53TG3B (152188 upstream) : SLC6A10P (47731 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32844735	32844735	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32844735delG								TP53TG3B (155857 upstream) : SLC6A10P (44062 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32851409	32851409	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32851409delA								TP53TG3B (162531 upstream) : SLC6A10P (37388 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	33530019	33530019	+	IGR	DEL	T	-	-	rs111564755		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33530019delT								SLC6A10P (633556 upstream) : MIR1826 (435489 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	33537029	33537030	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33537029_33537030insT								SLC6A10P (640566 upstream) : MIR1826 (428478 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	33589953	33589953	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33589953delA								SLC6A10P (693490 upstream) : MIR1826 (375555 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	33860349	33860350	+	IGR	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33860349_33860350delAC								SLC6A10P (963886 upstream) : MIR1826 (105158 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	33955970	33955970	+	IGR	DEL	T	-	-	rs113634398		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33955970delT								None (None upstream) : MIR1826 (9538 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	33967631	33967631	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33967631delA								MIR1826 (2039 upstream) : UBE2MP1 (436171 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	33997296	33997297	+	IGR	INS	-	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33997296_33997297insC								MIR1826 (31704 upstream) : UBE2MP1 (406505 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	34728572	34728575	+	IGR	DEL	AAAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:34728572_34728575delAAAA								LOC146481 (13605 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	34943751	34943751	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:34943751delT								LOC146481 (228784 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	34998943	34998944	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:34998943_34998944delAA								LOC146481 (283976 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	35230210	35230210	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:35230210delC								LOC146481 (515243 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	46464230	46464231	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46464230_46464231delTT								None (None upstream) : ANKRD26P1 (39018 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	47058294	47058297	+	IGR	DEL	TGTG	-	-	rs68189281		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47058294_47058297delTGTG								DNAJA2 (50669 upstream) : NETO2 (57145 downstream)																																			---	---	---	---
NETO2	81831	broad.mit.edu	37	16	47165311	47165311	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47165311delT	uc002eer.1	-						NETO2_uc010vgf.1_5'Flank|NETO2_uc002ees.1_Intron	NM_018092	NP_060562			neuropilin- and tolloid-like protein 2							integral to membrane	receptor activity				0		all_cancers(37;0.00114)|all_lung(18;0.00432)|Lung NSC(13;0.0384)|Breast(268;0.174)													HNSCC(25;0.065)			---	---	---	---
ITFG1	81533	broad.mit.edu	37	16	47292700	47292700	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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)																---	---	---	---
Unknown	0	broad.mit.edu	37	16	48042009	48042009	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48042009delA								PHKB (306576 upstream) : ABCC12 (74875 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	48193750	48193750	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48193750delA								ABCC12 (3821 upstream) : ABCC11 (7072 downstream)																																			---	---	---	---
LONP2	83752	broad.mit.edu	37	16	48311580	48311580	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48311580delT	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	48381942	48381942	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48381942delT	uc002efi.1	+						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																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	48709879	48709880	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48709879_48709880delTT								N4BP1 (65759 upstream) : CBLN1 (602331 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	48965465	48965468	+	IGR	DEL	CACT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48965465_48965468delCACT								N4BP1 (321345 upstream) : CBLN1 (346743 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	49308578	49308578	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49308578delT								N4BP1 (664458 upstream) : CBLN1 (3633 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	49350578	49350579	+	IGR	DEL	GA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49350578_49350579delGA								CBLN1 (34863 upstream) : C16orf78 (57229 downstream)																																			---	---	---	---
ZNF423	23090	broad.mit.edu	37	16	49620177	49620177	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49620177delT	uc002efs.2	-						ZNF423_uc010vgn.1_Intron	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	50023053	50023063	+	IGR	DEL	AAAACAAAAAC	-	-	rs143111940	by1000genomes;by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50023053_50023063delAAAACAAAAAC								ZNF423 (162135 upstream) : TMEM188 (36126 downstream)																																			---	---	---	---
HEATR3	55027	broad.mit.edu	37	16	50138270	50138270	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50138270delA	uc002efw.2	+						HEATR3_uc002efx.2_Intron|uc002efy.2_5'Flank	NM_182922	NP_891552			HEAT repeat containing 3								binding			ovary(1)|skin(1)	2																		---	---	---	---
PAPD5	64282	broad.mit.edu	37	16	50252247	50252247	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50252247delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	50275630	50275632	+	IGR	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50275630_50275632delTTT								PAPD5 (6413 upstream) : ADCY7 (24830 downstream)																																			---	---	---	---
NOD2	64127	broad.mit.edu	37	16	50761805	50761805	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50761805delT	uc002egm.1	+						NOD2_uc010vgq.1_Intron	NM_022162	NP_071445			nucleotide-binding oligomerization domain						activation of MAPK activity involved in innate immune response|cytokine production involved in immune response|detection of bacterium|detection of muramyl dipeptide|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of macrophage apoptosis|nucleotide-binding oligomerization domain containing 2 signaling pathway|positive regulation of B cell activation|positive regulation of dendritic cell antigen processing and presentation|positive regulation of epithelial cell proliferation|positive regulation of ERK1 and ERK2 cascade|positive regulation of gamma-delta T cell activation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-1 beta secretion|positive regulation of interleukin-10 production|positive regulation of interleukin-17 production|positive regulation of interleukin-6 production|positive regulation of JNK cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of nitric-oxide synthase biosynthetic process|positive regulation of Notch signaling pathway|positive regulation of phosphatidylinositol 3-kinase activity|positive regulation of prostaglandin-E synthase activity|positive regulation of prostaglandin-endoperoxide synthase activity|positive regulation of stress-activated MAPK cascade|positive regulation of tumor necrosis factor production|positive regulation of type 2 immune response|protein oligomerization|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cell surface|cytosol|plasma membrane|vesicle	ATP binding|CARD domain binding|muramyl dipeptide binding|protein kinase binding			ovary(3)|skin(1)	4		all_cancers(37;0.0156)																---	---	---	---
SALL1	6299	broad.mit.edu	37	16	51187249	51187251	+	5'Flank	DEL	TTA	-	-	rs143328865		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:51187249_51187251delTTA	uc010vgs.1	-						SALL1_uc010vgr.1_5'Flank|SALL1_uc010cbv.2_5'Flank	NM_002968	NP_002959			sal-like 1 isoform a						adrenal gland development|branching involved in ureteric bud morphogenesis|embryonic digestive tract development|embryonic digit morphogenesis|gonad development|histone deacetylation|inductive cell-cell signaling|mesenchymal to epithelial transition involved in metanephros morphogenesis|negative regulation of transcription from RNA polymerase II promoter|olfactory bulb interneuron differentiation|olfactory bulb mitral cell layer development|olfactory nerve development|outer ear morphogenesis|pituitary gland development|positive regulation of transcription from RNA polymerase II promoter|positive regulation of Wnt receptor signaling pathway|ureteric bud invasion|ventricular septum development	chromocenter|cytoplasm|heterochromatin|nucleus	beta-catenin binding|DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(5)|ovary(3)	8		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)															---	---	---	---
Unknown	0	broad.mit.edu	37	16	51249447	51249447	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:51249447delT								SALL1 (64264 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	51958379	51958380	+	IGR	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:51958379_51958380delTG								SALL1 (773196 upstream) : TOX3 (513538 downstream)																																	OREG0002645	type=REGULATORY REGION|Gene=SALL1-CHD9|Dataset=Vista Enhancers|EvidenceSubtype=In-vivo LacZ Expression Assay	---	---	---	---
Unknown	0	broad.mit.edu	37	16	52665234	52665234	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:52665234delT								TOX3 (83520 upstream) : CHD9 (423711 downstream)																																			---	---	---	---
RBL2	5934	broad.mit.edu	37	16	53480056	53480056	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53480056delA	uc002ehi.3	+						RBL2_uc010vgv.1_Intron|RBL2_uc002ehj.2_Intron	NM_005611	NP_005602			retinoblastoma-like 2 (p130)						cell cycle|chromatin modification|regulation of cell cycle|regulation of lipid kinase activity|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus	DNA binding|protein binding			ovary(2)|lung(2)|upper_aerodigestive_tract(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	54532299	54532300	+	IGR	DEL	AA	-	-	rs113948872		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54532299_54532300delAA								IRX3 (211921 upstream) : IRX5 (432811 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	54613493	54613507	+	IGR	DEL	AGAGGAAGAAGAAGC	-	-	rs62034184	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54613493_54613507delAGAGGAAGAAGAAGC								IRX3 (293115 upstream) : IRX5 (351604 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	54996069	54996069	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54996069delT								IRX5 (27676 upstream) : IRX6 (362402 downstream)																																			---	---	---	---
GNAO1	2775	broad.mit.edu	37	16	56320608	56320609	+	Intron	DEL	TG	-	-	rs149898139		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56320608_56320609delTG	uc002eit.3	+						GNAO1_uc002eiu.3_Intron	NM_138736	NP_620073			guanine nucleotide binding protein, alpha						dopamine receptor signaling pathway|G-protein signaling, coupled to cAMP nucleotide second messenger|muscle contraction	heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|GTP binding|GTPase activity|metabotropic serotonin receptor binding|signal transducer activity			lung(1)|breast(1)	2		all_neural(199;0.159)																---	---	---	---
Unknown	0	broad.mit.edu	37	16	56747919	56747919	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56747919delC								MT1X (29812 upstream) : NUP93 (16098 downstream)																																			---	---	---	---
NUP93	9688	broad.mit.edu	37	16	56876401	56876401	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56876401delA	uc002eka.2	+						NUP93_uc002ekb.2_Intron|NUP93_uc010vhi.1_Intron	NM_014669	NP_055484			nucleoporin 93kDa						carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear pore	protein binding			ovary(1)|lung(1)	2																		---	---	---	---
POLR2C	5432	broad.mit.edu	37	16	57501852	57501852	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57501852delT	uc002elt.1	+						POLR2C_uc010vhq.1_Intron	NM_032940	NP_116558			DNA directed RNA polymerase II polypeptide C						mRNA capping|nuclear mRNA splicing, via spliceosome|positive regulation of viral transcription|protein phosphorylation|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	DNA-directed RNA polymerase II, core complex	DNA binding|DNA-directed RNA polymerase activity|protein dimerization activity				0																		---	---	---	---
GPR56	9289	broad.mit.edu	37	16	57665020	57665020	+	Intron	DEL	T	-	-	rs34379257		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57665020delT	uc002emb.2	+						GPR56_uc002elz.1_Intron|GPR56_uc002ema.1_Intron|GPR56_uc002emc.2_Intron|GPR56_uc002emf.2_Intron|GPR56_uc010vhs.1_Intron|GPR56_uc002emd.2_Intron|GPR56_uc002eme.2_Intron|GPR56_uc010vht.1_Intron	NM_005682	NP_005673			G protein-coupled receptor 56 isoform a						brain development|cell adhesion|cell-cell signaling|neuropeptide signaling pathway	integral to plasma membrane	G-protein coupled receptor activity				0																		---	---	---	---
CSNK2A2	1459	broad.mit.edu	37	16	58208606	58208606	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58208606delA	uc002enc.2	-							NM_001896	NP_001887			casein kinase 2, alpha prime polypeptide						axon guidance|Wnt receptor signaling pathway	cytosol|nucleus	ATP binding|protein N-terminus binding|protein serine/threonine kinase activity			central_nervous_system(1)	1																		---	---	---	---
CCDC113	29070	broad.mit.edu	37	16	58285927	58285928	+	Intron	INS	-	AT	AT	rs9746500		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58285927_58285928insAT	uc002ene.2	+						CCDC113_uc010vid.1_Intron	NM_014157	NP_054876			coiled-coil domain containing 113 isoform 1							protein complex					0																		---	---	---	---
PRSS54	221191	broad.mit.edu	37	16	58326700	58326700	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58326700delG	uc002enf.2	-						PRSS54_uc002eng.2_Intron|PRSS54_uc010vie.1_Intron	NM_001080492	NP_001073961			plasma kallikrein-like protein 4 precursor						proteolysis	extracellular region	serine-type endopeptidase activity			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	58371680	58371684	+	IGR	DEL	AAAAA	-	-	rs35129928		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58371680_58371684delAAAAA								PRSS54 (42729 upstream) : GINS3 (54614 downstream)																																			---	---	---	---
NDRG4	65009	broad.mit.edu	37	16	58504509	58504509	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58504509delT	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	58577316	58577318	+	Intron	DEL	AAA	-	-	rs34232342		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58577316_58577318delAAA	uc002env.2	-						CNOT1_uc002enw.2_Intron|CNOT1_uc002enu.3_Intron|CNOT1_uc002enx.2_In_Frame_Del_p.F1543del|CNOT1_uc010vik.1_Intron	NM_016284	NP_057368			CCR4-NOT transcription complex, subunit 1						nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol				ovary(4)|central_nervous_system(2)	6				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)														---	---	---	---
CNOT1	23019	broad.mit.edu	37	16	58622985	58622986	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58622985_58622986delTT	uc002env.2	-						CNOT1_uc002enw.2_Intron|CNOT1_uc002enu.3_Intron|CNOT1_uc002enx.2_Intron|CNOT1_uc002enz.1_Intron	NM_016284	NP_057368			CCR4-NOT transcription complex, subunit 1						nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol				ovary(4)|central_nervous_system(2)	6				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	58731755	58731756	+	IGR	DEL	AG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58731755_58731756delAG								SLC38A7 (13081 upstream) : GOT2 (9279 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	59338910	59338911	+	IGR	DEL	GA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:59338910_59338911delGA								GOT2 (570664 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	59479523	59479523	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:59479523delT								GOT2 (711277 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	59764207	59764207	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:59764207delA								GOT2 (995961 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	60282050	60282050	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:60282050delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	60451494	60451494	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:60451494delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	61515804	61515804	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:61515804delA								None (None upstream) : CDH8 (171431 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	62791016	62791016	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:62791016delA								CDH8 (720980 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	63676628	63676628	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:63676628delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	64971513	64971513	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:64971513delT								None (None upstream) : CDH11 (9172 downstream)																																			---	---	---	---
LOC283867	283867	broad.mit.edu	37	16	65593913	65593913	+	Intron	DEL	A	-	-	rs5817533		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:65593913delA	uc010cdp.1	-						LOC283867_uc002eol.1_Intron					Homo sapiens cDNA clone IMAGE:5276218.												0				OV - Ovarian serous cystadenocarcinoma(108;0.17)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	65995958	65995965	+	IGR	DEL	GAGGGAGG	-	-	rs117450009		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:65995958_65995965delGAGGGAGG								LOC283867 (385755 upstream) : CDH5 (404560 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	66071325	66071326	+	IGR	INS	-	G	G	rs7192910		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66071325_66071326insG								LOC283867 (461122 upstream) : CDH5 (329199 downstream)																																			---	---	---	---
BEAN	146227	broad.mit.edu	37	16	66491689	66491689	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66491689delA	uc002eoq.2	+						BEAN_uc002eop.1_Intron	NM_001136106	NP_001129578			brain expressed, associated with Nedd4						cell death	integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	66736052	66736052	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66736052delA								CMTM4 (5442 upstream) : DYNC1LI2 (18747 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	66747486	66747486	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66747486delT								CMTM4 (16876 upstream) : DYNC1LI2 (7313 downstream)																																			---	---	---	---
CCDC79	283847	broad.mit.edu	37	16	66817622	66817624	+	Intron	DEL	TTG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66817622_66817624delTTG	uc010viv.1	-						CCDC79_uc002eqc.1_Intron|CCDC79_uc002eqd.1_Intron	NM_001136505	NP_001129977			coiled-coil domain containing 79						regulation of transcription, DNA-dependent		DNA binding				0																		---	---	---	---
NAE1	8883	broad.mit.edu	37	16	66839541	66839542	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66839541_66839542delAA	uc002eqf.2	-						NAE1_uc002eqe.2_Intron|NAE1_uc002eqg.2_Intron|NAE1_uc010cdv.2_Intron	NM_003905	NP_003896			NEDD8 activating enzyme E1 subunit 1 isoform a						apoptosis|cell cycle|DNA replication|mitotic cell cycle DNA replication checkpoint|protein neddylation|signal transduction	cytoplasm|insoluble fraction|plasma membrane	catalytic activity|protein heterodimerization activity			ovary(1)	1		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0914)|Epithelial(162;0.214)	Adenosine triphosphate(DB00171)													---	---	---	---
PDP2	57546	broad.mit.edu	37	16	66920652	66920652	+	3'UTR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66920652delA	uc002eqk.1	+	2						NM_020786	NP_065837			pyruvate dehydrogenase phosphatase isoenzyme 2						pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix|protein serine/threonine phosphatase complex	[pyruvate dehydrogenase (lipoamide)] phosphatase activity|metal ion binding			ovary(1)	1		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.088)|Epithelial(162;0.204)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	66933713	66933714	+	IGR	DEL	GA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66933713_66933714delGA								PDP2 (11858 upstream) : CDH16 (8312 downstream)																																			---	---	---	---
KCTD19	146212	broad.mit.edu	37	16	67345207	67345207	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67345207delT	uc002esu.2	-						KCTD19_uc002est.2_Intron|KCTD19_uc010vjj.1_Intron	NM_001100915	NP_001094385			potassium channel tetramerisation domain							voltage-gated potassium channel complex	voltage-gated potassium channel activity			skin(1)	1		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0311)|Epithelial(162;0.0906)														---	---	---	---
NUTF2	10204	broad.mit.edu	37	16	67902988	67902991	+	Intron	DEL	TTTT	-	-	rs71721636		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67902988_67902991delTTTT	uc002eup.2	+						NUTF2_uc002euq.3_5'Flank	NM_005796	NP_005787			nuclear transport factor 2						protein transport	cytosol|nuclear pore	protein binding|transporter activity				0		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00443)|Epithelial(162;0.0199)|all cancers(182;0.129)														---	---	---	---
PSKH1	5681	broad.mit.edu	37	16	67935032	67935032	+	Intron	DEL	T	-	-	rs113272713		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67935032delT	uc002euv.2	+						PSKH1_uc010cet.2_Intron	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	68033664	68033664	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68033664delA	uc002evg.2	-						DPEP2_uc002eve.2_5'Flank|DPEP2_uc002evf.2_Intron					SubName: Full=cDNA FLJ55113, moderately similar to Dipeptidase 2 (EC 3.4.13.19);						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	68489395	68489395	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68489395delA								SMPD3 (6986 upstream) : ZFP90 (74653 downstream)																																			---	---	---	---
CDH3	1001	broad.mit.edu	37	16	68689584	68689585	+	Intron	INS	-	AAC	AAC	rs137903416	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68689584_68689585insAAC	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			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)														---	---	---	---
TMCO7	79613	broad.mit.edu	37	16	69092579	69092579	+	Intron	DEL	T	-	-	rs114068667	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69092579delT	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)														---	---	---	---
SNTB2	6645	broad.mit.edu	37	16	69328722	69328725	+	Intron	DEL	TTTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69328722_69328725delTTTT	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)														---	---	---	---
TERF2	7014	broad.mit.edu	37	16	69404897	69404898	+	Intron	INS	-	AC	AC	rs138648749	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69404897_69404898insAC	uc002exd.2	-						TERF2_uc002exe.2_Intron	NM_005652	NP_005643			telomeric repeat binding factor 2						age-dependent telomere shortening|cell cycle|cellular senescence|negative regulation of telomere maintenance via semi-conservative replication|protection from non-homologous end joining at telomere|protein localization to chromosome, telomeric region|regulation of transcription, DNA-dependent|telomeric loop formation	Golgi apparatus|nuclear telomere cap complex|nucleoplasm	double-stranded telomeric DNA binding|protein C-terminus binding|protein homodimerization activity			lung(1)	1		Ovarian(137;0.101)																---	---	---	---
WWP2	11060	broad.mit.edu	37	16	69952178	69952178	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69952178delA	uc002exu.1	+						WWP2_uc002exv.1_Intron|WWP2_uc010vlm.1_Intron|WWP2_uc010vln.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																		---	---	---	---
PDPR	55066	broad.mit.edu	37	16	70190165	70190167	+	Intron	DEL	TGT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70190165_70190167delTGT	uc002eyf.1	+						CLEC18C_uc002exy.2_Intron|PDPR_uc010vlr.1_Intron|PDPR_uc002eyg.1_Intron|PDPR_uc002eyh.2_Intron|PDPR_uc010vls.1_Intron	NM_017990	NP_060460			pyruvate dehydrogenase phosphatase regulatory						glycine catabolic process|pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix	aminomethyltransferase activity|oxidoreductase activity			breast(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.124)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	70280996	70280996	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70280996delA								CLEC18C (60200 upstream) : EXOSC6 (3138 downstream)																																			---	---	---	---
AARS	16	broad.mit.edu	37	16	70292474	70292475	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70292474_70292475delTT	uc002eyn.1	-						AARS_uc010vlu.1_Intron	NM_001605	NP_001596			alanyl-tRNA synthetase						alanyl-tRNA aminoacylation|tRNA processing	cytosol|soluble fraction	alanine-tRNA ligase activity|ATP binding|metal ion binding|tRNA binding			pancreas(1)	1		Ovarian(137;0.0365)		BRCA - Breast invasive adenocarcinoma(221;0.161)	L-Alanine(DB00160)													---	---	---	---
Unknown	0	broad.mit.edu	37	16	70644107	70644111	+	IGR	DEL	AAAAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70644107_70644111delAAAAA								SF3B3 (32537 upstream) : IL34 (36357 downstream)																																			---	---	---	---
IL34	146433	broad.mit.edu	37	16	70690422	70690422	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70690422delA	uc002ezh.1	+						IL34_uc002ezi.1_Intron	NM_152456	NP_689669			interleukin 34 precursor						positive regulation of cell proliferation|positive regulation of protein phosphorylation	extracellular space	cytokine activity|growth factor activity|macrophage colony-stimulating factor receptor binding			central_nervous_system(1)|skin(1)	2																		---	---	---	---
CALB2	794	broad.mit.edu	37	16	71415920	71415922	+	Intron	DEL	GAG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71415920_71415922delGAG	uc002faa.3	+						CALB2_uc010vme.1_Intron|CALB2_uc002fac.3_Intron	NM_001740	NP_001731			calbindin 2 isoform 1								calcium ion binding				0		Ovarian(137;0.125)																---	---	---	---
AP1G1	164	broad.mit.edu	37	16	71808633	71808633	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71808633delT	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)																---	---	---	---
KIAA0174	9798	broad.mit.edu	37	16	71949731	71949731	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71949731delT	uc002fbj.1	+						KIAA0174_uc010cgh.1_Intron|KIAA0174_uc002fbk.1_Intron|KIAA0174_uc002fbm.1_Intron|KIAA0174_uc002fbl.1_Intron|KIAA0174_uc002fbn.1_Intron|KIAA0174_uc010cgi.1_Intron|KIAA0174_uc010cgj.1_5'Flank|KIAA0174_uc010vmk.1_Intron					SubName: Full=cDNA FLJ32696 fis, clone TESTI2000358; SubName: Full=cDNA FLJ77725;						cell cycle|cell division	cytoplasmic membrane-bounded vesicle|ER-Golgi intermediate compartment	protein binding			ovary(1)	1																		---	---	---	---
PKD1L3	342372	broad.mit.edu	37	16	72035181	72035181	+	5'Flank	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72035181delT	uc010vmm.1	-							NM_181536	NP_853514			polycystin 1-like 3 precursor												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	72299663	72299665	+	IGR	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72299663_72299665delTTT								PMFBP1 (93314 upstream) : ZFHX3 (517123 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	72385991	72385992	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72385991_72385992delTT								PMFBP1 (179642 upstream) : ZFHX3 (430796 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	72630546	72630546	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72630546delT								PMFBP1 (424197 upstream) : ZFHX3 (186242 downstream)																																			---	---	---	---
ZFHX3	463	broad.mit.edu	37	16	72982961	72982963	+	Intron	DEL	CTC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72982961_72982963delCTC	uc002fck.2	-						ZFHX3_uc002fcl.2_Intron	NM_006885	NP_008816			zinc finger homeobox 3 isoform A						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)																---	---	---	---
Unknown	0	broad.mit.edu	37	16	73323940	73323951	+	IGR	DEL	ACACACACACAT	-	-	rs10560787		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:73323940_73323951delACACACACACAT								HTA (196270 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	73469427	73469428	+	IGR	DEL	GG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:73469427_73469428delGG								HTA (341757 upstream) : PSMD7 (861253 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	73535328	73535328	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:73535328delA								HTA (407658 upstream) : PSMD7 (795353 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	73612525	73612525	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:73612525delT								HTA (484855 upstream) : PSMD7 (718156 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	74152702	74152703	+	IGR	INS	-	AG	AG			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74152702_74152703insAG								None (None upstream) : PSMD7 (177978 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	74200908	74200908	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74200908delT								None (None upstream) : PSMD7 (129773 downstream)																																			---	---	---	---
MLKL	197259	broad.mit.edu	37	16	74723021	74723021	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74723021delT	uc002fdb.2	-						MLKL_uc002fdc.2_Intron	NM_152649	NP_689862			mixed lineage kinase domain-like isoform 1								ATP binding|protein binding|protein kinase activity			stomach(2)	2																		---	---	---	---
FA2H	79152	broad.mit.edu	37	16	74795689	74795689	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74795689delA	uc002fde.1	-						FA2H_uc010vmy.1_Intron	NM_024306	NP_077282			fatty acid 2-hydroxylase						cell death|electron transport chain|fatty acid biosynthetic process|sphingolipid metabolic process|transport	endoplasmic reticulum membrane|integral to membrane|microsome	heme binding|oxidoreductase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	75026196	75026196	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75026196delT								WDR59 (7179 upstream) : ZNRF1 (6719 downstream)																																			---	---	---	---
BCAR1	9564	broad.mit.edu	37	16	75268061	75268062	+	Intron	DEL	AG	-	-	rs71985613		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75268061_75268062delAG	uc002fdv.2	-						BCAR1_uc002fdt.2_Intron|BCAR1_uc002fdu.2_Intron|BCAR1_uc010cgu.2_Intron|BCAR1_uc010vna.1_Intron|BCAR1_uc010vnb.1_Intron|BCAR1_uc002fdw.2_Intron|BCAR1_uc010vnc.1_Intron|BCAR1_uc010vnd.1_Intron|BCAR1_uc002fdx.2_Intron	NM_014567	NP_055382			breast cancer anti-estrogen resistance 1						actin filament organization|B cell receptor signaling pathway|blood coagulation|cell adhesion|cell division|cell migration|cell proliferation|epidermal growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|insulin receptor signaling pathway|integrin-mediated signaling pathway|nerve growth factor receptor signaling pathway|platelet-derived growth factor receptor signaling pathway|positive regulation of cell migration|regulation of apoptosis|regulation of cell growth|T cell receptor signaling pathway	cytosol|focal adhesion|membrane fraction|ruffle	protein kinase binding|protein phosphatase binding|SH3 domain binding|signal transducer activity			central_nervous_system(5)|breast(2)|prostate(1)	8				BRCA - Breast invasive adenocarcinoma(221;0.169)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	76147514	76147514	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:76147514delC								TERF2IP (456186 upstream) : CNTNAP4 (163662 downstream)																																			---	---	---	---
CNTNAP4	85445	broad.mit.edu	37	16	76406036	76406037	+	Intron	DEL	TT	-	-	rs139802997		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:76406036_76406037delTT	uc002feu.1	+						CNTNAP4_uc002fev.1_Intron|CNTNAP4_uc010chb.1_Intron|CNTNAP4_uc002fex.1_Intron|CNTNAP4_uc002few.2_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																		---	---	---	---
CNTNAP4	85445	broad.mit.edu	37	16	76439713	76439713	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:76439713delT	uc002feu.1	+						CNTNAP4_uc002fev.1_Intron|CNTNAP4_uc010chb.1_Intron|CNTNAP4_uc002fex.1_Intron|CNTNAP4_uc002few.2_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	77193829	+	IGR	DEL	TT	-	-	rs68066912		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77193828_77193829delTT								CNTNAP4 (600693 upstream) : MON1B (31007 downstream)																																			---	---	---	---
WWOX	51741	broad.mit.edu	37	16	79219865	79219866	+	Intron	DEL	GT	-	-	rs113299262		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:79219865_79219866delGT	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	80386054	80386054	+	IGR	DEL	A	-	-	rs2019809	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:80386054delA								MAF (751432 upstream) : DYNLRB2 (188800 downstream)																																			---	---	---	---
CDYL2	124359	broad.mit.edu	37	16	80702131	80702131	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:80702131delA	uc002ffs.2	-							NM_152342	NP_689555			chromodomain protein, Y-like 2							nucleus	catalytic activity|protein binding			central_nervous_system(1)	1																		---	---	---	---
PKD1L2	114780	broad.mit.edu	37	16	81146166	81146167	+	Intron	INS	-	TGATGA	TGATGA			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81146166_81146167insTGATGA	uc002fgh.1	-						PKD1L2_uc002fgf.1_Intron|PKD1L2_uc002fgg.1_Intron	NM_052892	NP_443124			polycystin 1-like 2 isoform a						neuropeptide signaling pathway	integral to membrane	calcium ion binding|ion channel activity|sugar binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3																		---	---	---	---
CMIP	80790	broad.mit.edu	37	16	81534101	81534101	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81534101delT	uc002fgp.2	+						CMIP_uc002fgq.1_Intron	NM_198390	NP_938204			c-Maf-inducing protein isoform C-mip							cytoplasm|nucleus					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	81775411	81775411	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81775411delA								CMIP (30046 upstream) : PLCG2 (37519 downstream)																																			---	---	---	---
PLCG2	5336	broad.mit.edu	37	16	81817438	81817438	+	Intron	DEL	T	-	-	rs74908827		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81817438delT	uc002fgt.2	+						PLCG2_uc010chg.1_5'Flank	NM_002661	NP_002652			phospholipase C, gamma 2						intracellular signal transduction|phospholipid catabolic process|platelet activation	plasma membrane	phosphatidylinositol phospholipase C activity|protein binding|signal transducer activity			large_intestine(4)|lung(2)|ovary(1)|skin(1)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	82293654	82293657	+	IGR	DEL	CCTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:82293654_82293657delCCTT								MPHOSPH6 (89825 upstream) : CDH13 (366921 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	82494804	82494804	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:82494804delA								MPHOSPH6 (290975 upstream) : CDH13 (165774 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	82559981	82559988	+	IGR	DEL	CCATCCAT	-	-	rs9935947		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:82559981_82559988delCCATCCAT								MPHOSPH6 (356152 upstream) : CDH13 (100590 downstream)																																			---	---	---	---
CDH13	1012	broad.mit.edu	37	16	82807736	82807736	+	Intron	DEL	A	-	-	rs72558693		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:82807736delA	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	82923603	82923603	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:82923603delT	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	83296198	83296198	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:83296198delT	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)														---	---	---	---
LRRC50	123872	broad.mit.edu	37	16	84183630	84183630	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84183630delA	uc002fhl.3	+						LRRC50_uc010chi.1_Intron	NM_178452	NP_848547			leucine rich repeat containing 50						axonemal dynein complex assembly|cilium morphogenesis	cilium axoneme|cytoplasm|spindle pole	dynein binding				0														Kartagener_syndrome				---	---	---	---
COX4NB	10328	broad.mit.edu	37	16	85812457	85812457	+	3'UTR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:85812457delC	uc002fjd.2	-	5					COX4NB_uc010vol.1_3'UTR	NM_006067	NP_006058			COX4 neighbor isoform 1							mitochondrion|nucleus					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	86000680	86000683	+	IGR	DEL	TCCG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86000680_86000683delTCCG								IRF8 (44471 upstream) : LOC732275 (364773 downstream)																																			---	---	---	---
LOC732275	732275	broad.mit.edu	37	16	86375384	86375384	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86375384delC	uc002fjj.2	-						LOC732275_uc010chr.2_Intron	NR_024406				Homo sapiens cDNA FLJ35925 fis, clone TESTI2010734.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	86892369	86892369	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86892369delA								FOXL1 (277066 upstream) : FBXO31 (470575 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	87309591	87309591	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87309591delG	uc002fjt.1	-											Homo sapiens cDNA FLJ43761 fis, clone TESTI2048109.																														---	---	---	---
KLHDC4	54758	broad.mit.edu	37	16	87744741	87744741	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87744741delG	uc002fki.2	-						KLHDC4_uc002fkh.1_5'Flank|KLHDC4_uc010cht.1_Intron|KLHDC4_uc002fkj.2_Intron|KLHDC4_uc002fkk.2_Intron|KLHDC4_uc002fkl.2_Intron|KLHDC4_uc010chu.1_Intron	NM_017566	NP_060036			kelch domain containing 4											pancreas(2)	2				BRCA - Breast invasive adenocarcinoma(80;0.0283)														---	---	---	---
CA5A	763	broad.mit.edu	37	16	87935199	87935199	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87935199delT	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)														---	---	---	---
CA5A	763	broad.mit.edu	37	16	87952489	87952489	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87952489delA	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	88116764	88116764	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88116764delA								BANP (5841 upstream) : ZNF469 (377115 downstream)																																			---	---	---	---
MVD	4597	broad.mit.edu	37	16	88724841	88724841	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88724841delT	uc002flg.1	-						MVD_uc002flf.1_5'Flank	NM_002461	NP_002452			diphosphomevalonate decarboxylase						cholesterol biosynthetic process|positive regulation of cell proliferation	cytosol	ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity				0				BRCA - Breast invasive adenocarcinoma(80;0.0478)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	88864751	88864752	+	IGR	INS	-	TGA	TGA	rs138052383	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88864751_88864752insTGA								FAM38A (13376 upstream) : CDT1 (5434 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	89153802	89153802	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89153802delT								CBFA2T3 (110401 upstream) : ACSF3 (6452 downstream)																																			---	---	---	---
DPEP1	1800	broad.mit.edu	37	16	89679869	89679882	+	Intron	DEL	CTCTCTCCCTCCTG	-	-	rs111857923		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89679869_89679882delCTCTCTCCCTCCTG	uc010cin.2	+							NM_001128141	NP_001121613			dipeptidase 1 precursor						proteolysis	anchored to membrane|apical plasma membrane|microvillus membrane	dipeptidase activity|dipeptidyl-peptidase activity|metal ion binding|metalloexopeptidase activity|protein binding			large_intestine(1)	1		all_lung(18;0.0054)|all_hematologic(23;0.094)		BRCA - Breast invasive adenocarcinoma(80;0.0258)	Cilastatin(DB01597)													---	---	---	---
DPEP1	1800	broad.mit.edu	37	16	89701210	89701210	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89701210delC	uc010cin.2	+						DPEP1_uc002fnr.3_Intron|DPEP1_uc002fns.3_Intron	NM_001128141	NP_001121613			dipeptidase 1 precursor						proteolysis	anchored to membrane|apical plasma membrane|microvillus membrane	dipeptidase activity|dipeptidyl-peptidase activity|metal ion binding|metalloexopeptidase activity|protein binding			large_intestine(1)	1		all_lung(18;0.0054)|all_hematologic(23;0.094)		BRCA - Breast invasive adenocarcinoma(80;0.0258)	Cilastatin(DB01597)													---	---	---	---
TCF25	22980	broad.mit.edu	37	16	89947000	89947002	+	Intron	DEL	AAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89947000_89947002delAAA	uc002fpb.2	+						TCF25_uc010vpp.1_Intron	NM_014972	NP_055787			NULP1						heart development|negative regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0		all_cancers(9;4.71e-08)|Lung NSC(15;0.000192)|all_lung(18;0.000319)|all_neural(9;0.0122)|all_hematologic(23;0.027)		BRCA - Breast invasive adenocarcinoma(80;0.0288)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	89981047	89981048	+	RNA	INS	-	TT	TT			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89981047_89981048insTT	uc010ciy.1	+	2		c.1550_1551insTT								Homo sapiens cDNA clone IMAGE:40002380.																														---	---	---	---
GAS8	2622	broad.mit.edu	37	16	90086714	90086715	+	5'Flank	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:90086714_90086715delAA	uc002fqi.1	+						DBNDD1_uc002fqf.1_5'Flank|DBNDD1_uc002fqg.1_5'Flank|GAS8_uc010vps.1_Intron|GAS8_uc002fqh.2_Intron|GAS8_uc010vpt.1_5'Flank|GAS8_uc010vpu.1_5'Flank|GAS8_uc010vpv.1_5'Flank|GAS8_uc010cjc.1_5'Flank|GAS8_uc010vpw.1_5'Flank|GAS8_uc002fqj.1_5'Flank	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	630649	630649	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:630649delT								VPS53 (12553 upstream) : FAM57A (5198 downstream)																																			---	---	---	---
GLOD4	51031	broad.mit.edu	37	17	678933	678933	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:678933delA	uc002frv.2	-						GLOD4_uc002frt.2_Intron|GLOD4_uc002fru.2_Intron|GLOD4_uc010vqc.1_Intron	NM_016080	NP_057164			glyoxalase domain containing 4							mitochondrion					0				UCEC - Uterine corpus endometrioid carcinoma (25;0.022)														---	---	---	---
NXN	64359	broad.mit.edu	37	17	744683	744684	+	Intron	INS	-	C	C	rs146246056		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:744683_744684insC	uc002fsa.2	-						NXN_uc002fsb.1_Intron|NXN_uc002frz.2_Intron|NXN_uc010vqe.1_Intron	NM_022463	NP_071908			nucleoredoxin						cell differentiation|cell redox homeostasis|multicellular organismal development|Wnt receptor signaling pathway	cytosol|nucleus	protein-disulfide reductase activity			ovary(2)|breast(1)|pancreas(1)	4				UCEC - Uterine corpus endometrioid carcinoma (25;0.0237)														---	---	---	---
NXN	64359	broad.mit.edu	37	17	775620	775621	+	Intron	DEL	GA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:775620_775621delGA	uc002fsa.2	-						NXN_uc002fsb.1_Intron	NM_022463	NP_071908			nucleoredoxin						cell differentiation|cell redox homeostasis|multicellular organismal development|Wnt receptor signaling pathway	cytosol|nucleus	protein-disulfide reductase activity			ovary(2)|breast(1)|pancreas(1)	4				UCEC - Uterine corpus endometrioid carcinoma (25;0.0237)														---	---	---	---
ABR	29	broad.mit.edu	37	17	990174	990175	+	Intron	DEL	TT	-	-	rs112446325		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:990174_990175delTT	uc002fsd.2	-						ABR_uc002fse.2_Intron|ABR_uc002fsg.2_Intron|ABR_uc002fsh.1_Intron	NM_021962	NP_068781			active breakpoint cluster region-related						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding|Rho guanyl-nucleotide exchange factor activity			upper_aerodigestive_tract(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.0228)														---	---	---	---
ABR	29	broad.mit.edu	37	17	1055710	1055712	+	Intron	DEL	AAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1055710_1055712delAAA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	1217228	1217228	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1217228delT								TUSC5 (12947 upstream) : YWHAE (30608 downstream)																																			---	---	---	---
PITPNA	5306	broad.mit.edu	37	17	1433665	1433666	+	Intron	INS	-	AGAG	AGAG	rs139887728	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1433665_1433666insAGAG	uc002fst.3	-						PITPNA_uc010cjt.2_Intron|PITPNA_uc010cju.2_Intron	NM_006224	NP_006215			phosphatidylinositol transfer protein, alpha						axon guidance|lipid metabolic process|visual perception	cytoplasm	phosphatidylcholine transmembrane transporter activity|phosphatidylinositol transporter activity|protein binding			ovary(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.0845)														---	---	---	---
RPA1	6117	broad.mit.edu	37	17	1795306	1795306	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1795306delT	uc002fto.2	+							NM_002945	NP_002936			replication protein A1						cell cycle checkpoint|DNA recombinase assembly|DNA strand elongation involved in DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	actin cytoskeleton|cytoplasm|DNA replication factor A complex|PML body	metal ion binding|protein binding|single-stranded DNA binding				0													NER					---	---	---	---
SMG6	23293	broad.mit.edu	37	17	2068235	2068237	+	Intron	DEL	AAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2068235_2068237delAAA	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																		---	---	---	---
P2RX1	5023	broad.mit.edu	37	17	3802503	3802504	+	Intron	INS	-	T	T	rs71381525		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3802503_3802504insT	uc002fww.2	-							NM_002558	NP_002549			purinergic receptor P2X1						platelet activation	integral to plasma membrane	calcium channel activity|extracellular ATP-gated cation channel activity|purinergic nucleotide receptor activity			ovary(1)|skin(1)	2				LUAD - Lung adenocarcinoma(2;1.9e-05)|Lung(3;0.0173)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	3895193	3895194	+	IGR	DEL	CT	-	-	rs60877824		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3895193_3895194delCT								ATP2A3 (27457 upstream) : ZZEF1 (12546 downstream)																																			---	---	---	---
ANKFY1	51479	broad.mit.edu	37	17	4136300	4136300	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4136300delA	uc002fxq.1	-						ANKFY1_uc002fxn.2_Intron|ANKFY1_uc002fxo.2_Intron|ANKFY1_uc002fxp.2_Intron|ANKFY1_uc010ckp.2_Intron|ANKFY1_uc002fxr.2_Intron|ANKFY1_uc010vrz.1_Intron	NM_016376	NP_057460			ankyrin repeat and FYVE domain containing 1							endosome membrane	metal ion binding|protein binding			ovary(2)|skin(1)	3																		---	---	---	---
SPNS3	201305	broad.mit.edu	37	17	4378154	4378155	+	Intron	DEL	AT	-	-	rs140016802		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4378154_4378155delAT	uc002fxt.2	+						SPNS3_uc002fxu.2_Intron|SPNS3_uc002fxv.2_Intron	NM_182538	NP_872344			spinster homolog 3						lipid transport|transmembrane transport	integral to membrane				large_intestine(1)	1																		---	---	---	---
MINK1	50488	broad.mit.edu	37	17	4773371	4773371	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4773371delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	4812058	4812059	+	IGR	INS	-	AC	AC	rs139957974	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4812058_4812059insAC								CHRNE (5689 upstream) : GP1BA (23533 downstream)																																			---	---	---	---
USP6	9098	broad.mit.edu	37	17	5052992	5052992	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5052992delT	uc002gau.1	+						USP6_uc002gav.1_Intron|USP6_uc010ckz.1_Intron	NM_004505	NP_004496			ubiquitin specific protease 6						protein deubiquitination|regulation of vesicle-mediated transport|ubiquitin-dependent protein catabolic process	lysosome|plasma membrane|recycling endosome	calmodulin binding|cysteine-type endopeptidase activity|nucleic acid binding|protein binding|Rab GTPase activator activity|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			skin(2)|upper_aerodigestive_tract(1)|lung(1)|breast(1)	5								T	COL1A1|CDH11|ZNF9|OMD	aneurysmal bone cysts								---	---	---	---
RABEP1	9135	broad.mit.edu	37	17	5191207	5191207	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5191207delA	uc002gbm.3	+						RABEP1_uc010clc.1_Intron|RABEP1_uc010cld.1_Intron|RABEP1_uc010vsw.1_Intron|RABEP1_uc002gbl.3_Intron|RABEP1_uc002gbj.2_Intron|RABEP1_uc002gbk.2_Intron	NM_004703	NP_004694			rabaptin, RAB GTPase binding effector protein 1						apoptosis|cellular membrane fusion|endocytosis|protein transport	centrosome|early endosome|endocytic vesicle|recycling endosome	growth factor activity|GTPase activator activity|protein homodimerization activity			large_intestine(1)|ovary(1)	2																		---	---	---	---
RABEP1	9135	broad.mit.edu	37	17	5272409	5272409	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5272409delA	uc002gbm.3	+						RABEP1_uc010clc.1_Intron|RABEP1_uc010cld.1_Intron|RABEP1_uc010vsw.1_Intron|RABEP1_uc002gbl.3_Intron|NUP88_uc002gbn.2_Intron	NM_004703	NP_004694			rabaptin, RAB GTPase binding effector protein 1						apoptosis|cellular membrane fusion|endocytosis|protein transport	centrosome|early endosome|endocytic vesicle|recycling endosome	growth factor activity|GTPase activator activity|protein homodimerization activity			large_intestine(1)|ovary(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	5559118	5559119	+	IGR	INS	-	TG	TG	rs140421591	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5559118_5559119insTG								NLRP1 (71286 upstream) : WSCD1 (413318 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	5714018	5714018	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5714018delT	uc002gcm.2	+											Homo sapiens hypothetical protein LOC339166, mRNA (cDNA clone IMAGE:5163423), partial cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	17	6181295	6181298	+	IGR	DEL	TTTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6181295_6181298delTTTT								WSCD1 (153550 upstream) : AIPL1 (145762 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	7076491	7076491	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7076491delA								ASGR2 (58199 upstream) : ASGR1 (261 downstream)																																			---	---	---	---
NLGN2	57555	broad.mit.edu	37	17	7309586	7309586	+	5'Flank	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7309586delG	uc002ggt.1	+						PLSCR3_uc002ggr.1_5'Flank|PLSCR3_uc010cmg.1_5'Flank|C17orf61_uc002ggs.2_5'Flank	NM_020795	NP_065846			neuroligin 2 precursor						cell-cell junction maintenance|neuron cell-cell adhesion|positive regulation of synaptogenesis|regulation of inhibitory postsynaptic membrane potential|synapse assembly	cell surface|integral to plasma membrane|postsynaptic membrane	neurexin binding|receptor activity			central_nervous_system(1)	1		Prostate(122;0.157)																---	---	---	---
FXR2	9513	broad.mit.edu	37	17	7496122	7496122	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7496122delG	uc002gia.1	-	14	1846	c.1619delC	c.(1618-1620)CCAfs	p.P540fs	SOX15_uc002ghy.1_5'Flank|SOX15_uc002ghz.1_5'Flank	NM_004860	NP_004851	P51116	FXR2_HUMAN	fragile X mental retardation syndrome related	540						cytosolic large ribosomal subunit	protein binding|RNA binding				0				READ - Rectum adenocarcinoma(115;0.17)														---	---	---	---
SHBG	6462	broad.mit.edu	37	17	7535598	7535598	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7535598delA	uc002gie.2	+						SHBG_uc010cmo.2_Intron|SHBG_uc010cmp.2_Intron|SHBG_uc010cmq.2_Intron|SHBG_uc010cmr.2_Intron|SHBG_uc010cms.2_Intron|SHBG_uc010cmt.2_Intron|SHBG_uc010cmu.2_Intron|SHBG_uc010cmz.2_Intron|SHBG_uc010cmv.2_Intron|SHBG_uc010cmw.2_Intron|SHBG_uc010cmx.2_Intron|SHBG_uc010cmy.2_Intron|SHBG_uc002gid.3_Intron|SHBG_uc010cnd.2_Intron|SHBG_uc010cna.2_Intron|SHBG_uc010vue.1_Intron|SHBG_uc010vuf.1_Intron|SHBG_uc010cnb.2_Intron|SHBG_uc010cnc.2_Intron	NM_001040	NP_001031			sex hormone-binding globulin isoform 1						hormone transport	extracellular region	androgen binding|protein homodimerization activity	p.0?(1)|p.?(1)			0		all_cancers(10;0.0867)		READ - Rectum adenocarcinoma(115;0.168)	Danazol(DB01406)|Dromostanolone(DB00858)|Estradiol(DB00783)|Estrone(DB00655)|Fluoxymesterone(DB01185)|Hydrocortisone(DB00741)|Mitotane(DB00648)|Norethindrone(DB00717)|Testosterone(DB00624)													---	---	---	---
MYH10	4628	broad.mit.edu	37	17	8533443	8533443	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8533443delC	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																		---	---	---	---
NTN1	9423	broad.mit.edu	37	17	9003790	9003790	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9003790delT	uc002glw.3	+							NM_004822	NP_004813			netrin 1 precursor						apoptosis|axon guidance		protein binding				0																		---	---	---	---
NTN1	9423	broad.mit.edu	37	17	9107564	9107565	+	Intron	DEL	TC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9107564_9107565delTC	uc002glw.3	+							NM_004822	NP_004813			netrin 1 precursor						apoptosis|axon guidance		protein binding				0																		---	---	---	---
STX8	9482	broad.mit.edu	37	17	9282137	9282137	+	Intron	DEL	A	-	-	rs139246965	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9282137delA	uc002glx.2	-							NM_004853	NP_004844			syntaxin 8						transport	endoplasmic reticulum|integral to plasma membrane				central_nervous_system(1)	1																		---	---	---	---
USP43	124739	broad.mit.edu	37	17	9572989	9572989	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9572989delG	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																		---	---	---	---
RCVRN	5957	broad.mit.edu	37	17	9803361	9803361	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9803361delA	uc002gme.1	-							NM_002903	NP_002894			recoverin						visual perception		calcium ion binding|calcium sensitive guanylate cyclase activator activity				0																		---	---	---	---
MYH3	4621	broad.mit.edu	37	17	10536521	10536521	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10536521delA	uc002gmq.1	-							NM_002470	NP_002461			myosin, heavy chain 3, skeletal muscle,						muscle filament sliding|muscle organ development	cytosol|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(4)|central_nervous_system(2)|pancreas(1)	7																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	10664038	10664038	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10664038delT								TMEM220 (30392 upstream) : PIRT (61755 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	11095050	11095050	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11095050delA								PIRT (353632 upstream) : SHISA6 (49690 downstream)																																			---	---	---	---
SHISA6	388336	broad.mit.edu	37	17	11303048	11303048	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11303048delT	uc002gna.3	+						SHISA6_uc002gnb.3_Intron|SHISA6_uc010com.2_Intron	NM_207386	NP_997269			shisa homolog 6							integral to membrane				breast(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	12435395	12435395	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:12435395delT								MAP2K4 (388345 upstream) : MYOCD (133812 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	13064732	13064733	+	IGR	DEL	TG	-	-	rs2529898	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:13064732_13064733delTG								ELAC2 (143373 upstream) : HS3ST3A1 (334273 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	13698258	13698258	+	5'Flank	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:13698258delT	uc002goc.1	-											Homo sapiens cDNA FLJ41269 fis, clone BRAMY2036079.																														---	---	---	---
HS3ST3B1	9953	broad.mit.edu	37	17	14229323	14229324	+	Intron	DEL	TG	-	-	rs72031973		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:14229323_14229324delTG	uc002goh.1	+							NM_006041	NP_006032			heparan sulfate D-glucosaminyl						heparan sulfate proteoglycan biosynthetic process, enzymatic modification	Golgi membrane|integral to plasma membrane	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity|[heparan sulfate]-glucosamine 3-sulfotransferase 3 activity				0				UCEC - Uterine corpus endometrioid carcinoma (92;0.0887)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	14417203	14417203	+	IGR	DEL	T	-	-	rs139366770		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:14417203delT								HS3ST3B1 (167711 upstream) : PMP22 (715894 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	14606709	14606709	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:14606709delT								HS3ST3B1 (357217 upstream) : PMP22 (526388 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	15053238	15053239	+	IGR	INS	-	A	A	rs145493545	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15053238_15053239insA								HS3ST3B1 (803746 upstream) : PMP22 (79858 downstream)																																			---	---	---	---
FAM18B2	201158	broad.mit.edu	37	17	15406041	15406064	+	3'UTR	DEL	TCTCTTTCTCTCTCCTCTCTCCCG	-	-	rs149635358	by1000genomes;by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15406041_15406064delTCTCTTTCTCTCTCCTCTCTCCCG	uc002goq.2	-	6					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	15496942	15496944	+	Intron	DEL	TTT	-	-	rs113426025		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15496942_15496944delTTT	uc002gor.1	-						CDRT1_uc010vvy.1_Intron|CDRT1_uc010vvz.1_Intron|CDRT1_uc002gov.3_Intron|CDRT1_uc002gou.2_Intron					SubName: Full=Putative uncharacterized protein; Flags: Fragment;						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)														---	---	---	---
TTC19	54902	broad.mit.edu	37	17	15906573	15906573	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15906573delT	uc002gph.1	+						TTC19_uc010cox.1_Intron	NM_017775	NP_060245			tetratricopeptide repeat domain 19						cell cycle|cytokinesis|mitochondrial respiratory chain complex III assembly	centrosome|midbody|mitochondrial inner membrane	protein binding			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (92;0.0837)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	16428746	16428746	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16428746delT								C17orf76 (33266 upstream) : ZNF287 (24885 downstream)																																			---	---	---	---
CCDC144A	9720	broad.mit.edu	37	17	16623498	16623498	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16623498delT	uc002gqk.1	+						CCDC144A_uc002gql.1_Intron|LOC162632_uc010cpj.1_Intron	NM_014695	NP_055510			coiled-coil domain containing 144A												0																		---	---	---	---
CCDC144A	9720	broad.mit.edu	37	17	16666468	16666469	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16666468_16666469insA	uc002gqk.1	+						CCDC144A_uc002gql.1_Intron|LOC162632_uc010cpj.1_Intron	NM_014695	NP_055510			coiled-coil domain containing 144A												0																		---	---	---	---
TNFRSF13B	23495	broad.mit.edu	37	17	16878048	16878048	+	5'Flank	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16878048delT	uc002gqs.1	-						TNFRSF13B_uc010vwt.1_5'Flank|TNFRSF13B_uc002gqt.1_5'Flank|TNFRSF13B_uc010vwu.1_5'Flank	NM_012452	NP_036584			tumor necrosis factor receptor 13B						cell surface receptor linked signaling pathway	integral to plasma membrane	protein binding|receptor activity			kidney(2)	2														IgA_Deficiency_Selective				---	---	---	---
NT5M	56953	broad.mit.edu	37	17	17227196	17227196	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17227196delT	uc002grf.2	+						NT5M_uc002gre.2_Intron|NT5M_uc002grg.2_Intron	NM_020201	NP_064586			5',3'-nucleotidase, mitochondrial precursor						DNA replication|pyrimidine base metabolic process|pyrimidine nucleoside catabolic process	mitochondrial matrix	5'-nucleotidase activity|metal ion binding|nucleotide binding				0																		---	---	---	---
TOP3A	7156	broad.mit.edu	37	17	18195035	18195035	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18195035delT	uc002gsx.1	-						TOP3A_uc010cpz.1_5'Flank|TOP3A_uc010vxr.1_Intron|TOP3A_uc002gsw.1_Intron|TOP3A_uc010vxs.1_Intron	NM_004618	NP_004609			topoisomerase (DNA) III alpha						DNA topological change|meiosis	chromosome|PML body	ATP binding|DNA topoisomerase type I activity|protein binding|zinc ion binding			skin(3)	3																		---	---	---	---
TBC1D28	254272	broad.mit.edu	37	17	18540062	18540063	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18540062_18540063insT	uc002gud.2	-							NM_001039397	NP_001034486			TBC1 domain family, member 28							intracellular	Rab GTPase activator activity			ovary(1)	1																		---	---	---	---
ZNF286B	729288	broad.mit.edu	37	17	18579677	18579677	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18579677delA	uc010vyd.1	-							NM_001145045	NP_001138517			zinc finger protein 286B						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
PRPSAP2	5636	broad.mit.edu	37	17	18795553	18795553	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18795553delT	uc002gup.1	+						PRPSAP2_uc002guo.1_Intron|PRPSAP2_uc010vyi.1_Intron|PRPSAP2_uc010vyj.1_Intron|PRPSAP2_uc010vyk.1_Intron	NM_002767	NP_002758			phosphoribosyl pyrophosphate						nucleotide biosynthetic process		enzyme inhibitor activity|magnesium ion binding|ribose phosphate diphosphokinase activity			skin(1)	1																		---	---	---	---
PRPSAP2	5636	broad.mit.edu	37	17	18818798	18818799	+	Intron	INS	-	A	A	rs143359431	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18818798_18818799insA	uc002gup.1	+						PRPSAP2_uc002guo.1_Intron|PRPSAP2_uc010vyi.1_Intron|PRPSAP2_uc010vyj.1_Intron|PRPSAP2_uc010vyk.1_Intron	NM_002767	NP_002758			phosphoribosyl pyrophosphate						nucleotide biosynthetic process		enzyme inhibitor activity|magnesium ion binding|ribose phosphate diphosphokinase activity			skin(1)	1																		---	---	---	---
SLC47A1	55244	broad.mit.edu	37	17	19435963	19435964	+	5'Flank	INS	-	G	G	rs72006292		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19435963_19435964insG	uc002gvy.1	+						SLC47A1_uc010vyy.1_5'Flank|SLC47A1_uc002gvx.2_5'Flank|SLC47A1_uc010vyz.1_5'Flank|SLC47A1_uc010cqp.1_5'Flank	NM_018242	NP_060712			solute carrier family 47, member 1							integral to membrane|plasma membrane	drug:hydrogen antiporter activity				0	all_cancers(12;2.49e-05)|all_epithelial(12;0.00263)|Hepatocellular(7;0.00345)																	---	---	---	---
ULK2	9706	broad.mit.edu	37	17	19676289	19676289	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19676289delA	uc002gwm.3	-						ULK2_uc002gwn.2_3'UTR	NM_001142610	NP_001136082			unc-51-like kinase 2						signal transduction		ATP binding|protein binding|protein serine/threonine kinase activity			skin(2)|large_intestine(1)|stomach(1)	4	all_cancers(12;4.97e-05)|all_epithelial(12;0.00362)|Breast(13;0.186)																	---	---	---	---
ULK2	9706	broad.mit.edu	37	17	19727358	19727358	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19727358delA	uc002gwm.3	-						ULK2_uc002gwn.2_Intron	NM_001142610	NP_001136082			unc-51-like kinase 2						signal transduction		ATP binding|protein binding|protein serine/threonine kinase activity			skin(2)|large_intestine(1)|stomach(1)	4	all_cancers(12;4.97e-05)|all_epithelial(12;0.00362)|Breast(13;0.186)																	---	---	---	---
CCDC144C	348254	broad.mit.edu	37	17	20266462	20266463	+	Intron	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20266462_20266463delAC	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	20377969	20377970	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20377969_20377970delAA								LGALS9B (7121 upstream) : CCDC144NL (388740 downstream)																																			---	---	---	---
MAP2K3	5606	broad.mit.edu	37	17	21199106	21199106	+	Intron	DEL	G	-	-	rs5819734		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21199106delG	uc002gys.2	+						MAP2K3_uc002gyt.2_Intron|MAP2K3_uc002gyu.2_Intron	NM_145109	NP_659731			mitogen-activated protein kinase kinase 3						activation of MAPK activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of transcription, DNA-dependent|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				0				COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	21237279	21237280	+	IGR	INS	-	AAGAAC	AAGAAC	rs77391560		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21237279_21237280insAAGAAC								MAP2K3 (18730 upstream) : KCNJ12 (42419 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21272027	21272027	+	IGR	DEL	A	-	-	rs34412151		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21272027delA								MAP2K3 (53478 upstream) : KCNJ12 (7672 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21333424	21333424	+	IGR	DEL	C	-	-	rs111937714		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21333424delC								KCNJ12 (10245 upstream) : C17orf51 (98148 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21349646	21349647	+	IGR	INS	-	TAA	TAA			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21349646_21349647insTAA								KCNJ12 (26467 upstream) : C17orf51 (81925 downstream)																																			---	---	---	---
C17orf51	339263	broad.mit.edu	37	17	21442867	21442867	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21442867delC	uc002gyw.3	-						C17orf51_uc002gyx.1_Intron	NM_001113434	NP_001106905			hypothetical protein LOC339263												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	21507129	21507129	+	IGR	DEL	A	-	-	rs113637029		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21507129delA								C17orf51 (29398 upstream) : FAM27L (318241 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21520240	21520241	+	IGR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21520240_21520241insA								C17orf51 (42509 upstream) : FAM27L (305129 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21525678	21525679	+	IGR	INS	-	TGT	TGT	rs141624412		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21525678_21525679insTGT								C17orf51 (47947 upstream) : FAM27L (299691 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21554408	21554409	+	IGR	DEL	CA	-	-	rs112964260		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21554408_21554409delCA								C17orf51 (76677 upstream) : FAM27L (270961 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21566237	21566238	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21566237_21566238delAA								C17orf51 (88506 upstream) : FAM27L (259132 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21929259	21929259	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21929259delA								FLJ36000 (16189 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	25264316	25264320	+	IGR	DEL	GGTGC	-	-	rs75651067		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25264316_25264320delGGTGC								None (None upstream) : WSB1 (356786 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	25305019	25305019	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25305019delA								None (None upstream) : WSB1 (316087 downstream)																																			---	---	---	---
NLK	51701	broad.mit.edu	37	17	26469254	26469254	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26469254delT	uc010crj.2	+						NLK_uc010cri.1_Intron	NM_016231	NP_057315			nemo like kinase						intracellular protein kinase cascade|negative regulation of Wnt receptor signaling pathway|peptidyl-threonine phosphorylation|regulation of transcription, DNA-dependent|serine phosphorylation of STAT3 protein|transcription, DNA-dependent|transforming growth factor beta receptor signaling pathway|Wnt receptor signaling pathway	cytoplasm|nucleus	ATP binding|magnesium ion binding|MAP kinase activity|SH2 domain binding|transcription factor binding|ubiquitin protein ligase binding			ovary(1)|lung(1)|central_nervous_system(1)	3	all_lung(13;0.000343)|Lung NSC(42;0.00184)			UCEC - Uterine corpus endometrioid carcinoma (53;0.168)														---	---	---	---
NLK	51701	broad.mit.edu	37	17	26512302	26512302	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26512302delT	uc010crj.2	+						NLK_uc010cri.1_Intron	NM_016231	NP_057315			nemo like kinase						intracellular protein kinase cascade|negative regulation of Wnt receptor signaling pathway|peptidyl-threonine phosphorylation|regulation of transcription, DNA-dependent|serine phosphorylation of STAT3 protein|transcription, DNA-dependent|transforming growth factor beta receptor signaling pathway|Wnt receptor signaling pathway	cytoplasm|nucleus	ATP binding|magnesium ion binding|MAP kinase activity|SH2 domain binding|transcription factor binding|ubiquitin protein ligase binding			ovary(1)|lung(1)|central_nervous_system(1)	3	all_lung(13;0.000343)|Lung NSC(42;0.00184)			UCEC - Uterine corpus endometrioid carcinoma (53;0.168)														---	---	---	---
FLJ40504	284085	broad.mit.edu	37	17	26617730	26617731	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26617730_26617731insT	uc002has.3	-							NM_173624	NP_775895			SubName: Full=Putative uncharacterized protein FLJ40504; SubName: Full=cDNA FLJ40504 fis, clone TESTI2045509, highly similar to KERATIN, TYPE I CYTOSKELETAL 18;												0	all_lung(13;0.000238)|Lung NSC(42;0.000789)			UCEC - Uterine corpus endometrioid carcinoma (53;0.155)														---	---	---	---
TMEM97	27346	broad.mit.edu	37	17	26655614	26655614	+	3'UTR	DEL	T	-	-	rs35381358		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26655614delT	uc002hat.2	+	3					IFT20_uc002hau.1_3'UTR|IFT20_uc002hav.1_3'UTR|IFT20_uc002haw.1_3'UTR|TNFAIP1_uc002hax.1_5'Flank	NM_014573	NP_055388			transmembrane protein 97						cholesterol homeostasis|regulation of cell growth	integral to membrane|lysosome|nuclear membrane|plasma membrane|rough endoplasmic reticulum	protein binding				0	all_lung(13;0.000238)|Lung NSC(42;0.000789)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	27356755	27356755	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27356755delT								SEZ6 (23297 upstream) : PIPOX (13163 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	27361723	27361723	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27361723delA								SEZ6 (28265 upstream) : PIPOX (8195 downstream)																																			---	---	---	---
MYO18A	399687	broad.mit.edu	37	17	27467820	27467821	+	Intron	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27467820_27467821delAC	uc002hdt.1	-						MYO18A_uc002hds.2_5'Flank|MYO18A_uc010csa.1_Intron|MYO18A_uc002hdu.1_Intron|MYO18A_uc010wbd.1_5'Flank	NM_078471	NP_510880			myosin 18A isoform a						anti-apoptosis|DNA metabolic process	ER-Golgi intermediate compartment|myosin complex	ATP binding|DNA binding|DNA-dependent ATPase activity|identical protein binding|motor activity				0			Epithelial(11;4.97e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000221)|all cancers(11;0.000234)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	27542670	27542675	+	IGR	DEL	ACACAC	-	-	rs148246642		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27542670_27542675delACACAC								MYO18A (35263 upstream) : CRYBA1 (31200 downstream)																																			---	---	---	---
SSH2	85464	broad.mit.edu	37	17	27962429	27962430	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27962429_27962430delTT	uc002heo.1	-						SSH2_uc010wbh.1_Intron	NM_033389	NP_203747			slingshot 2						actin cytoskeleton organization|regulation of actin polymerization or depolymerization|regulation of axonogenesis|regulation of lamellipodium assembly	cytoplasm|cytoskeleton	actin binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			skin(2)	2																		---	---	---	---
SSH2	85464	broad.mit.edu	37	17	28047745	28047746	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28047745_28047746delAA	uc002heo.1	-						SSH2_uc010wbh.1_Intron|SSH2_uc002hep.1_Intron|SSH2_uc002heq.2_Intron|SSH2_uc002her.2_Intron|SSH2_uc010csc.1_Intron	NM_033389	NP_203747			slingshot 2						actin cytoskeleton organization|regulation of actin polymerization or depolymerization|regulation of axonogenesis|regulation of lamellipodium assembly	cytoplasm|cytoskeleton	actin binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			skin(2)	2																		---	---	---	---
EFCAB5	374786	broad.mit.edu	37	17	28314844	28314844	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28314844delA	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																		---	---	---	---
EFCAB5	374786	broad.mit.edu	37	17	28331641	28331643	+	Intron	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28331641_28331643delTTT	uc002het.2	+						EFCAB5_uc010wbi.1_Intron|EFCAB5_uc010wbj.1_Intron|EFCAB5_uc010wbk.1_Intron|EFCAB5_uc010csd.2_Intron|EFCAB5_uc010cse.2_Intron|EFCAB5_uc010csf.2_Intron	NM_198529	NP_940931			EF-hand calcium binding domain 5 isoform a								calcium ion binding			ovary(1)|skin(1)	2																		---	---	---	---
CPD	1362	broad.mit.edu	37	17	28731725	28731727	+	Intron	DEL	TCT	-	-	rs66500745		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28731725_28731727delTCT	uc002hfb.1	+						CPD_uc010wbo.1_Intron|CPD_uc010wbp.1_Intron	NM_001304	NP_001295			carboxypeptidase D precursor						proteolysis	integral to membrane	metallocarboxypeptidase activity|serine-type carboxypeptidase activity|zinc ion binding			liver(1)|skin(1)	2																		---	---	---	---
CPD	1362	broad.mit.edu	37	17	28750489	28750489	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28750489delA	uc002hfb.1	+						CPD_uc010wbo.1_Intron|CPD_uc010wbp.1_Intron	NM_001304	NP_001295			carboxypeptidase D precursor						proteolysis	integral to membrane	metallocarboxypeptidase activity|serine-type carboxypeptidase activity|zinc ion binding			liver(1)|skin(1)	2																		---	---	---	---
SUZ12P	440423	broad.mit.edu	37	17	29068784	29068785	+	Intron	INS	-	AGA	AGA	rs139963035	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29068784_29068785insAGA	uc002hfn.1	+						SUZ12P_uc002hfo.2_Intron|SUZ12P_uc002hfp.2_Intron|SUZ12P_uc002hfq.2_Intron					Homo sapiens cDNA clone IMAGE:5299523, containing frame-shift errors.												0																		---	---	---	---
CRLF3	51379	broad.mit.edu	37	17	29115464	29115464	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29115464delG	uc002hfr.3	-						CRLF3_uc010wbr.1_Intron	NM_015986	NP_057070			cytokine receptor-like factor 3						negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|positive regulation of cell cycle arrest|positive regulation of JAK-STAT cascade|positive regulation of transcription from RNA polymerase II promoter	cytoplasm					0		all_hematologic(16;0.014)|Acute lymphoblastic leukemia(14;0.0236)|Myeloproliferative disorder(56;0.0255)																---	---	---	---
NF1	4763	broad.mit.edu	37	17	29474593	29474594	+	Intron	INS	-	TG	TG	rs149796650	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29474593_29474594insTG	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.?(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)			---	---	---	---
Unknown	0	broad.mit.edu	37	17	29957464	29957465	+	IGR	INS	-	G	G	rs150952760	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29957464_29957465insG								MIR365-2 (54924 upstream) : C17orf79 (221420 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	30071619	30071619	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30071619delT								MIR365-2 (169079 upstream) : C17orf79 (107266 downstream)																																			---	---	---	---
ACCN1	40	broad.mit.edu	37	17	31795828	31795828	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:31795828delT	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	17	32496594	32496594	+	Intron	DEL	A	-	-	rs34848565		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:32496594delA	uc002hhx.1	-											Homo sapiens cDNA clone IMAGE:6103254, partial cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	17	32700161	32700161	+	IGR	DEL	C	-	-	rs80176951		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:32700161delC								CCL1 (9909 upstream) : C17orf102 (200981 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	33518944	33518944	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33518944delT								UNC45B (2581 upstream) : AMAC1 (595 downstream)																																			---	---	---	---
SLFN11	91607	broad.mit.edu	37	17	33678459	33678459	+	3'UTR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33678459delA	uc010ctp.2	-	7					SLFN11_uc010ctq.2_3'UTR|SLFN11_uc002hjh.3_3'UTR|SLFN11_uc002hjg.3_3'UTR|SLFN11_uc010ctr.2_3'UTR	NM_001104588	NP_001098058			schlafen family member 11							nucleus	ATP binding			large_intestine(1)|ovary(1)|skin(1)	3		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	33734828	33734828	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33734828delG								SLFN11 (34108 upstream) : SLFN12 (3255 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	34217074	34217075	+	IGR	DEL	TT	-	-	rs113886465		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34217074_34217075delTT								CCL5 (9697 upstream) : RDM1 (28012 downstream)																																			---	---	---	---
TBC1D3C	414060	broad.mit.edu	37	17	34587956	34587957	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34587956_34587957delAA	uc002hlk.1	-						TBC1D3C_uc002hll.1_Intron|TBC1D3G_uc010wcv.1_Intron|TBC1D3G_uc002hlm.2_Intron|uc002hlo.1_5'Flank	NM_001001418	NP_001001418			TBC1 domain family member 3C							intracellular	Rab GTPase activator activity				0		Breast(25;0.102)|Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)														---	---	---	---
TBC1D3C	414060	broad.mit.edu	37	17	34758859	34758859	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34758859delG	uc002hme.3	-						TBC1D3C_uc002hll.1_Intron|TBC1D3G_uc010wcv.1_Intron|TBC1D3G_uc002hlm.2_Intron|TBC1D3H_uc002hmb.2_5'Flank|TBC1D3H_uc002hmc.3_5'Flank|TBC1D3H_uc010wcx.1_5'Flank|TBC1D3H_uc002hmd.3_5'Flank	NM_001001418	NP_001001418			TBC1 domain family member 3C							intracellular	Rab GTPase activator activity				0		Breast(25;0.102)|Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	35188580	35188580	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35188580delA								MRM1 (223174 upstream) : LHX1 (105919 downstream)																																			---	---	---	---
AATF	26574	broad.mit.edu	37	17	35400341	35400341	+	Intron	DEL	T	-	-	rs34084439		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35400341delT	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	35723728	35723729	+	Intron	DEL	AA	-	-	rs113396306		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35723728_35723729delAA	uc002hno.2	-						ACACA_uc002hnn.2_Intron|ACACA_uc002hnq.2_Intron|ACACA_uc002hnr.1_5'Flank	NM_198834	NP_942131			acetyl-Coenzyme A carboxylase alpha isoform 1						acetyl-CoA metabolic process|energy reserve metabolic process|fatty acid biosynthetic process|long-chain fatty-acyl-CoA biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|triglyceride biosynthetic process	cytosol	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding			large_intestine(1)|ovary(1)	2		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)													---	---	---	---
ACACA	31	broad.mit.edu	37	17	35762769	35762769	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35762769delT	uc002hno.2	-						ACACA_uc002hnn.2_Intron|ACACA_uc002hnq.2_Intron	NM_198834	NP_942131			acetyl-Coenzyme A carboxylase alpha isoform 1						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)													---	---	---	---
C17orf98	388381	broad.mit.edu	37	17	36993202	36993202	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36993202delA	uc002hqv.2	-							NM_001080465	NP_001073934			hypothetical protein LOC388381												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	37214421	37214421	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37214421delT	uc002hre.1	+						uc002hrf.1_5'Flank					Homo sapiens cDNA FLJ37796 fis, clone BRSSN1000092.																														---	---	---	---
FBXL20	84961	broad.mit.edu	37	17	37420364	37420364	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37420364delA	uc010wed.1	-						FBXL20_uc002hrt.2_Intron|FBXL20_uc010cvu.2_Intron	NM_032875	NP_116264			F-box and leucine-rich repeat protein 20							cytoplasm				ovary(1)	1			LUAD - Lung adenocarcinoma(14;0.146)															---	---	---	---
ERBB2	2064	broad.mit.edu	37	17	37844465	37844465	+	5'UTR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37844465delT	uc010cwa.2	+	1					ERBB2_uc002hsm.2_5'UTR|PGAP3_uc002hsj.2_5'Flank|PGAP3_uc010wej.1_5'Flank|PGAP3_uc002hsk.2_5'Flank|PGAP3_uc010cvz.2_5'Flank|ERBB2_uc002hsl.2_5'UTR	NM_001005862	NP_001005862			erbB-2 isoform b						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)			---	---	---	---
Unknown	0	broad.mit.edu	37	17	37891035	37891035	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37891035delT								C17orf37 (4247 upstream) : GRB7 (3152 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	39450261	39450261	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39450261delT								KRTAP9-9 (37646 upstream) : KRTAP17-1 (20910 downstream)																																			---	---	---	---
JUP	3728	broad.mit.edu	37	17	39762265	39762266	+	Intron	INS	-	A	A	rs143665923	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39762265_39762266insA	uc010wfs.1	-							NM_021991	NP_068831			junction plakoglobin						adherens junction organization|atrioventricular valve morphogenesis|cell migration|cell morphogenesis|cellular response to indole-3-methanol|cytoskeletal anchoring at plasma membrane|detection of mechanical stimulus|ectoderm development|endothelial cell-cell adhesion|gastrulation|morphogenesis of embryonic epithelium|negative regulation of heart induction by canonical Wnt receptor signaling pathway|negative regulation of Wnt receptor signaling pathway involved in heart development|nervous system development|oocyte development|positive regulation of protein import into nucleus|positive regulation of sequence-specific DNA binding transcription factor activity|skin development	actin cytoskeleton|Axin-APC-beta-catenin-GSK3B complex|basolateral plasma membrane|catenin complex|desmosome|fascia adherens|gamma-catenin-TCF7L2 complex|internal side of plasma membrane|nucleus|protein-DNA complex|Z disc|zonula adherens	alpha-catenin binding|cadherin binding|protein homodimerization activity|protein kinase binding|protein phosphatase binding|RPTP-like protein binding|specific RNA polymerase II transcription factor activity|transcription coactivator activity			ovary(2)|lung(2)|breast(1)	5		Breast(137;0.000162)	BRCA - Breast invasive adenocarcinoma(4;0.233)	BRCA - Breast invasive adenocarcinoma(366;0.15)														---	---	---	---
JUP	3728	broad.mit.edu	37	17	39859994	39859994	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39859994delA	uc010wfs.1	-							NM_021991	NP_068831			junction plakoglobin						adherens junction organization|atrioventricular valve morphogenesis|cell migration|cell morphogenesis|cellular response to indole-3-methanol|cytoskeletal anchoring at plasma membrane|detection of mechanical stimulus|ectoderm development|endothelial cell-cell adhesion|gastrulation|morphogenesis of embryonic epithelium|negative regulation of heart induction by canonical Wnt receptor signaling pathway|negative regulation of Wnt receptor signaling pathway involved in heart development|nervous system development|oocyte development|positive regulation of protein import into nucleus|positive regulation of sequence-specific DNA binding transcription factor activity|skin development	actin cytoskeleton|Axin-APC-beta-catenin-GSK3B complex|basolateral plasma membrane|catenin complex|desmosome|fascia adherens|gamma-catenin-TCF7L2 complex|internal side of plasma membrane|nucleus|protein-DNA complex|Z disc|zonula adherens	alpha-catenin binding|cadherin binding|protein homodimerization activity|protein kinase binding|protein phosphatase binding|RPTP-like protein binding|specific RNA polymerase II transcription factor activity|transcription coactivator activity			ovary(2)|lung(2)|breast(1)	5		Breast(137;0.000162)	BRCA - Breast invasive adenocarcinoma(4;0.233)	BRCA - Breast invasive adenocarcinoma(366;0.15)														---	---	---	---
JUP	3728	broad.mit.edu	37	17	39914431	39914431	+	Intron	DEL	T	-	-	rs150430167		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39914431delT	uc002hxq.2	-						JUP_uc010wfs.1_Intron|JUP_uc002hxr.2_Intron|JUP_uc002hxs.2_Intron	NM_021991	NP_068831			junction plakoglobin						adherens junction organization|atrioventricular valve morphogenesis|cell migration|cell morphogenesis|cellular response to indole-3-methanol|cytoskeletal anchoring at plasma membrane|detection of mechanical stimulus|ectoderm development|endothelial cell-cell adhesion|gastrulation|morphogenesis of embryonic epithelium|negative regulation of heart induction by canonical Wnt receptor signaling pathway|negative regulation of Wnt receptor signaling pathway involved in heart development|nervous system development|oocyte development|positive regulation of protein import into nucleus|positive regulation of sequence-specific DNA binding transcription factor activity|skin development	actin cytoskeleton|Axin-APC-beta-catenin-GSK3B complex|basolateral plasma membrane|catenin complex|desmosome|fascia adherens|gamma-catenin-TCF7L2 complex|internal side of plasma membrane|nucleus|protein-DNA complex|Z disc|zonula adherens	alpha-catenin binding|cadherin binding|protein homodimerization activity|protein kinase binding|protein phosphatase binding|RPTP-like protein binding|specific RNA polymerase II transcription factor activity|transcription coactivator activity			ovary(2)|lung(2)|breast(1)	5		Breast(137;0.000162)	BRCA - Breast invasive adenocarcinoma(4;0.233)	BRCA - Breast invasive adenocarcinoma(366;0.15)														---	---	---	---
STAT5A	6776	broad.mit.edu	37	17	40447289	40447289	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40447289delT	uc002hzj.1	+						STAT5A_uc010cya.1_Intron|STAT5A_uc010cyb.1_Intron|STAT5A_uc010cyc.1_Intron	NM_003152	NP_003143			signal transducer and activator of transcription						2-oxoglutarate metabolic process|allantoin metabolic process|citrate metabolic process|creatine metabolic process|creatinine metabolic process|fatty acid metabolic process|isoleucine metabolic process|oxaloacetate metabolic process|succinate metabolic process|taurine metabolic process|valine metabolic process	cytosol|nucleoplasm	calcium ion binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			lung(1)	1		all_cancers(22;1.56e-06)|all_epithelial(22;3.17e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.128)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	40769004	40769004	+	IGR	DEL	A	-	-	rs112785121		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40769004delA								TUBG1 (1750 upstream) : TUBG2 (42262 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	40803824	40803824	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40803824delC								TUBG1 (36570 upstream) : TUBG2 (7442 downstream)																																			---	---	---	---
CNTNAP1	8506	broad.mit.edu	37	17	40842542	40842547	+	Intron	DEL	AAAAAA	-	-	rs139890629		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40842542_40842547delAAAAAA	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)														---	---	---	---
LOC388387	388387	broad.mit.edu	37	17	41042463	41042464	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41042463_41042464delTT	uc010whe.1	-						LOC388387_uc002ibz.2_Intron|LOC388387_uc002iby.2_Intron|LOC388387_uc002ica.2_Intron					SubName: Full=cDNA FLJ57415;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	41387406	41387406	+	IGR	DEL	T	-	-	rs141505550		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41387406delT								TMEM106A (15817 upstream) : LOC100130581 (59807 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	41819538	41819538	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41819538delT								MEOX1 (80276 upstream) : SOST (11561 downstream)																																			---	---	---	---
MPP3	4356	broad.mit.edu	37	17	41884685	41884687	+	Intron	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41884685_41884687delTTT	uc002iei.3	-						MPP3_uc002ieh.2_Intron|MPP3_uc002iej.2_Intron	NM_001932	NP_001923			palmitoylated membrane protein 3						signal transduction	cell surface|integral to plasma membrane	guanylate kinase activity			large_intestine(1)|skin(1)	2		Breast(137;0.00394)		BRCA - Breast invasive adenocarcinoma(366;0.119)														---	---	---	---
CCDC43	124808	broad.mit.edu	37	17	42757271	42757271	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42757271delA	uc002ihc.2	-						CCDC43_uc010czw.1_Intron	NM_144609	NP_653210			coiled-coil domain containing 43 isoform 1												0		Prostate(33;0.0322)																---	---	---	---
Unknown	0	broad.mit.edu	37	17	43297431	43297431	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43297431delA	uc002iil.3	-						uc002iim.2_Intron|FMNL1_uc002iin.2_5'Flank					Homo sapiens hypothetical protein LOC339192, mRNA (cDNA clone IMAGE:4638737), partial cds.																														---	---	---	---
FMNL1	752	broad.mit.edu	37	17	43313838	43313839	+	Intron	INS	-	G	G	rs145223547	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43313838_43313839insG	uc002iin.2	+							NM_005892	NP_005883			formin-like 1						actin cytoskeleton organization		actin binding|Rho GTPase binding			pancreas(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	43616612	43616612	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43616612delA	uc002ijh.2	-						uc010wjv.1_Intron					Homo sapiens cDNA FLJ45049 fis, clone BRAWH3022347.																														---	---	---	---
KIAA1267	284058	broad.mit.edu	37	17	44166765	44166765	+	Intron	DEL	T	-	-	rs67516111		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44166765delT	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	44263749	44263750	+	Intron	INS	-	A	A	rs67118224		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44263749_44263750insA	uc002ikc.2	-						KIAA1267_uc002ikd.2_Intron|KIAA1267_uc010dav.2_Intron	NM_015443	NP_056258			hypothetical protein LOC284058							MLL1 complex	protein binding			skin(2)	2		Melanoma(429;0.211)																---	---	---	---
KIAA1267	284058	broad.mit.edu	37	17	44291283	44291284	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44291283_44291284delAA	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	44307938	44307938	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44307938delA								KIAA1267 (5221 upstream) : ARL17B (55925 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	44329744	44329747	+	IGR	DEL	TTTT	-	-	rs7502848	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44329744_44329747delTTTT								KIAA1267 (27027 upstream) : ARL17B (34116 downstream)																																			---	---	---	---
WNT3	7473	broad.mit.edu	37	17	44858779	44858779	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44858779delA	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)															---	---	---	---
CDC27	996	broad.mit.edu	37	17	45198679	45198682	+	Intron	DEL	AAAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45198679_45198682delAAAA	uc002ild.3	-						CDC27_uc002ile.3_Intron|CDC27_uc002ilf.3_Intron|CDC27_uc010wkp.1_Intron	NM_001256	NP_001247			cell division cycle protein 27 isoform 2						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell proliferation|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase/anaphase transition|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	protein phosphatase binding			lung(2)|breast(2)|ovary(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	45708978	45708979	+	IGR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45708978_45708979insA								NPEPPS (8337 upstream) : KPNB1 (18296 downstream)																																			---	---	---	---
SNX11	29916	broad.mit.edu	37	17	46183269	46183269	+	5'Flank	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46183269delT	uc002inf.1	+						SNX11_uc010wlg.1_5'Flank|SNX11_uc010wlh.1_5'Flank|SNX11_uc010wli.1_5'Flank|SNX11_uc010wlj.1_5'Flank|SNX11_uc002ing.1_5'Flank	NM_152244	NP_689450			sorting nexin 11						cell communication|protein transport	membrane	phosphatidylinositol binding				0																		---	---	---	---
SKAP1	8631	broad.mit.edu	37	17	46234244	46234244	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46234244delT	uc002ini.1	-						SKAP1_uc002inj.1_Intron|SKAP1_uc010dbd.1_Intron|SKAP1_uc010dbe.1_Intron|MIR1203_hsa-mir-1203|MI0006335_5'Flank	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	46478675	46478675	+	Intron	DEL	A	-	-	rs71366871		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46478675delA	uc002ini.1	-						SKAP1_uc002inj.1_Intron|SKAP1_uc010dbd.1_Intron|SKAP1_uc010dbe.1_Intron	NM_003726	NP_003717			src kinase associated phosphoprotein 1 isoform						positive regulation of transcription from RNA polymerase II promoter|T cell receptor signaling pathway	cytoplasm|nucleus|plasma membrane	antigen binding|protein kinase binding|SH2 domain binding				0																		---	---	---	---
HOXB3	3213	broad.mit.edu	37	17	46658040	46658040	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46658040delC	uc010dbf.2	-						HOXB3_uc010wlm.1_Intron|HOXB3_uc010dbg.2_Intron|HOXB3_uc010wll.1_Intron|HOXB4_uc002inp.2_5'Flank|uc002inq.3_5'Flank|MIR10A_hsa-mir-10a|MI0000266_5'Flank	NM_002146	NP_002137			homeobox B3						angiogenesis	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
HOXB7	3217	broad.mit.edu	37	17	46685066	46685066	+	3'UTR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46685066delT	uc002inv.2	-	2					HOXB6_uc002ins.1_5'Flank|HOXB6_uc010dbh.1_5'Flank	NM_004502	NP_004493			homeobox B7							nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	47328771	47328774	+	Intron	DEL	TTTT	-	-	rs147782122		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47328771_47328774delTTTT	uc002iot.1	+											Homo sapiens cDNA FLJ40194 fis, clone TESTI2019481.																														---	---	---	---
Unknown	0	broad.mit.edu	37	17	47607046	47607046	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47607046delC								NGFR (14681 upstream) : NXPH3 (46252 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	47615324	47615324	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47615324delA								NGFR (22959 upstream) : NXPH3 (37974 downstream)																																			---	---	---	---
SLC35B1	10237	broad.mit.edu	37	17	47780109	47780109	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47780109delA	uc002iph.1	-						SLC35B1_uc002ipi.1_Intron|SLC35B1_uc002ipj.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																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	48043517	48043517	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48043517delT								TAC4 (118138 upstream) : DLX4 (3045 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	48347757	48347757	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48347757delG								COL1A1 (68757 upstream) : TMEM92 (4080 downstream)																																	OREG0024562	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
MYCBPAP	84073	broad.mit.edu	37	17	48602072	48602073	+	Intron	INS	-	GT	GT			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48602072_48602073insGT	uc010wmr.1	+						MYCBPAP_uc002iqz.2_Intron	NM_032133	NP_115509			Myc-binding protein-associated protein						cell differentiation|multicellular organismal development|spermatogenesis|synaptic transmission	cytoplasm|membrane	protein binding			urinary_tract(2)|skin(2)|ovary(1)|pancreas(1)	6	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;1.23e-09)															---	---	---	---
LUC7L3	51747	broad.mit.edu	37	17	48821044	48821044	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48821044delT	uc002isr.2	+						LUC7L3_uc002isp.1_Intron|LUC7L3_uc010wmw.1_Intron|LUC7L3_uc002isq.2_Intron|LUC7L3_uc002iss.2_Intron	NM_006107	NP_006098			LUC7-like 3						apoptosis|mRNA processing|response to stress|RNA splicing	focal adhesion|nuclear speck	DNA binding|mRNA binding|protein binding				0																		---	---	---	---
C17orf73	55018	broad.mit.edu	37	17	48839303	48839304	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48839303_48839304delTT	uc010wmx.1	-							NR_024626				Homo sapiens cDNA FLJ20663 fis, clone KAIA798.												0																		---	---	---	---
SPAG9	9043	broad.mit.edu	37	17	49066820	49066820	+	Intron	DEL	T	-	-	rs74399022		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49066820delT	uc002itc.2	-						SPAG9_uc002itb.2_Intron|SPAG9_uc002itd.2_Intron|SPAG9_uc002ita.2_Intron	NM_001130528	NP_001124000			sperm associated antigen 9 isoform 1						positive regulation of cell migration|positive regulation of muscle cell differentiation|retrograde transport, endosome to Golgi|spermatogenesis	acrosomal vesicle|integral to membrane|perinuclear region of cytoplasm				lung(4)|breast(1)	5			BRCA - Breast invasive adenocarcinoma(22;4.24e-07)															---	---	---	---
SPAG9	9043	broad.mit.edu	37	17	49154366	49154367	+	Intron	INS	-	CTAT	CTAT	rs62062982		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49154366_49154367insCTAT	uc002itc.2	-						SPAG9_uc002itb.2_Intron|SPAG9_uc002itd.2_Intron|SPAG9_uc002itf.2_Intron	NM_001130528	NP_001124000			sperm associated antigen 9 isoform 1						positive regulation of cell migration|positive regulation of muscle cell differentiation|retrograde transport, endosome to Golgi|spermatogenesis	acrosomal vesicle|integral to membrane|perinuclear region of cytoplasm				lung(4)|breast(1)	5			BRCA - Breast invasive adenocarcinoma(22;4.24e-07)															---	---	---	---
SPAG9	9043	broad.mit.edu	37	17	49177990	49177990	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49177990delA	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)															---	---	---	---
UTP18	51096	broad.mit.edu	37	17	49353083	49353084	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49353083_49353084delTT	uc002its.2	+							NM_016001	NP_057085			UTP18, small subunit processome component						rRNA processing	nucleolus					0			BRCA - Breast invasive adenocarcinoma(22;2.09e-07)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	49456038	49456038	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49456038delT								UTP18 (80748 upstream) : CA10 (251637 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	49567654	49567654	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49567654delA								UTP18 (192364 upstream) : CA10 (140021 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	49670629	49670629	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49670629delT								UTP18 (295339 upstream) : CA10 (37046 downstream)																																			---	---	---	---
CA10	56934	broad.mit.edu	37	17	50180340	50180340	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:50180340delT	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	50440992	50440993	+	IGR	DEL	AC	-	-	rs113415135		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:50440992_50440993delAC								CA10 (203615 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	51054827	51054827	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:51054827delT								CA10 (817450 upstream) : KIF2B (845412 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	51521793	51521794	+	IGR	DEL	CA	-	-	rs72364154		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:51521793_51521794delCA								None (None upstream) : KIF2B (378445 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	51653316	51653317	+	IGR	DEL	CA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:51653316_51653317delCA								None (None upstream) : KIF2B (246922 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	53671036	53671036	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:53671036delT								MMD (171695 upstream) : TMEM100 (125954 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	54068944	54068944	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54068944delT								PCTP (214197 upstream) : ANKFN1 (161892 downstream)																																			---	---	---	---
ANKFN1	162282	broad.mit.edu	37	17	54237896	54237896	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54237896delT	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	54552497	54552498	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54552497_54552498insA	uc002iun.1	+							NM_153228	NP_694960			ankyrin-repeat and fibronectin type III domain											large_intestine(1)|ovary(1)	2																		---	---	---	---
MSI2	124540	broad.mit.edu	37	17	55550259	55550260	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55550259_55550260delTT	uc002iuz.1	+						MSI2_uc010wnm.1_Intron|MSI2_uc002iva.2_Intron	NM_138962	NP_620412			musashi 2 isoform a							cytoplasm	nucleotide binding|RNA binding			central_nervous_system(1)|pancreas(1)	2	Breast(9;1.78e-08)			GBM - Glioblastoma multiforme(1;0.0025)				T	HOXA9	CML								---	---	---	---
MSI2	124540	broad.mit.edu	37	17	55589001	55589002	+	Intron	INS	-	C	C	rs150488970	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55589001_55589002insC	uc002iuz.1	+						MSI2_uc010wnm.1_Intron|MSI2_uc002iva.2_Intron	NM_138962	NP_620412			musashi 2 isoform a							cytoplasm	nucleotide binding|RNA binding			central_nervous_system(1)|pancreas(1)	2	Breast(9;1.78e-08)			GBM - Glioblastoma multiforme(1;0.0025)				T	HOXA9	CML								---	---	---	---
Unknown	0	broad.mit.edu	37	17	55843498	55843499	+	IGR	DEL	GA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55843498_55843499delGA								MSI2 (86199 upstream) : MRPS23 (73345 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	55865069	55865069	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55865069delA								MSI2 (107770 upstream) : MRPS23 (51775 downstream)																																			---	---	---	---
VEZF1	7716	broad.mit.edu	37	17	56056916	56056916	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56056916delA	uc002ivf.1	-						VEZF1_uc010dcn.1_Intron	NM_007146	NP_009077			zinc finger protein 161						cellular defense response|regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	DNA binding|zinc ion binding			ovary(1)|breast(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	56177389	56177390	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56177389_56177390delTT								DYNLL2 (9771 upstream) : OR4D1 (55125 downstream)																																			---	---	---	---
RNF43	54894	broad.mit.edu	37	17	56454406	56454410	+	Intron	DEL	CTTAA	-	-	rs3030929		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56454406_56454410delCTTAA	uc002iwf.2	-						RNF43_uc010wnv.1_Intron|RNF43_uc002iwh.3_Intron|RNF43_uc002iwg.3_Intron|RNF43_uc010dcw.2_Intron	NM_017763	NP_060233			ring finger protein 43 precursor							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)																	---	---	---	---
SEPT4	5414	broad.mit.edu	37	17	56615994	56615994	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56615994delC	uc010wnx.1	-						SEPT4_uc010wny.1_Intron	NM_080416	NP_536341			septin 4 isoform 3						apoptosis|cell cycle|cytokinesis|regulation of apoptosis	cytoskeleton|mitochondrion|nucleus	GTP binding|GTPase activity|protein binding|structural molecule activity				0	Medulloblastoma(34;0.127)|all_neural(34;0.237)																	---	---	---	---
RAD51C	5889	broad.mit.edu	37	17	56774399	56774399	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56774399delT	uc002iwu.2	+						RAD51C_uc010woa.1_Intron|RAD51C_uc010ddc.2_Intron|RAD51C_uc002iwv.2_Intron|RAD51C_uc002iww.2_Intron|RAD51C_uc010wob.1_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				---	---	---	---
RAD51C	5889	broad.mit.edu	37	17	56779363	56779363	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56779363delT	uc002iwu.2	+						RAD51C_uc010woa.1_Intron|RAD51C_uc010ddc.2_Intron|RAD51C_uc002iwv.2_Intron|RAD51C_uc002iww.2_Intron|RAD51C_uc010wob.1_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	56841982	56841983	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56841982_56841983insT	uc002iwx.2	+						PPM1E_uc010ddd.2_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)															---	---	---	---
PPM1E	22843	broad.mit.edu	37	17	56842541	56842545	+	Intron	DEL	TTTTT	-	-	rs11298918		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56842541_56842545delTTTTT	uc002iwx.2	+						PPM1E_uc010ddd.2_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)															---	---	---	---
PPM1E	22843	broad.mit.edu	37	17	57060352	57060352	+	3'UTR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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	57149028	57149029	+	Intron	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57149028_57149029delAC	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				---	---	---	---
GDPD1	284161	broad.mit.edu	37	17	57311744	57311744	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57311744delC	uc002ixk.1	+						GDPD1_uc002ixj.2_Intron	NM_182569	NP_872375			glycerophosphodiester phosphodiesterase domain						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)																	---	---	---	---
TUBD1	51174	broad.mit.edu	37	17	57966089	57966089	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57966089delT	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)															---	---	---	---
RNFT1	51136	broad.mit.edu	37	17	58037277	58037280	+	Intron	DEL	AAAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58037277_58037280delAAAA	uc002iya.2	-						RNFT1_uc002iyb.2_Intron|RNFT1_uc002iyc.2_Intron|RNFT1_uc010wop.1_3'UTR	NM_016125	NP_057209			PTD016 protein							integral to membrane	zinc ion binding				0	all_cancers(5;1.58e-13)|Breast(5;2.91e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;7.95e-12)|all cancers(12;1.34e-10)															---	---	---	---
CA4	762	broad.mit.edu	37	17	58232860	58232861	+	Intron	DEL	AC	-	-	rs3830362		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58232860_58232861delAC	uc002iym.3	+						CA4_uc010wou.1_Intron	NM_000717	NP_000708			carbonic anhydrase IV precursor						bicarbonate transport|one-carbon metabolic process	anchored to external side of plasma membrane|apical plasma membrane|brush border membrane|ER-Golgi intermediate compartment|membrane fraction|perinuclear region of cytoplasm|rough endoplasmic reticulum|secretory granule membrane|trans-Golgi network|transport vesicle membrane	carbonate dehydratase activity|protein binding|zinc ion binding				0	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;3.83e-12)|all cancers(12;6.83e-11)		Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Cyclothiazide(DB00606)|Diazoxide(DB01119)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Quinethazone(DB01325)|Topiramate(DB00273)|Trichlormethiazide(DB01021)													---	---	---	---
APPBP2	10513	broad.mit.edu	37	17	58585337	58585342	+	Intron	DEL	TTTTTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58585337_58585342delTTTTTT	uc002iys.1	-						APPBP2_uc010ddl.1_Intron	NM_006380	NP_006371			amyloid beta precursor protein-binding protein						intracellular protein transport	cytoplasmic vesicle membrane|microtubule|microtubule associated complex|nucleus	microtubule motor activity|protein binding				0	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;3.67e-13)|all cancers(12;1.44e-11)|Colorectal(3;0.01)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	58639092	58639096	+	IGR	DEL	AAAAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58639092_58639096delAAAAA								APPBP2 (35512 upstream) : PPM1D (38458 downstream)																																			---	---	---	---
BCAS3	54828	broad.mit.edu	37	17	58888882	58888882	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58888882delA	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)															---	---	---	---
BCAS3	54828	broad.mit.edu	37	17	58933052	58933052	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58933052delT	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)															---	---	---	---
BCAS3	54828	broad.mit.edu	37	17	59015379	59015379	+	Intron	DEL	T	-	-	rs142673156		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59015379delT	uc002iyv.3	+						BCAS3_uc010wow.1_Intron|BCAS3_uc002iyu.3_Intron|BCAS3_uc002iyw.3_Intron|BCAS3_uc002iyx.1_Intron|BCAS3_uc002iyy.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)															---	---	---	---
BCAS3	54828	broad.mit.edu	37	17	59064184	59064184	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59064184delT	uc002iyv.3	+						BCAS3_uc010wow.1_Intron|BCAS3_uc002iyu.3_Intron|BCAS3_uc002iyw.3_Intron|BCAS3_uc002iyx.1_Intron|BCAS3_uc002iyy.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)															---	---	---	---
BCAS3	54828	broad.mit.edu	37	17	59364605	59364608	+	Intron	DEL	AAAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59364605_59364608delAAAA	uc002iyv.3	+						BCAS3_uc002iyu.3_Intron|BCAS3_uc002iyw.3_Intron|BCAS3_uc002iyy.3_Intron|BCAS3_uc002iyz.3_Intron|BCAS3_uc002iza.3_Intron|BCAS3_uc002izb.3_Intron|BCAS3_uc002izc.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-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	59502721	59502722	+	IGR	DEL	AT	-	-	rs147175167		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59502721_59502722delAT								C17orf82 (12080 upstream) : TBX4 (27057 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	59610470	59610470	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59610470delT								TBX4 (48001 upstream) : NACA2 (57324 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	59715096	59715097	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59715096_59715097delAA								NACA2 (46533 upstream) : BRIP1 (44888 downstream)																																			---	---	---	---
TLK2	11011	broad.mit.edu	37	17	60654328	60654328	+	Intron	DEL	T	-	-	rs72108433		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60654328delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	60952112	60952112	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60952112delT								MARCH10 (66407 upstream) : MIR633 (69464 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	61073847	61073848	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61073847_61073848delTT								MIR633 (52174 upstream) : TANC2 (13050 downstream)																																			---	---	---	---
TANC2	26115	broad.mit.edu	37	17	61417855	61417855	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61417855delA	uc002jal.3	+						TANC2_uc010wpe.1_Intron	NM_025185	NP_079461			tetratricopeptide repeat, ankyrin repeat and								binding			ovary(2)	2																		---	---	---	---
DDX42	11325	broad.mit.edu	37	17	61866907	61866912	+	Intron	DEL	TTTTTT	-	-	rs56786359		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61866907_61866912delTTTTTT	uc002jbu.2	+						DDX42_uc002jbv.2_Intron|DDX42_uc002jbw.1_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																		---	---	---	---
DDX42	11325	broad.mit.edu	37	17	61888619	61888619	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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																		---	---	---	---
ERN1	2081	broad.mit.edu	37	17	62209240	62209240	+	5'Flank	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62209240delC	uc002jdz.2	-							NM_001433	NP_001424			endoplasmic reticulum to nucleus signalling 1						activation of signaling protein activity involved in unfolded protein response|apoptosis|cell cycle arrest|induction of apoptosis|mRNA processing|regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to endoplasmic reticulum membrane	ATP binding|endoribonuclease activity, producing 5'-phosphomonoesters|magnesium ion binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(4)|lung(2)|stomach(1)|ovary(1)|kidney(1)	9																		---	---	---	---
TEX2	55852	broad.mit.edu	37	17	62312252	62312252	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62312252delT	uc002jed.2	-						TEX2_uc002jee.2_Intron	NM_018469	NP_060939			testis expressed sequence 2						signal transduction|sphingolipid metabolic process	integral to membrane				ovary(1)	1			BRCA - Breast invasive adenocarcinoma(8;1.33e-10)	READ - Rectum adenocarcinoma(1115;0.0689)														---	---	---	---
CCDC45	90799	broad.mit.edu	37	17	62521442	62521442	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62521442delA	uc002jem.2	+						CCDC45_uc002jen.2_Intron|CCDC45_uc010wqb.1_Intron	NM_138363	NP_612372			coiled-coil domain containing 45							centrosome|spindle pole	protein binding				0	Breast(5;1.32e-14)		BRCA - Breast invasive adenocarcinoma(8;8.6e-12)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	63496491	63496491	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63496491delG								RGS9 (272672 upstream) : AXIN2 (28194 downstream)																																			---	---	---	---
CCDC46	201134	broad.mit.edu	37	17	64019986	64019986	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64019986delA	uc002jfl.2	-						CCDC46_uc010deo.2_Intron|CCDC46_uc002jfm.2_Intron|CCDC46_uc010dep.2_Intron	NM_145036	NP_659473			coiled-coil domain containing 46 isoform a							centrosome					0			BRCA - Breast invasive adenocarcinoma(6;1.53e-06)															---	---	---	---
PRKCA	5578	broad.mit.edu	37	17	64462027	64462027	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64462027delT	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	64552106	64552106	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64552106delT	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	64752674	64752675	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64752674_64752675delAA	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)													---	---	---	---
HELZ	9931	broad.mit.edu	37	17	65167954	65167954	+	Intron	DEL	T	-	-	rs66660717		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65167954delT	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	65633404	65633404	+	Intron	DEL	T	-	-	rs79219203		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65633404delT	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	65836221	65836221	+	Intron	DEL	T	-	-	rs113437066		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65836221delT	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)															---	---	---	---
PRKAR1A	5573	broad.mit.edu	37	17	66520326	66520326	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66520326delT	uc002jhg.2	+						PRKAR1A_uc002jhh.2_Intron|PRKAR1A_uc002jhi.2_Intron|PRKAR1A_uc002jhj.2_Intron|PRKAR1A_uc002jhk.2_Intron|PRKAR1A_uc002jhl.2_Intron|PRKAR1A_uc002jhm.2_Intron	NM_212471	NP_997636			cAMP-dependent protein kinase, regulatory						activation of phospholipase C activity|activation of protein kinase A activity|blood coagulation|cellular response to glucagon stimulus|energy reserve metabolic process|intracellular signal transduction|nerve growth factor receptor signaling pathway|regulation of insulin secretion|regulation of transcription from RNA polymerase II promoter|transmembrane transport|water transport	cAMP-dependent protein kinase complex|cytosol	cAMP binding|cAMP-dependent protein kinase regulator activity|protein binding			adrenal_gland(4)|lung(3)|thyroid(2)|soft_tissue(2)|breast(1)	12	Breast(10;1.64e-13)							T|Mis|N|F|S	RET	papillary thyroid	myxoma|endocrine|papillary thyroid			Carney_Complex|Primary_Pigmented_Nodular_Adrenocortical_Disease_Familial|Cardiac_Myxomas_Familial_Clustering_of				---	---	---	---
Unknown	0	broad.mit.edu	37	17	66813837	66813840	+	IGR	DEL	TTTT	-	-	rs75656033		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66813837_66813840delTTTT								FAM20A (216742 upstream) : ABCA8 (49593 downstream)																																			---	---	---	---
ABCA5	23461	broad.mit.edu	37	17	67248055	67248055	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67248055delA	uc002jif.2	-						ABCA5_uc002jib.2_Intron|ABCA5_uc002jic.2_Intron|ABCA5_uc002jid.2_Intron|ABCA5_uc002jie.2_Intron|ABCA5_uc002jig.2_Intron	NM_018672	NP_061142			ATP-binding cassette, sub-family A , member 5						cholesterol efflux|high-density lipoprotein particle remodeling|negative regulation of macrophage derived foam cell differentiation	Golgi membrane|integral to membrane|late endosome membrane|lysosomal membrane	ATP binding|ATPase activity			ovary(2)|central_nervous_system(1)|skin(1)	4	Breast(10;3.72e-11)																	---	---	---	---
Unknown	0	broad.mit.edu	37	17	67374745	67374745	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67374745delA								ABCA5 (51422 upstream) : MAP2K6 (36093 downstream)																																			---	---	---	---
MAP2K6	5608	broad.mit.edu	37	17	67414671	67414671	+	Intron	DEL	T	-	-	rs35592724		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67414671delT	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)																	---	---	---	---
MAP2K6	5608	broad.mit.edu	37	17	67482120	67482121	+	Intron	INS	-	T	T	rs141459579	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67482120_67482121insT	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	67958815	67958815	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67958815delA								MAP2K6 (420353 upstream) : KCNJ16 (112611 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	68227979	68227979	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:68227979delT								KCNJ2 (51798 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	68810232	68810232	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:68810232delT								KCNJ2 (634051 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	69015018	69015018	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:69015018delA								KCNJ2 (838837 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	69432631	69432631	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:69432631delA								None (None upstream) : SOX9 (684530 downstream)																																			---	---	---	---
SLC39A11	201266	broad.mit.edu	37	17	70720243	70720244	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:70720243_70720244delTT	uc002jjb.2	-						SLC39A11_uc002jja.2_Intron	NM_001159770	NP_001153242			solute carrier family 39, member 11 isoform 1						zinc ion transport	integral to membrane	metal ion transmembrane transporter activity			ovary(1)	1																		---	---	---	---
SLC39A11	201266	broad.mit.edu	37	17	70944226	70944227	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:70944226_70944227insA	uc002jjb.2	-						SLC39A11_uc002jja.2_Intron|SLC39A11_uc002jjc.1_Intron	NM_001159770	NP_001153242			solute carrier family 39, member 11 isoform 1						zinc ion transport	integral to membrane	metal ion transmembrane transporter activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	72417945	72417949	+	IGR	DEL	TTTTC	-	-	rs148512920		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72417945_72417949delTTTTC								GPR142 (49184 upstream) : GPRC5C (9718 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	72872929	72872929	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72872929delA								FDXR (3773 upstream) : FADS6 (544 downstream)																																			---	---	---	---
GRB2	2885	broad.mit.edu	37	17	73326789	73326791	+	Intron	DEL	AAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73326789_73326791delAAA	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	73329937	73329938	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73329937_73329938insA	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)													---	---	---	---
RECQL5	9400	broad.mit.edu	37	17	73649998	73649998	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73649998delA	uc010dgl.2	-						RECQL5_uc010dgk.2_Intron|RECQL5_uc002jpb.1_Intron|RECQL5_uc002joz.3_Intron|RECQL5_uc002jpa.3_Intron	NM_004259	NP_004250			RecQ protein-like 5 isoform 1						DNA recombination|DNA repair	cytoplasm|nuclear membrane|nucleolus|nucleoplasm	ATP binding|ATP-dependent helicase activity|DNA helicase activity|nucleic acid binding			kidney(3)	3	all_cancers(13;2.73e-08)|Breast(9;6.04e-09)|all_epithelial(9;6.79e-09)		all cancers(21;1.15e-06)|Epithelial(20;2.19e-06)|Lung(188;0.101)|LUSC - Lung squamous cell carcinoma(166;0.112)										Other_identified_genes_with_known_or_suspected_DNA_repair_function					---	---	---	---
UNC13D	201294	broad.mit.edu	37	17	73833154	73833155	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73833154_73833155delTT	uc002jpp.2	-						UNC13D_uc010wsk.1_Intron|UNC13D_uc002jpq.1_Intron|UNC13D_uc010dgq.1_Intron	NM_199242	NP_954712			unc-13 homolog D						positive regulation of exocytosis|regulation of mast cell degranulation	exocytic vesicle|late endosome|lysosome|membrane|recycling endosome	protein binding			upper_aerodigestive_tract(1)|skin(1)	2			all cancers(21;2.11e-06)|Epithelial(20;2.32e-06)|BRCA - Breast invasive adenocarcinoma(9;0.000618)|LUSC - Lung squamous cell carcinoma(166;0.154)											Familial_Hemophagocytic_Lymphohistiocytosis				---	---	---	---
UNC13D	201294	broad.mit.edu	37	17	73835181	73835181	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73835181delA	uc002jpp.2	-						UNC13D_uc010wsk.1_Intron|UNC13D_uc002jpq.1_Intron|UNC13D_uc010dgq.1_Intron	NM_199242	NP_954712			unc-13 homolog D						positive regulation of exocytosis|regulation of mast cell degranulation	exocytic vesicle|late endosome|lysosome|membrane|recycling endosome	protein binding			upper_aerodigestive_tract(1)|skin(1)	2			all cancers(21;2.11e-06)|Epithelial(20;2.32e-06)|BRCA - Breast invasive adenocarcinoma(9;0.000618)|LUSC - Lung squamous cell carcinoma(166;0.154)											Familial_Hemophagocytic_Lymphohistiocytosis				---	---	---	---
CDK3	1018	broad.mit.edu	37	17	73999833	73999833	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73999833delT	uc010dgt.2	+						CDK3_uc002jqg.3_Intron	NM_001258	NP_001249			cyclin-dependent kinase 3						cell division|cell proliferation|mitosis		ATP binding|cyclin-dependent protein kinase activity			central_nervous_system(1)	1																		---	---	---	---
RNF157	114804	broad.mit.edu	37	17	74167749	74167749	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74167749delT	uc002jqz.2	-						RNF157_uc002jra.2_Intron	NM_052916	NP_443148			ring finger protein 157								zinc ion binding			ovary(1)	1			LUSC - Lung squamous cell carcinoma(166;0.187)															---	---	---	---
RNF157	114804	broad.mit.edu	37	17	74198210	74198213	+	Intron	DEL	CACA	-	-	rs59025820	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74198210_74198213delCACA	uc002jqz.2	-						RNF157_uc002jra.2_Intron	NM_052916	NP_443148			ring finger protein 157								zinc ion binding			ovary(1)	1			LUSC - Lung squamous cell carcinoma(166;0.187)															---	---	---	---
RNF157	114804	broad.mit.edu	37	17	74228471	74228471	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74228471delA	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	74325825	74325827	+	Intron	DEL	AAC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74325825_74325827delAAC	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	74601218	74601219	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74601218_74601219delTT								ST6GALNAC2 (19073 upstream) : ST6GALNAC1 (19628 downstream)																																			---	---	---	---
MXRA7	439921	broad.mit.edu	37	17	74697440	74697440	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74697440delG	uc002jsk.1	-						MXRA7_uc002jsl.2_Intron|MXRA7_uc002jsm.2_Intron	NM_001008528	NP_001008528			transmembrane anchor protein 1 isoform 1							integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	75617832	75617832	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75617832delT								SEPT9 (121156 upstream) : FLJ45079 (257277 downstream)																																			---	---	---	---
TNRC6C	57690	broad.mit.edu	37	17	76074093	76074094	+	Intron	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76074093_76074094delAC	uc002jud.2	+						TNRC6C_uc002juf.2_Intron	NM_018996	NP_061869			trinucleotide repeat containing 6C isoform 2						gene silencing by RNA|regulation of translation		nucleotide binding|RNA binding			ovary(1)|central_nervous_system(1)	2			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)															---	---	---	---
DNAH17	8632	broad.mit.edu	37	17	76425005	76425006	+	Intron	INS	-	A	A	rs60351485		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76425005_76425006insA	uc010dhp.1	-						DNAH17_uc002jvq.2_Intron|DNAH17_uc002jvs.2_Intron					SubName: Full=DNAH17 variant protein; Flags: Fragment;											ovary(6)|breast(2)|skin(1)	9			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)															---	---	---	---
CYTH1	9267	broad.mit.edu	37	17	76698914	76698914	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76698914delT	uc002jvw.2	-						CYTH1_uc010wtw.1_Intron|CYTH1_uc010wtx.1_Intron	NM_017456	NP_059430			cytohesin 1 isoform 2						regulation of ARF protein signal transduction|regulation of cell adhesion|vesicle-mediated transport	cytoplasm|plasma membrane	ARF guanyl-nucleotide exchange factor activity|protein binding			ovary(1)	1																		---	---	---	---
HRNBP3	146713	broad.mit.edu	37	17	77099443	77099444	+	Intron	DEL	GA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77099443_77099444delGA	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	77395563	77395563	+	Intron	DEL	T	-	-	rs35720544		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77395563delT	uc010dhs.2	-						HRNBP3_uc010wua.1_Intron	NM_001082575	NP_001076044			hexaribonucleotide binding protein 3						mRNA processing|RNA splicing	cytoplasm|nucleus	nucleotide binding|RNA binding				0			BRCA - Breast invasive adenocarcinoma(99;0.0577)|OV - Ovarian serous cystadenocarcinoma(97;0.112)															---	---	---	---
HRNBP3	146713	broad.mit.edu	37	17	77424854	77424854	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77424854delC	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	77777540	77777541	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77777540_77777541insT								CBX8 (6650 upstream) : CBX4 (29415 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	77796069	77796072	+	IGR	DEL	TGTG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77796069_77796072delTGTG								CBX8 (25179 upstream) : CBX4 (10884 downstream)																																			---	---	---	---
TBC1D16	125058	broad.mit.edu	37	17	77988156	77988156	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77988156delA	uc002jxj.2	-							NM_019020	NP_061893			TBC1 domain family, member 16							intracellular	Rab GTPase activator activity				0	all_neural(118;0.167)		OV - Ovarian serous cystadenocarcinoma(97;0.00739)|BRCA - Breast invasive adenocarcinoma(99;0.0819)															---	---	---	---
RPTOR	57521	broad.mit.edu	37	17	78600214	78600214	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78600214delA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	78977272	78977273	+	RNA	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78977272_78977273insA	uc002jyx.1	+	1		c.138_139insA								Homo sapiens clone PP552 unknown mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	17	79345875	79345875	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79345875delG								TMEM105 (41401 upstream) : BAHCC1 (27665 downstream)																																			---	---	---	---
BAHCC1	57597	broad.mit.edu	37	17	79408713	79408717	+	Intron	DEL	AAAAG	-	-	rs56121832		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79408713_79408717delAAAAG	uc002kaf.2	+						BAHCC1_uc002kae.2_5'Flank	NM_001080519	NP_001073988			BAH domain and coiled-coil containing 1								DNA binding			ovary(1)	1	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0224)|OV - Ovarian serous cystadenocarcinoma(97;0.116)															---	---	---	---
BAHCC1	57597	broad.mit.edu	37	17	79414897	79414897	+	Intron	DEL	C	-	-	rs11650750	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79414897delC	uc002kaf.2	+						BAHCC1_uc002kae.2_Intron	NM_001080519	NP_001073988			BAH domain and coiled-coil containing 1								DNA binding			ovary(1)	1	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0224)|OV - Ovarian serous cystadenocarcinoma(97;0.116)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	80000799	80000800	+	IGR	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80000799_80000800delAC								DCXR (5226 upstream) : RFNG (4979 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	80467728	80467729	+	IGR	DEL	AG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80467728_80467729delAG								NARF (21587 upstream) : FOXK2 (9865 downstream)																																			---	---	---	---
FOXK2	3607	broad.mit.edu	37	17	80525803	80525809	+	Intron	DEL	TTTTTTT	-	-	rs5822539		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80525803_80525809delTTTTTTT	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)															---	---	---	---
TBCD	6904	broad.mit.edu	37	17	80771147	80771148	+	Intron	DEL	CT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80771147_80771148delCT	uc002kfz.2	+						TBCD_uc002kfx.1_Intron|TBCD_uc002kfy.1_Intron	NM_005993	NP_005984			beta-tubulin cofactor D						'de novo' posttranslational protein folding|adherens junction assembly|negative regulation of cell-substrate adhesion|negative regulation of microtubule polymerization|post-chaperonin tubulin folding pathway|tight junction assembly	adherens junction|cytoplasm|lateral plasma membrane|microtubule|tight junction	beta-tubulin binding|chaperone binding|GTPase activator activity				0	Breast(20;0.000523)|all_neural(118;0.0779)	all_cancers(8;0.0266)|all_epithelial(8;0.0696)	OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.18)															---	---	---	---
Unknown	0	broad.mit.edu	37	18	947871	947871	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:947871delT								ADCYAP1 (35700 upstream) : C18orf2 (306519 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	1013317	1013319	+	IGR	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:1013317_1013319delTTT								ADCYAP1 (101146 upstream) : C18orf2 (241071 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	1092425	1092425	+	IGR	DEL	T	-	-	rs78144898		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:1092425delT								ADCYAP1 (180254 upstream) : C18orf2 (161965 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	2068176	2068177	+	IGR	INS	-	A	A	rs138377378	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2068176_2068177insA								C18orf2 (660995 upstream) : METTL4 (469348 downstream)																																			---	---	---	---
SMCHD1	23347	broad.mit.edu	37	18	2760782	2760782	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2760782delT	uc002klm.3	+						SMCHD1_uc002klk.3_Intron|SMCHD1_uc002kll.3_Intron	NM_015295	NP_056110			structural maintenance of chromosomes flexible						chromosome organization		ATP binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	3020295	3020295	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3020295delA								LPIN2 (8350 upstream) : MYOM1 (46511 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	3039609	3039609	+	IGR	DEL	T	-	-	rs72126878		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3039609delT								LPIN2 (27664 upstream) : MYOM1 (27197 downstream)																																			---	---	---	---
MYOM1	8736	broad.mit.edu	37	18	3155228	3155228	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3155228delT	uc002klp.2	-						MYOM1_uc002klq.2_Intron	NM_003803	NP_003794			myomesin 1 isoform a							striated muscle myosin thick filament	structural constituent of muscle			ovary(3)|central_nervous_system(1)|pancreas(1)	5																		---	---	---	---
MYL12B	103910	broad.mit.edu	37	18	3260473	3260473	+	5'Flank	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3260473delA	uc010dkl.2	+						MYL12B_uc002klt.3_5'Flank|MYL12B_uc010wyv.1_5'Flank	NM_001144944	NP_001138416			myosin regulatory light chain MRCL2 isoform A						axon guidance|muscle contraction	cytosol|myosin complex	calcium ion binding				0																		---	---	---	---
DLGAP1	9229	broad.mit.edu	37	18	3541905	3541905	+	Intron	DEL	A	-	-	rs11339725		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3541905delA	uc002kmf.2	-						DLGAP1_uc010wyz.1_Intron|DLGAP1_uc002kme.1_Intron|DLGAP1_uc010dkn.2_Intron|DLGAP1_uc010wyw.1_Intron|DLGAP1_uc010wyx.1_Intron|DLGAP1_uc010wyy.1_Intron|DLGAP1_uc002kmg.2_Intron	NM_004746	NP_004737			discs large homolog-associated protein 1 isoform						synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)																---	---	---	---
DLGAP1	9229	broad.mit.edu	37	18	3613928	3613929	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3613928_3613929delTT	uc002kmf.2	-						DLGAP1_uc010wyz.1_Intron|DLGAP1_uc002kme.1_Intron|DLGAP1_uc010dkn.2_Intron|DLGAP1_uc010wyw.1_Intron|DLGAP1_uc010wyx.1_Intron|DLGAP1_uc010wyy.1_Intron|DLGAP1_uc002kmg.2_Intron	NM_004746	NP_004737			discs large homolog-associated protein 1 isoform						synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)																---	---	---	---
DLGAP1	9229	broad.mit.edu	37	18	3942970	3942971	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3942970_3942971delTT	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	4010875	4010876	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:4010875_4010876delAA	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	4144436	4144436	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:4144436delC	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	4166823	4166823	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:4166823delA	uc010wyz.1	-						uc002kmm.2_Intron	NM_004746	NP_004737			discs large homolog-associated protein 1 isoform						synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)																---	---	---	---
Unknown	0	broad.mit.edu	37	18	4959146	4959146	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:4959146delA								DLGAP1 (503880 upstream) : LOC642597 (184526 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	5328386	5328389	+	IGR	DEL	AAAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5328386_5328389delAAAA								ZFP161 (32347 upstream) : EPB41L3 (63999 downstream)																																			---	---	---	---
L3MBTL4	91133	broad.mit.edu	37	18	6225832	6225833	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:6225832_6225833delAA	uc002kmz.3	-						L3MBTL4_uc010dkt.2_Intron|L3MBTL4_uc002kmy.3_Intron	NM_173464	NP_775735			l(3)mbt-like 4						chromatin modification	nucleus	sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)|pancreas(1)	3		Colorectal(10;0.0249)																---	---	---	---
L3MBTL4	91133	broad.mit.edu	37	18	6321923	6321923	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:6321923delA	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)																---	---	---	---
L3MBTL4	91133	broad.mit.edu	37	18	6408686	6408689	+	Intron	DEL	TTTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:6408686_6408689delTTTT	uc010dkt.2	-							NM_173464	NP_775735			l(3)mbt-like 4						chromatin modification	nucleus	sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)|pancreas(1)	3		Colorectal(10;0.0249)																---	---	---	---
Unknown	0	broad.mit.edu	37	18	7391783	7391783	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:7391783delT								LRRC30 (159742 upstream) : PTPRM (175531 downstream)																																			---	---	---	---
PTPRM	5797	broad.mit.edu	37	18	7612122	7612122	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:7612122delT	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	7824426	7824427	+	Intron	DEL	TG	-	-	rs10565296		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:7824426_7824427delTG	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	8386381	8386382	+	Intron	DEL	AG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8386381_8386382delAG	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	8497230	8497231	+	IGR	DEL	TT	-	-	rs112532764		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8497230_8497231delTT								PTPRM (90372 upstream) : RAB12 (112204 downstream)																																			---	---	---	---
KIAA0802	23255	broad.mit.edu	37	18	8785017	8785019	+	Intron	DEL	TTG	-	-	rs71168010		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8785017_8785019delTTG	uc002knr.2	+						KIAA0802_uc002knq.2_Intron|KIAA0802_uc010dkw.1_Intron	NM_015210	NP_056025			hypothetical protein LOC23255												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	8988595	8988595	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8988595delT								KIAA0802 (155820 upstream) : NDUFV2 (114080 downstream)																																	OREG0024860	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
ANKRD12	23253	broad.mit.edu	37	18	9211367	9211367	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9211367delT	uc002knv.2	+						ANKRD12_uc010wzn.1_Intron|ANKRD12_uc002knw.2_Intron|ANKRD12_uc002knx.2_Intron	NM_015208	NP_056023			ankyrin repeat domain 12 isoform 1							nucleus				ovary(2)|central_nervous_system(1)	3																		---	---	---	---
TWSG1	57045	broad.mit.edu	37	18	9369625	9369625	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9369625delT	uc002knz.2	+						TWSG1_uc002koa.2_Intron	NM_020648	NP_065699			twisted gastrulation precursor											ovary(1)|pancreas(1)	2																		---	---	---	---
TWSG1	57045	broad.mit.edu	37	18	9382730	9382730	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9382730delA	uc002knz.2	+						TWSG1_uc002koa.2_Intron	NM_020648	NP_065699			twisted gastrulation precursor											ovary(1)|pancreas(1)	2																		---	---	---	---
FAM38B	63895	broad.mit.edu	37	18	10693353	10693356	+	Intron	DEL	TTTG	-	-	rs138554997		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10693353_10693356delTTTG	uc002kor.3	-						FAM38B_uc002koq.2_Intron	NM_022068	NP_071351			family with sequence similarity 38, member B							integral to membrane	ion channel activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	10898419	10898419	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10898419delA								FAM38B (196440 upstream) : GNAL (790717 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	11274944	11274945	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11274944_11274945insT								FAM38B (572965 upstream) : GNAL (414191 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	11381901	11381901	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11381901delG								FAM38B (679922 upstream) : GNAL (307235 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	11632872	11632874	+	IGR	DEL	AAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11632872_11632874delAAA								FAM38B (930893 upstream) : GNAL (56262 downstream)																																			---	---	---	---
GNAL	2774	broad.mit.edu	37	18	11715144	11715144	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11715144delA	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																		---	---	---	---
CIDEA	1149	broad.mit.edu	37	18	12259407	12259407	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12259407delA	uc002kqt.3	+						CIDEA_uc002kqu.3_Intron|CIDEA_uc010dlc.2_Intron	NM_001279	NP_001270			cell death-inducing DFFA-like effector a isoform						DNA damage response, signal transduction resulting in induction of apoptosis|DNA fragmentation involved in apoptotic nuclear change|lipid metabolic process|lipid storage|negative regulation of apoptosis|negative regulation of cytokine secretion|negative regulation of lipid catabolic process|negative regulation of transforming growth factor beta receptor signaling pathway|negative regulation of tumor necrosis factor production|positive regulation of sequestering of triglyceride|temperature homeostasis	mitochondrial envelope|nucleus	protein homodimerization activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
AFG3L2	10939	broad.mit.edu	37	18	12330780	12330780	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12330780delA	uc002kqz.1	-							NM_006796	NP_006787			AFG3 ATPase family gene 3-like 2						cell death|protein catabolic process|proteolysis	integral to membrane	ATP binding|metalloendopeptidase activity|nucleoside-triphosphatase activity|unfolded protein binding|zinc ion binding				0					Adenosine triphosphate(DB00171)													---	---	---	---
SPIRE1	56907	broad.mit.edu	37	18	12451072	12451072	+	Intron	DEL	A	-	-	rs76865998		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12451072delA	uc002kre.2	-						SPIRE1_uc002krc.2_Intron|SPIRE1_uc010wzw.1_Intron|SPIRE1_uc010wzx.1_Intron|SPIRE1_uc010wzy.1_Intron	NM_001128626	NP_001122098			spire homolog 1 isoform a							cytoskeleton|perinuclear region of cytoplasm	actin binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	13158822	13158823	+	IGR	INS	-	TTTC	TTTC	rs141632549	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13158822_13158823insTTTC								CEP192 (33773 upstream) : C18orf1 (59963 downstream)																																			---	---	---	---
C18orf1	753	broad.mit.edu	37	18	13408827	13408827	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13408827delT	uc002ksa.2	+						C18orf1_uc002ksb.2_Intron	NM_181481	NP_852146			hypothetical protein LOC753 isoform alpha 1							integral to membrane|plasma membrane				ovary(2)|skin(1)	3				READ - Rectum adenocarcinoma(73;0.0642)														---	---	---	---
Unknown	0	broad.mit.edu	37	18	13851583	13851585	+	IGR	DEL	CAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13851583_13851585delCAA								MC5R (24843 upstream) : MC2R (30458 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	13946675	13946678	+	IGR	DEL	CTCC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13946675_13946678delCTCC								MC2R (31140 upstream) : ZNF519 (129311 downstream)																																			---	---	---	---
ZNF519	162655	broad.mit.edu	37	18	14081300	14081300	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14081300delA	uc002ksq.1	-						ZNF519_uc002ksr.1_Intron					Homo sapiens cDNA FLJ39429 fis, clone PROST2002101.						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	14186372	14186372	+	Intron	DEL	C	-	-	rs113236427		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14186372delC	uc002ksv.1	+											Homo sapiens cDNA FLJ34795 fis, clone NT2NE2005921.																														---	---	---	---
Unknown	0	broad.mit.edu	37	18	14666312	14666312	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14666312delT								POTEC (122713 upstream) : ANKRD30B (81927 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	14906041	14906041	+	IGR	DEL	T	-	-	rs113304759		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14906041delT								ANKRD30B (53304 upstream) : LOC644669 (407514 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	15171424	15171425	+	IGR	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:15171424_15171425delAC								ANKRD30B (318687 upstream) : LOC644669 (142130 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	15407196	15407197	+	IGR	DEL	CA	-	-	rs150221454		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:15407196_15407197delCA								LOC644669 (81278 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	18802646	18802647	+	IGR	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:18802646_18802647delAC								ROCK1 (110834 upstream) : GREB1L (19556 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	19490817	19490817	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19490817delT								MIB1 (39907 upstream) : GATA6 (258599 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	20411203	20411203	+	IGR	DEL	A	-	-	rs35739208		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:20411203delA								CTAGE1 (413325 upstream) : RBBP8 (102092 downstream)																																			---	---	---	---
NPC1	4864	broad.mit.edu	37	18	21139924	21139924	+	Intron	DEL	A	-	-	rs112490232		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21139924delA	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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	18	22099101	22099102	+	IGR	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:22099101_22099102delTG								HRH4 (39181 upstream) : ZNF521 (542786 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	22232013	22232014	+	Intron	INS	-	C	C	rs12953893		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:22232013_22232014insC	uc002kvj.1	+											Homo sapiens cDNA FLJ42358 fis, clone UTERU2023262.																														---	---	---	---
ZNF521	25925	broad.mit.edu	37	18	22798813	22798813	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:22798813delA	uc002kvk.2	-						ZNF521_uc010xbe.1_Intron|ZNF521_uc010dly.2_Intron|ZNF521_uc002kvl.2_Intron	NM_015461	NP_056276			zinc finger protein 521						cell differentiation|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein domain specific binding|zinc ion binding			ovary(4)|large_intestine(2)|lung(1)	7	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)							T	PAX5	ALL								---	---	---	---
Unknown	0	broad.mit.edu	37	18	23023848	23023848	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:23023848delA								ZNF521 (91634 upstream) : SS18 (572371 downstream)																																			---	---	---	---
KCTD1	284252	broad.mit.edu	37	18	24168289	24168289	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:24168289delA	uc010xbk.1	-							NM_198991	NP_945342			potassium channel tetramerisation domain						negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|voltage-gated potassium channel complex	transcription corepressor activity|transcription factor binding|voltage-gated potassium channel activity			ovary(1)	1	all_cancers(21;0.00191)|Lung NSC(5;0.000698)|all_lung(6;0.0019)|Ovarian(20;0.0848)		Epithelial(2;7.8e-06)|OV - Ovarian serous cystadenocarcinoma(3;9.02e-06)|all cancers(3;3.37e-05)															---	---	---	---
KCTD1	284252	broad.mit.edu	37	18	24221333	24221333	+	5'Flank	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:24221333delT	uc010xbk.1	-							NM_198991	NP_945342			potassium channel tetramerisation domain						negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|voltage-gated potassium channel complex	transcription corepressor activity|transcription factor binding|voltage-gated potassium channel activity			ovary(1)	1	all_cancers(21;0.00191)|Lung NSC(5;0.000698)|all_lung(6;0.0019)|Ovarian(20;0.0848)		Epithelial(2;7.8e-06)|OV - Ovarian serous cystadenocarcinoma(3;9.02e-06)|all cancers(3;3.37e-05)															---	---	---	---
Unknown	0	broad.mit.edu	37	18	24264156	24264159	+	IGR	DEL	TTTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:24264156_24264159delTTTT								KCTD1 (43848 upstream) : LOC728606 (3426 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	24856469	24856471	+	IGR	DEL	AAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:24856469_24856471delAAA								C18orf16 (85819 upstream) : CDH2 (674459 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	24933692	24933692	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:24933692delT	uc002kwf.1	-											Homo sapiens cDNA FLJ45994 fis, clone SKMUS2009557.																														---	---	---	---
CDH2	1000	broad.mit.edu	37	18	25598281	25598281	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:25598281delA	uc002kwg.2	-						CDH2_uc010xbn.1_Intron	NM_001792	NP_001783			cadherin 2, type 1 preproprotein						adherens junction organization|cell junction assembly|positive regulation of muscle cell differentiation	catenin complex|integral to membrane	alpha-catenin binding|beta-catenin binding|calcium ion binding|gamma-catenin binding			ovary(3)|lung(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	26018025	26018025	+	IGR	DEL	T	-	-	rs74171379		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:26018025delT								CDH2 (260580 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	28126532	28126532	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28126532delA								MIR302F (247606 upstream) : DSC3 (443521 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	28211938	28211938	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28211938delG								MIR302F (333012 upstream) : DSC3 (358115 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	28563986	28563987	+	IGR	DEL	AA	-	-	rs79354647		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28563986_28563987delAA								MIR302F (685060 upstream) : DSC3 (6066 downstream)																																			---	---	---	---
DSG1	1828	broad.mit.edu	37	18	28923779	28923779	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28923779delT	uc002kwp.2	+						DSG1_uc010xbp.1_5'UTR	NM_001942	NP_001933			desmoglein 1 preproprotein						calcium-dependent cell-cell adhesion|cell-cell junction assembly|cellular component disassembly involved in apoptosis|homophilic cell adhesion|protein stabilization	cytosol|desmosome|integral to membrane|internal side of plasma membrane	calcium ion binding|gamma-catenin binding|toxin binding			skin(3)|ovary(2)|central_nervous_system(2)	7			OV - Ovarian serous cystadenocarcinoma(10;0.00559)															---	---	---	---
Unknown	0	broad.mit.edu	37	18	29149778	29149778	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29149778delA								DSG2 (20965 upstream) : TTR (21952 downstream)																																			---	---	---	---
B4GALT6	9331	broad.mit.edu	37	18	29253903	29253904	+	Intron	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29253903_29253904delAC	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	18	30407001	30407002	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:30407001_30407002delTT								KLHL14 (54027 upstream) : C18orf34 (110364 downstream)																																			---	---	---	---
ASXL3	80816	broad.mit.edu	37	18	31167735	31167735	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:31167735delA	uc010dmg.1	+						ASXL3_uc002kxq.2_Intron	NM_030632	NP_085135			additional sex combs like 3						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding			ovary(2)|pancreas(1)	3																		---	---	---	---
DTNA	1837	broad.mit.edu	37	18	32405028	32405029	+	Intron	DEL	TT	-	-	rs77685796		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:32405028_32405029delTT	uc010dmn.1	+						DTNA_uc002kxu.2_Intron|DTNA_uc010xbx.1_Intron|DTNA_uc002kxv.3_Intron|DTNA_uc002kxw.2_Intron|DTNA_uc002kxx.2_Intron|DTNA_uc010dmj.2_Intron|DTNA_uc002kxz.2_Intron|DTNA_uc002kxy.2_Intron|DTNA_uc010dmk.1_Intron|DTNA_uc010dml.2_Intron|DTNA_uc002kyb.3_Intron|DTNA_uc010dmm.2_Intron|DTNA_uc010xby.1_Intron|DTNA_uc010dmo.2_Intron|DTNA_uc002kyd.3_Intron|DTNA_uc010xbz.1_Intron|DTNA_uc010xca.1_Intron|DTNA_uc002kye.2_Intron	NM_001390	NP_001381			dystrobrevin alpha isoform 1						neuromuscular synaptic transmission|signal transduction|striated muscle contraction	cell junction|cytoplasm|synapse	calcium ion binding|protein binding|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	33304004	33304004	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33304004delT								GALNT1 (12207 upstream) : MIR187 (180777 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	33390855	33390856	+	IGR	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33390855_33390856delTG								GALNT1 (99058 upstream) : MIR187 (93925 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	33489539	33489539	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33489539delA								MIR187 (4650 upstream) : C18orf21 (63049 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	33663117	33663117	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33663117delA								RPRD1A (15744 upstream) : SLC39A6 (25378 downstream)																																			---	---	---	---
FHOD3	80206	broad.mit.edu	37	18	34230512	34230512	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34230512delC	uc002kzt.1	+						FHOD3_uc002kzr.1_Intron|FHOD3_uc002kzs.1_Intron|FHOD3_uc002kzu.1_Intron|FHOD3_uc010dmz.1_Intron	NM_025135	NP_079411			formin homology 2 domain containing 3						actin cytoskeleton organization	cytoplasm|cytoskeleton	actin binding			skin(3)|large_intestine(2)|breast(2)|ovary(1)	8		all_epithelial(2;0.0181)|Colorectal(2;0.0195)																---	---	---	---
FHOD3	80206	broad.mit.edu	37	18	34235709	34235710	+	Intron	DEL	CA	-	-	rs137998269		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34235709_34235710delCA	uc002kzt.1	+						FHOD3_uc002kzr.1_Intron|FHOD3_uc002kzs.1_Intron|FHOD3_uc002kzu.1_Intron|FHOD3_uc010dmz.1_Intron	NM_025135	NP_079411			formin homology 2 domain containing 3						actin cytoskeleton organization	cytoplasm|cytoskeleton	actin binding			skin(3)|large_intestine(2)|breast(2)|ovary(1)	8		all_epithelial(2;0.0181)|Colorectal(2;0.0195)																---	---	---	---
KIAA1328	57536	broad.mit.edu	37	18	34805114	34805115	+	3'UTR	DEL	AG	-	-	rs35952844		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34805114_34805115delAG	uc002kzz.2	+	10					KIAA1328_uc002lab.2_3'UTR|KIAA1328_uc002lac.1_3'UTR|KIAA1328_uc010dnc.1_RNA	NM_020776	NP_065827			hypothetical protein LOC57536											central_nervous_system(1)	1				COAD - Colon adenocarcinoma(74;0.195)														---	---	---	---
Unknown	0	broad.mit.edu	37	18	35316322	35316323	+	IGR	DEL	GT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:35316322_35316323delGT								CELF4 (170322 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	35998530	35998530	+	IGR	DEL	A	-	-	rs75563681		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:35998530delA								CELF4 (852530 upstream) : LOC647946 (788358 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	36431963	36431964	+	IGR	INS	-	G	G	rs149020769	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:36431963_36431964insG								None (None upstream) : LOC647946 (354924 downstream)																																			---	---	---	---
LOC647946	647946	broad.mit.edu	37	18	36906014	36906014	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:36906014delA	uc002lak.1	-						LOC647946_uc010xcj.1_Intron|LOC647946_uc002lal.1_Intron					Homo sapiens cDNA FLJ33284 fis, clone ASTRO2009458.												0																		---	---	---	---
LOC647946	647946	broad.mit.edu	37	18	37020131	37020131	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:37020131delT	uc010xcj.1	-						LOC647946_uc002lal.1_Intron	NR_024391				Homo sapiens cDNA FLJ33284 fis, clone ASTRO2009458.												0																		---	---	---	---
LOC647946	647946	broad.mit.edu	37	18	37045187	37045187	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:37045187delT	uc010xcj.1	-						LOC647946_uc002lal.1_Intron	NR_024391				Homo sapiens cDNA FLJ33284 fis, clone ASTRO2009458.												0																		---	---	---	---
LOC647946	647946	broad.mit.edu	37	18	37045893	37045893	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:37045893delC	uc010xcj.1	-						LOC647946_uc002lal.1_Intron	NR_024391				Homo sapiens cDNA FLJ33284 fis, clone ASTRO2009458.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	37458073	37458073	+	5'Flank	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:37458073delA	uc010xck.1	-											Homo sapiens cDNA, FLJ99758.																														---	---	---	---
Unknown	0	broad.mit.edu	37	18	37603089	37603089	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:37603089delT								LOC647946 (222807 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	37642142	37642142	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:37642142delT								LOC647946 (261860 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	37915790	37915790	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:37915790delT								LOC647946 (535508 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	37948680	37948680	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:37948680delG								LOC647946 (568398 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	38001959	38001959	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:38001959delA								LOC647946 (621677 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	38030445	38030446	+	IGR	INS	-	CTC	CTC	rs151157295	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:38030445_38030446insCTC								LOC647946 (650163 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	38988796	38988796	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:38988796delA								None (None upstream) : KC6 (71442 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	39129541	39129542	+	IGR	INS	-	CA	CA	rs138053529	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:39129541_39129542insCA								KC6 (28980 upstream) : PIK3C3 (405657 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	39307320	39307320	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:39307320delA								KC6 (206759 upstream) : PIK3C3 (227879 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	39352032	39352032	+	IGR	DEL	A	-	-	rs34354119		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:39352032delA								KC6 (251471 upstream) : PIK3C3 (183167 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	39508251	39508251	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:39508251delA								KC6 (407690 upstream) : PIK3C3 (26948 downstream)																																			---	---	---	---
PIK3C3	5289	broad.mit.edu	37	18	39569061	39569062	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:39569061_39569062insT	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	40016626	40016627	+	Intron	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:40016626_40016627delTG	uc002las.1	+						uc002lat.2_Intron|uc002lau.2_Intron					Homo sapiens hypothetical gene supported by BC011527; BC021928; BC011527; BC021928, mRNA (cDNA clone IMAGE:3872963), with apparent retained intron.																														---	---	---	---
Unknown	0	broad.mit.edu	37	18	40153994	40153994	+	Intron	DEL	C	-	-	rs4643422	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:40153994delC	uc002lau.2	+											Homo sapiens hypothetical gene supported by BC011527; BC021928; BC011527; BC021928, mRNA (cDNA clone IMAGE:3872963), with apparent retained intron.																														---	---	---	---
Unknown	0	broad.mit.edu	37	18	42062765	42062768	+	Intron	DEL	TGTG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:42062765_42062768delTGTG	uc002lax.3	-											Homo sapiens cDNA clone IMAGE:5265929.																														---	---	---	---
KIAA1632	57724	broad.mit.edu	37	18	43489253	43489253	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43489253delA	uc002lbm.2	-						KIAA1632_uc002lbo.1_Intron|KIAA1632_uc010xcq.1_Intron|KIAA1632_uc010xcr.1_Intron|KIAA1632_uc010xcs.1_Intron|KIAA1632_uc002lbn.2_Intron	NM_020964	NP_066015			hypothetical protein LOC57724						autophagy						0																		---	---	---	---
KIAA1632	57724	broad.mit.edu	37	18	43529365	43529365	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43529365delT	uc002lbm.2	-						KIAA1632_uc002lbo.1_Intron	NM_020964	NP_066015			hypothetical protein LOC57724						autophagy						0																		---	---	---	---
HAUS1	115106	broad.mit.edu	37	18	43702270	43702271	+	Intron	INS	-	CA	CA	rs12968820		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43702270_43702271insCA	uc002lbu.2	+						HAUS1_uc002lbv.2_Intron	NM_138443	NP_612452			coiled-coil domain containing 5						cell division|centrosome organization|mitosis|spindle assembly	centrosome|HAUS complex|microtubule|spindle pole				ovary(1)	1																		---	---	---	---
C18orf25	147339	broad.mit.edu	37	18	43844698	43844699	+	3'UTR	INS	-	T	T	rs11405758		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43844698_43844699insT	uc002lbw.2	+	6					C18orf25_uc002lbx.2_3'UTR	NM_145055	NP_659492			ARKadia-like 1 isoform a											central_nervous_system(2)	2																		---	---	---	---
RNF165	494470	broad.mit.edu	37	18	43909322	43909322	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43909322delT	uc002lby.1	+							NM_152470	NP_689683			ring finger protein 165								zinc ion binding				0				READ - Rectum adenocarcinoma(1;0.0873)														---	---	---	---
RNF165	494470	broad.mit.edu	37	18	43917517	43917517	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43917517delT	uc002lcb.1	+						RNF165_uc002lby.1_Intron|RNF165_uc010dnn.1_Intron|RNF165_uc002lbz.2_RNA|RNF165_uc002lca.1_RNA	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	44154352	44154353	+	Intron	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44154352_44154353delAC	uc010xcw.1	-						LOXHD1_uc002lcg.1_Intron	NM_144612	NP_653213			lipoxygenase homology domains 1 isoform 1						sensory perception of sound	stereocilium	protein binding				0																		---	---	---	---
IER3IP1	51124	broad.mit.edu	37	18	44683645	44683649	+	Intron	DEL	AAAAA	-	-	rs35638006		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44683645_44683649delAAAAA	uc002lcu.2	-							NM_016097	NP_057181			immediate early response 3 interacting protein							endoplasmic reticulum membrane|Golgi apparatus|integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	44763150	44763150	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44763150delT	uc010dnt.1	-											RecName: Full=Ladybird homeobox corepressor 1-like protein; AltName: Full=LBX1 corepressor 1-like protein; AltName: Full=Functional Smad-suppressing element on chromosome 18;          Short=Fussel-18;																														---	---	---	---
Unknown	0	broad.mit.edu	37	18	45101373	45101373	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:45101373delA	uc002lcx.2	+											Homo sapiens, clone IMAGE:5538207, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	18	45154974	45154975	+	IGR	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:45154974_45154975delAC								IER3IP1 (452229 upstream) : SMAD2 (204492 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	45195641	45195642	+	IGR	INS	-	A	A	rs140866940	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:45195641_45195642insA								IER3IP1 (492896 upstream) : SMAD2 (163825 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	45216704	45216704	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:45216704delA								IER3IP1 (513959 upstream) : SMAD2 (142763 downstream)																																			---	---	---	---
ZBTB7C	201501	broad.mit.edu	37	18	45701515	45701515	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:45701515delA	uc010dnw.2	-						ZBTB7C_uc010dny.1_Intron|ZBTB7C_uc010dnz.1_Intron|ZBTB7C_uc010dob.1_Intron|ZBTB7C_uc010doc.1_Intron|ZBTB7C_uc010dod.1_Intron|ZBTB7C_uc010doe.1_Intron|ZBTB7C_uc010dof.1_Intron|ZBTB7C_uc010dog.1_Intron|ZBTB7C_uc010doh.1_Intron|ZBTB7C_uc010doi.1_Intron|ZBTB7C_uc010doj.1_Intron|ZBTB7C_uc010dok.1_Intron|ZBTB7C_uc010dol.1_Intron|ZBTB7C_uc010doa.1_Intron|ZBTB7C_uc010don.1_Intron|ZBTB7C_uc010doo.1_Intron|ZBTB7C_uc010dop.1_Intron|ZBTB7C_uc010doq.1_Intron|ZBTB7C_uc010dor.1_Intron|ZBTB7C_uc010dos.1_Intron|ZBTB7C_uc010dot.1_Intron|ZBTB7C_uc010dou.1_Intron|ZBTB7C_uc010dom.1_Intron	NM_001039360	NP_001034449			zinc finger and BTB domain containing 7C							intracellular	nucleic acid binding|zinc ion binding			ovary(1)	1																		---	---	---	---
ZBTB7C	201501	broad.mit.edu	37	18	45706101	45706102	+	Intron	DEL	CT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:45706101_45706102delCT	uc010dnw.2	-						ZBTB7C_uc010dny.1_Intron|ZBTB7C_uc010dnz.1_Intron|ZBTB7C_uc010dob.1_Intron|ZBTB7C_uc010doc.1_Intron|ZBTB7C_uc010dod.1_Intron|ZBTB7C_uc010doe.1_Intron|ZBTB7C_uc010dof.1_Intron|ZBTB7C_uc010dog.1_Intron|ZBTB7C_uc010doh.1_Intron|ZBTB7C_uc010doi.1_Intron|ZBTB7C_uc010doj.1_Intron|ZBTB7C_uc010dok.1_Intron|ZBTB7C_uc010dol.1_Intron|ZBTB7C_uc010doa.1_Intron|ZBTB7C_uc010don.1_Intron|ZBTB7C_uc010doo.1_Intron|ZBTB7C_uc010dop.1_Intron|ZBTB7C_uc010doq.1_Intron|ZBTB7C_uc010dor.1_Intron|ZBTB7C_uc010dos.1_Intron|ZBTB7C_uc010dot.1_Intron|ZBTB7C_uc010dou.1_Intron|ZBTB7C_uc010dom.1_Intron	NM_001039360	NP_001034449			zinc finger and BTB domain containing 7C							intracellular	nucleic acid binding|zinc ion binding			ovary(1)	1																		---	---	---	---
KIAA0427	9811	broad.mit.edu	37	18	46107573	46107573	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:46107573delT	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																		---	---	---	---
MYO5B	4645	broad.mit.edu	37	18	47462153	47462153	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47462153delG	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)														---	---	---	---
MAPK4	5596	broad.mit.edu	37	18	48089831	48089831	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48089831delG	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)														---	---	---	---
MAPK4	5596	broad.mit.edu	37	18	48219629	48219629	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48219629delA	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)														---	---	---	---
MRO	83876	broad.mit.edu	37	18	48342405	48342405	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48342405delA	uc002lew.3	-						MRO_uc010xdn.1_Intron|MRO_uc010dpa.2_Intron|MRO_uc010dpb.2_Intron|MRO_uc010dpc.2_Intron|MRO_uc002lex.3_Intron	NM_031939	NP_114145			maestro isoform a							nucleolus	binding				0		Colorectal(6;0.0596)		Colorectal(21;0.082)														---	---	---	---
Unknown	0	broad.mit.edu	37	18	48803908	48803909	+	IGR	DEL	GT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48803908_48803909delGT								MEX3C (80218 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	49148906	49148907	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:49148906_49148907insT								MEX3C (425216 upstream) : DCC (717664 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	49237151	49237151	+	IGR	DEL	T	-	-	rs35819595		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:49237151delT								MEX3C (513461 upstream) : DCC (629420 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	49435122	49435122	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:49435122delT								MEX3C (711432 upstream) : DCC (431449 downstream)																																			---	---	---	---
DCC	1630	broad.mit.edu	37	18	49882707	49882708	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:49882707_49882708insT	uc002lfe.1	+							NM_005215	NP_005206			netrin receptor DCC precursor						apoptosis|induction of apoptosis|negative regulation of collateral sprouting|negative regulation of dendrite development	cytosol|integral to membrane				skin(8)|ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	17		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)														---	---	---	---
DCC	1630	broad.mit.edu	37	18	50408791	50408791	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:50408791delT	uc002lfe.1	+						DCC_uc010xdr.1_Intron	NM_005215	NP_005206			netrin receptor DCC precursor						apoptosis|induction of apoptosis|negative regulation of collateral sprouting|negative regulation of dendrite development	cytosol|integral to membrane				skin(8)|ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	17		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)														---	---	---	---
DCC	1630	broad.mit.edu	37	18	50554196	50554196	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:50554196delT	uc002lfe.1	+						DCC_uc010xdr.1_Intron|DCC_uc010dpf.1_Intron	NM_005215	NP_005206			netrin receptor DCC precursor						apoptosis|induction of apoptosis|negative regulation of collateral sprouting|negative regulation of dendrite development	cytosol|integral to membrane				skin(8)|ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	17		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)														---	---	---	---
DCC	1630	broad.mit.edu	37	18	50586380	50586381	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:50586380_50586381delTT	uc002lfe.1	+						DCC_uc010xdr.1_Intron|DCC_uc010dpf.1_Intron	NM_005215	NP_005206			netrin receptor DCC precursor						apoptosis|induction of apoptosis|negative regulation of collateral sprouting|negative regulation of dendrite development	cytosol|integral to membrane				skin(8)|ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	17		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)														---	---	---	---
DCC	1630	broad.mit.edu	37	18	50817539	50817539	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:50817539delA	uc002lfe.1	+						DCC_uc010xdr.1_Intron|DCC_uc010dpf.1_Intron	NM_005215	NP_005206			netrin receptor DCC precursor						apoptosis|induction of apoptosis|negative regulation of collateral sprouting|negative regulation of dendrite development	cytosol|integral to membrane				skin(8)|ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	17		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)														---	---	---	---
DCC	1630	broad.mit.edu	37	18	50920283	50920284	+	Intron	DEL	CC	-	-	rs77045594	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:50920283_50920284delCC	uc002lfe.1	+						DCC_uc010xdr.1_Intron|DCC_uc010dpf.1_Intron	NM_005215	NP_005206			netrin receptor DCC precursor						apoptosis|induction of apoptosis|negative regulation of collateral sprouting|negative regulation of dendrite development	cytosol|integral to membrane				skin(8)|ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	17		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)														---	---	---	---
Unknown	0	broad.mit.edu	37	18	52372123	52372124	+	IGR	INS	-	T	T	rs113213231		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:52372123_52372124insT								C18orf26 (105399 upstream) : RAB27B (123716 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	52655889	52655889	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:52655889delA								CCDC68 (29150 upstream) : TCF4 (233673 downstream)																																			---	---	---	---
TCF4	6925	broad.mit.edu	37	18	52953537	52953538	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:52953537_52953538delTT	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_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)														---	---	---	---
Unknown	0	broad.mit.edu	37	18	54188091	54188091	+	IGR	DEL	A	-	-	rs111616994		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54188091delA								TCF4 (884906 upstream) : TXNL1 (81964 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	54267118	54267118	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54267118delA								TCF4 (963933 upstream) : TXNL1 (2937 downstream)																																			---	---	---	---
TXNL1	9352	broad.mit.edu	37	18	54283363	54283363	+	Intron	DEL	A	-	-	rs35834292		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54283363delA	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)														---	---	---	---
WDR7	23335	broad.mit.edu	37	18	54421517	54421520	+	Intron	DEL	TATA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54421517_54421520delTATA	uc002lgk.1	+						WDR7_uc010dpk.1_Intron|WDR7_uc002lgl.1_Intron	NM_015285	NP_056100			rabconnectin-3 beta isoform 1											ovary(2)|skin(1)	3				Lung(128;0.0238)|Colorectal(16;0.0296)														---	---	---	---
WDR7	23335	broad.mit.edu	37	18	54616816	54616816	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54616816delT	uc002lgk.1	+						WDR7_uc002lgl.1_Intron	NM_015285	NP_056100			rabconnectin-3 beta isoform 1											ovary(2)|skin(1)	3				Lung(128;0.0238)|Colorectal(16;0.0296)														---	---	---	---
Unknown	0	broad.mit.edu	37	18	54906062	54906063	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54906062_54906063delAA								WDR7 (209026 upstream) : ST8SIA3 (113658 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	55425711	55425711	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55425711delA								ATP8B1 (26672 upstream) : NEDD4L (285908 downstream)																																			---	---	---	---
NEDD4L	23327	broad.mit.edu	37	18	55809566	55809567	+	Intron	DEL	CA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55809566_55809567delCA	uc002lgy.2	+						NEDD4L_uc002lgz.2_Intron|NEDD4L_uc002lgx.2_Intron|NEDD4L_uc010xee.1_Intron|NEDD4L_uc002lha.1_Intron	NM_001144967	NP_001138439			neural precursor cell expressed, developmentally						cellular sodium ion homeostasis|excretion|interspecies interaction between organisms|positive regulation of endocytosis|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of protein catabolic process|response to metal ion|sodium ion transport|water homeostasis	cytoplasm	protein binding|sodium channel regulator activity|ubiquitin-protein ligase activity			lung(4)	4																		---	---	---	---
NEDD4L	23327	broad.mit.edu	37	18	55903589	55903589	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55903589delA	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																		---	---	---	---
NEDD4L	23327	broad.mit.edu	37	18	56054652	56054652	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56054652delT	uc002lgy.2	+						NEDD4L_uc002lgz.2_Intron|NEDD4L_uc002lgx.2_Intron|NEDD4L_uc010xee.1_Intron|NEDD4L_uc002lhc.2_Intron|NEDD4L_uc002lhd.2_Intron|NEDD4L_uc002lhb.2_Intron|NEDD4L_uc002lhe.2_Intron|NEDD4L_uc002lhf.2_Intron|NEDD4L_uc002lhg.2_Intron|NEDD4L_uc002lhh.2_Intron|NEDD4L_uc010dpn.2_Intron	NM_001144967	NP_001138439			neural precursor cell expressed, developmentally						cellular sodium ion homeostasis|excretion|interspecies interaction between organisms|positive regulation of endocytosis|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of protein catabolic process|response to metal ion|sodium ion transport|water homeostasis	cytoplasm	protein binding|sodium channel regulator activity|ubiquitin-protein ligase activity			lung(4)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	56873187	56873187	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56873187delA								SEC11C (47126 upstream) : GRP (14213 downstream)																																			---	---	---	---
RAX	30062	broad.mit.edu	37	18	56935368	56935368	+	3'UTR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56935368delG	uc002lhx.2	-	3					RAX_uc010dpp.2_3'UTR	NM_013435	NP_038463			retina and anterior neural fold homeobox						visual perception	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)	1		Lung NSC(161;0.0804)|Colorectal(73;0.0946)		STAD - Stomach adenocarcinoma(84;0.18)														---	---	---	---
Unknown	0	broad.mit.edu	37	18	57685956	57685956	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:57685956delA								PMAIP1 (114418 upstream) : MC4R (352608 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	57896292	57896292	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:57896292delT								PMAIP1 (324754 upstream) : MC4R (142272 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	58545750	58545751	+	IGR	DEL	GC	-	-	rs57342160		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:58545750_58545751delGC								MC4R (505749 upstream) : CDH20 (455237 downstream)																																			---	---	---	---
CDH20	28316	broad.mit.edu	37	18	59137840	59137840	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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	59434802	59434802	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59434802delA								CDH20 (212437 upstream) : RNF152 (47502 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	59620242	59620243	+	IGR	INS	-	GGAA	GGAA			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59620242_59620243insGGAA								RNF152 (59938 upstream) : PIGN (91217 downstream)																																			---	---	---	---
PHLPP1	23239	broad.mit.edu	37	18	60482381	60482382	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:60482381_60482382delTT	uc002lis.2	+							NM_194449	NP_919431			PH domain and leucine rich repeat protein						apoptosis|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling	cytosol|membrane|nucleus	metal ion binding|protein serine/threonine phosphatase activity				0																		---	---	---	---
PHLPP1	23239	broad.mit.edu	37	18	60598883	60598883	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:60598883delT	uc002lis.2	+							NM_194449	NP_919431			PH domain and leucine rich repeat protein						apoptosis|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling	cytosol|membrane|nucleus	metal ion binding|protein serine/threonine phosphatase activity				0																		---	---	---	---
KDSR	2531	broad.mit.edu	37	18	61020415	61020415	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61020415delA	uc010dpw.2	-						KDSR_uc010xem.1_Intron	NM_002035	NP_002026			3-ketodihydrosphingosine reductase precursor						3-keto-sphinganine metabolic process	endoplasmic reticulum membrane|extracellular space|integral to membrane	3-dehydrosphinganine reductase activity|binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	61607580	61607580	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61607580delA								SERPINB10 (5106 upstream) : HMSD (9008 downstream)																																			---	---	---	---
SERPINB8	5271	broad.mit.edu	37	18	61638018	61638019	+	Intron	INS	-	CC	CC			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61638018_61638019insCC	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	62172155	62172155	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:62172155delA								C18orf20 (355895 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	62228613	62228613	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:62228613delA								C18orf20 (412353 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	62426350	62426350	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:62426350delG								C18orf20 (610090 upstream) : CDH7 (991138 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	63188998	63188998	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:63188998delA								None (None upstream) : CDH7 (228490 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	63213571	63213572	+	IGR	INS	-	T	T	rs4144733		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:63213571_63213572insT								None (None upstream) : CDH7 (203916 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	63668954	63668954	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:63668954delT								CDH7 (120780 upstream) : CDH19 (502367 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	64848388	64848388	+	IGR	DEL	A	-	-	rs114449569	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:64848388delA								CDH19 (577172 upstream) : DSEL (325431 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	65385587	65385587	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:65385587delT								DSEL (201620 upstream) : TMX3 (955340 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	65963037	65963040	+	IGR	DEL	GTGT	-	-	rs74175313		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:65963037_65963040delGTGT								DSEL (779070 upstream) : TMX3 (377887 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	66857965	66857965	+	IGR	DEL	T	-	-	rs36081354		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:66857965delT								CCDC102B (135539 upstream) : DOK6 (210326 downstream)																																			---	---	---	---
SOCS6	9306	broad.mit.edu	37	18	67971616	67971616	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:67971616delA	uc002lkr.1	+							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	68660077	68660077	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:68660077delT								SOCS6 (662643 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	69034370	69034370	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:69034370delG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	69224737	69224738	+	Intron	DEL	GA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:69224737_69224738delGA	uc002lks.1	-						uc002lkt.1_Intron					Homo sapiens cDNA FLJ36657 fis, clone UTERU2001876.																														---	---	---	---
Unknown	0	broad.mit.edu	37	18	71166354	71166354	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:71166354delT								NETO1 (631544 upstream) : FBXO15 (574234 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	72852206	72852207	+	IGR	DEL	CT	-	-	rs67886317		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:72852206_72852207delCT								ZNF407 (74578 upstream) : ZADH2 (57072 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	73774758	73774758	+	IGR	DEL	T	-	-	rs34038237		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:73774758delT								C18orf62 (635169 upstream) : ZNF516 (296861 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	73825371	73825371	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:73825371delA								C18orf62 (685782 upstream) : ZNF516 (246248 downstream)																																			---	---	---	---
MBP	4155	broad.mit.edu	37	18	74836292	74836292	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74836292delT	uc010xfd.1	-						MBP_uc002lmr.2_Intron	NM_001025101	NP_001020272			Golli-mbp isoform 1						central nervous system development|immune response|synaptic transmission	plasma membrane	structural constituent of myelin sheath			haematopoietic_and_lymphoid_tissue(1)	1		Prostate(75;0.0865)|Esophageal squamous(42;0.129)|Melanoma(33;0.211)		OV - Ovarian serous cystadenocarcinoma(15;1.79e-06)|BRCA - Breast invasive adenocarcinoma(31;0.113)|READ - Rectum adenocarcinoma(1;0.188)														---	---	---	---
Unknown	0	broad.mit.edu	37	18	75289823	75289826	+	IGR	DEL	GACT	-	-	rs141137402		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:75289823_75289826delGACT								GALR1 (307729 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	76217122	76217123	+	IGR	INS	-	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:76217122_76217123insC								None (None upstream) : SALL3 (523152 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	76378149	76378149	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:76378149delG								None (None upstream) : SALL3 (362126 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	76666787	76666789	+	IGR	DEL	AAA	-	-	rs113738178		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:76666787_76666789delAAA								None (None upstream) : SALL3 (73486 downstream)																																			---	---	---	---
NFATC1	4772	broad.mit.edu	37	18	77191713	77191713	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77191713delT	uc010xfg.1	+						NFATC1_uc002lnc.1_Intron|NFATC1_uc010xff.1_Intron|NFATC1_uc002lnd.2_Intron|NFATC1_uc002lne.2_Intron|NFATC1_uc010xfh.1_Intron|NFATC1_uc010xfi.1_Intron|NFATC1_uc010xfj.1_Intron|NFATC1_uc002lnf.2_Intron|NFATC1_uc002lng.2_Intron|NFATC1_uc010xfk.1_Intron	NM_006162	NP_006153			nuclear factor of activated T-cells, cytosolic						intracellular signal transduction|positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleus	FK506 binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			large_intestine(1)|ovary(1)	2		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;3.73e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0257)														---	---	---	---
CTDP1	9150	broad.mit.edu	37	18	77445005	77445006	+	Intron	DEL	GG	-	-	rs71974203		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77445005_77445006delGG	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)														---	---	---	---
PQLC1	80148	broad.mit.edu	37	18	77672108	77672108	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77672108delG	uc002lnl.2	-						PQLC1_uc010dre.2_Intron|PQLC1_uc002lnk.2_Intron|PQLC1_uc010xfm.1_Intron	NM_025078	NP_079354			PQ loop repeat containing 1 isoform 1							integral to membrane				large_intestine(1)|ovary(1)	2		Esophageal squamous(42;0.0212)|Melanoma(33;0.2)		OV - Ovarian serous cystadenocarcinoma(15;8.2e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0258)														---	---	---	---
PARD6G	84552	broad.mit.edu	37	18	77954890	77954890	+	Intron	DEL	A	-	-	rs34001539		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77954890delA	uc002lny.2	-						PARD6G_uc010xfp.1_Intron	NM_032510	NP_115899			PAR-6 gamma protein						cell cycle|cell division|tight junction assembly	cytosol|tight junction	protein binding				0		all_cancers(4;5.63e-22)|all_epithelial(4;5.86e-15)|all_lung(4;1.32e-05)|Ovarian(4;1.33e-05)|Lung NSC(4;2.77e-05)|Esophageal squamous(42;0.0157)|all_hematologic(56;0.13)|Melanoma(33;0.144)		Epithelial(2;1.48e-13)|all cancers(1;5.77e-13)|OV - Ovarian serous cystadenocarcinoma(15;2.74e-10)|BRCA - Breast invasive adenocarcinoma(31;0.00166)|STAD - Stomach adenocarcinoma(84;0.18)|Lung(128;0.23)														---	---	---	---
MED16	10025	broad.mit.edu	37	19	892175	892175	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:892175delG	uc002lqd.1	-						MED16_uc002lqe.2_Intron|MED16_uc002lqf.2_Intron|MED16_uc010xfv.1_5'Flank|MED16_uc010xfw.1_5'Flank|MED16_uc010xfx.1_5'Flank|MED16_uc010xfy.1_5'Flank|MED16_uc010xga.1_Intron	NM_005481	NP_005472			mediator complex subunit 16						androgen receptor signaling pathway|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	receptor activity|thyroid hormone receptor binding|thyroid hormone receptor coactivator activity|vitamin D receptor binding				0		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
ADAMTSL5	339366	broad.mit.edu	37	19	1509610	1509611	+	Intron	INS	-	GGAA	GGAA	rs141155053	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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	1729504	1729505	+	IGR	DEL	GT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1729504_1729505delGT								TCF3 (77178 upstream) : ONECUT3 (24157 downstream)																																			---	---	---	---
AP3D1	8943	broad.mit.edu	37	19	2114529	2114529	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2114529delC	uc002luz.2	-						AP3D1_uc002luy.2_Intron|AP3D1_uc002lva.2_Intron	NM_003938	NP_003929			adaptor-related protein complex 3, delta 1						eye pigment biosynthetic process|intracellular protein transport|regulation of sequestering of zinc ion|vesicle-mediated transport	endosome membrane|Golgi membrane|membrane coat	binding|protein transporter activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
SPPL2B	56928	broad.mit.edu	37	19	2349867	2349868	+	Intron	DEL	TC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2349867_2349868delTC	uc002lvs.2	+						SPPL2B_uc002lvr.2_Intron	NM_152988	NP_694533			signal peptide peptidase-like 2B isoform 2							Golgi membrane|integral to membrane	aspartic-type endopeptidase activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	2371712	2371713	+	IGR	DEL	AA	-	-	rs57906471		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2371712_2371713delAA								SPPL2B (16613 upstream) : TMPRSS9 (18071 downstream)																																			---	---	---	---
C19orf77	284422	broad.mit.edu	37	19	3476853	3476860	+	Intron	DEL	GATGGATG	-	-	rs111284772		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3476853_3476860delGATGGATG	uc010xhk.1	-							NM_001136503	NP_001129975			hypothetical protein LOC284422 precursor							integral to membrane					0																		---	---	---	---
PIP5K1C	23396	broad.mit.edu	37	19	3650758	3650758	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3650758delT	uc002lyj.1	-						PIP5K1C_uc010xhq.1_Intron|PIP5K1C_uc010xhr.1_Intron	NM_012398	NP_036530			phosphatidylinositol-4-phosphate 5-kinase, type						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	3737193	3737195	+	Intron	DEL	TTG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3737193_3737195delTTG	uc010xhv.1	+						TJP3_uc010xhs.1_Intron|TJP3_uc010xht.1_Intron|TJP3_uc010xhu.1_Intron|TJP3_uc010xhw.1_Intron	NM_014428	NP_055243			tight junction protein 3							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)														---	---	---	---
CHAF1A	10036	broad.mit.edu	37	19	4438978	4438979	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4438978_4438979insA	uc002mal.2	+							NM_005483	NP_005474			chromatin assembly factor 1, subunit A (p150)						cell cycle|DNA repair|DNA replication|DNA replication-dependent nucleosome assembly|protein complex assembly|regulation of transcription, DNA-dependent|transcription, DNA-dependent	CAF-1 complex|WINAC complex	chromatin binding|chromo shadow domain binding|unfolded protein binding			ovary(1)|skin(1)	2		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0148)|STAD - Stomach adenocarcinoma(1328;0.18)									Chromatin_Structure					---	---	---	---
KDM4B	23030	broad.mit.edu	37	19	4995334	4995334	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4995334delT	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																		---	---	---	---
PTPRS	5802	broad.mit.edu	37	19	5231449	5231449	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5231449delG	uc002mbv.2	-	14	2261	c.2027delC	c.(2026-2028)CCGfs	p.P676fs	PTPRS_uc002mbu.1_Intron|PTPRS_uc010xin.1_Intron|PTPRS_uc002mbw.2_Frame_Shift_Del_p.P663fs|PTPRS_uc002mbx.2_Intron|PTPRS_uc002mby.2_Intron	NM_002850	NP_002841	Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type,	676	Extracellular (Potential).|Fibronectin type-III 4.				cell adhesion	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			large_intestine(2)|ovary(1)|central_nervous_system(1)	4				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0321)|Lung(535;0.182)														---	---	---	---
PTPRS	5802	broad.mit.edu	37	19	5239112	5239113	+	Intron	DEL	GA	-	-	rs36155090		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5239112_5239113delGA	uc002mbv.2	-						PTPRS_uc002mbu.1_Intron|PTPRS_uc010xin.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)														---	---	---	---
SAFB	6294	broad.mit.edu	37	19	5627321	5627321	+	Intron	DEL	A	-	-	rs144918619		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5627321delA	uc002mcf.2	+						SAFB_uc010xiq.1_Intron|SAFB_uc002mcg.2_Intron|SAFB_uc002mce.3_Intron|SAFB_uc010xir.1_Intron|SAFB_uc010xis.1_Intron|SAFB_uc010xit.1_Intron|SAFB_uc010xiu.1_Intron	NM_002967	NP_002958			scaffold attachment factor B						chromatin organization|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	double-stranded DNA binding|nucleotide binding|protein binding|RNA binding			ovary(1)|liver(1)|skin(1)	3				UCEC - Uterine corpus endometrioid carcinoma (162;0.000222)														---	---	---	---
RFX2	5990	broad.mit.edu	37	19	6070170	6070171	+	Intron	INS	-	ATAGA	ATAGA			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6070170_6070171insATAGA	uc002meb.2	-						RFX2_uc002mec.2_Intron|RFX2_uc010xiy.1_Intron	NM_000635	NP_000626			regulatory factor X2 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			breast(4)|ovary(1)|skin(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	6522467	6522467	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6522467delC								TUBB4 (20137 upstream) : TNFSF9 (8543 downstream)																																			---	---	---	---
TRIP10	9322	broad.mit.edu	37	19	6739847	6739847	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6739847delC	uc002mfs.2	+						GPR108_uc002mfo.3_5'Flank|GPR108_uc002mfp.2_5'Flank|GPR108_uc010duw.2_5'Flank|TRIP10_uc010dux.1_Intron|TRIP10_uc002mfr.2_Intron|TRIP10_uc010duy.2_Intron|TRIP10_uc010duz.2_Intron	NM_004240	NP_004231			thyroid hormone receptor interactor 10						actin cytoskeleton organization|cell communication|endocytosis|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cell cortex|cell projection|cytoskeleton|cytosol|Golgi apparatus|lysosome|perinuclear region of cytoplasm|phagocytic cup	GTPase activator activity|identical protein binding|lipid binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	6877417	6877418	+	IGR	DEL	GA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6877417_6877418delGA								VAV1 (20046 upstream) : EMR1 (10164 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	6877964	6877965	+	IGR	DEL	GA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6877964_6877965delGA								VAV1 (20593 upstream) : EMR1 (9617 downstream)																																			---	---	---	---
EMR4P	326342	broad.mit.edu	37	19	6970274	6970275	+	Intron	INS	-	AC	AC			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6970274_6970275insAC	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	7106510	7106510	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7106510delG								ZNF557 (18534 upstream) : INSR (5756 downstream)																																			---	---	---	---
INSR	3643	broad.mit.edu	37	19	7121012	7121013	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7121012_7121013delTT	uc002mgd.1	-						INSR_uc002mge.1_Intron	NM_000208	NP_000199			insulin receptor isoform Long precursor						activation of MAPK activity|activation of protein kinase B activity|carbohydrate metabolic process|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|glucose homeostasis|heart morphogenesis|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of developmental growth|positive regulation of DNA replication|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of glycolysis|positive regulation of MAPKKK cascade|positive regulation of mitosis|positive regulation of nitric oxide biosynthetic process|positive regulation of protein kinase B signaling cascade|positive regulation of protein phosphorylation|positive regulation of respiratory burst|protein autophosphorylation|protein heterotetramerization|regulation of embryonic development|regulation of transcription, DNA-dependent|transformation of host cell by virus	caveola|endosome membrane|insulin receptor complex|microsome	ATP binding|GTP binding|insulin binding|insulin receptor activity|insulin receptor substrate binding|insulin-like growth factor I binding|insulin-like growth factor II binding|insulin-like growth factor receptor binding|metal ion binding|phosphatidylinositol 3-kinase binding|PTB domain binding|receptor signaling protein tyrosine kinase activity|SH2 domain binding			ovary(4)|lung(3)|central_nervous_system(2)|large_intestine(1)|stomach(1)|skin(1)	12					Insulin Glargine recombinant(DB00047)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)													---	---	---	---
INSR	3643	broad.mit.edu	37	19	7251278	7251278	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7251278delT	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)													---	---	---	---
ARHGEF18	23370	broad.mit.edu	37	19	7464117	7464117	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7464117delT	uc010xjm.1	+						ARHGEF18_uc002mgh.2_Intron	NM_015318	NP_056133			Rho/Rac guanine nucleotide exchange factor 18						actin cytoskeleton organization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of cell shape|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity			ovary(1)	1		Renal(5;0.0902)																---	---	---	---
PNPLA6	10908	broad.mit.edu	37	19	7620693	7620693	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7620693delA	uc010xjq.1	+						PNPLA6_uc002mgq.1_Intron|PNPLA6_uc010xjp.1_Intron|PNPLA6_uc002mgr.1_Intron|PNPLA6_uc002mgs.2_Intron|PNPLA6_uc002mgt.1_Intron	NM_006702	NP_006693			neuropathy target esterase isoform b						cell death|lipid catabolic process|phosphatidylcholine metabolic process	endoplasmic reticulum membrane|integral to membrane	lysophospholipase activity			ovary(3)	3																		---	---	---	---
CD209	30835	broad.mit.edu	37	19	7806378	7806378	+	3'UTR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7806378delA	uc002mht.2	-	7					CD209_uc010xju.1_3'UTR|CD209_uc010dvp.2_3'UTR|CD209_uc002mhr.2_3'UTR|CD209_uc002mhs.2_3'UTR|CD209_uc002mhu.2_3'UTR|CD209_uc010dvq.2_3'UTR|CD209_uc002mhq.2_3'UTR|CD209_uc002mhv.2_3'UTR|CD209_uc002mhx.2_3'UTR|CD209_uc002mhw.2_3'UTR|CD209_uc010dvr.2_3'UTR	NM_021155	NP_066978			CD209 molecule isoform 1						cell-cell recognition|endocytosis|heterophilic cell-cell adhesion|innate immune response|intracellular signal transduction|intracellular virion transport|leukocyte cell-cell adhesion|peptide antigen transport|viral genome replication|virion attachment to host cell surface receptor	cytoplasm|extracellular region|integral to membrane|plasma membrane	mannose binding|metal ion binding|peptide antigen binding|receptor activity|virion binding			skin(1)	1																		---	---	---	---
ELAVL1	1994	broad.mit.edu	37	19	8026637	8026638	+	3'UTR	INS	-	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8026637_8026638insC	uc002mjb.2	-	6						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																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	8262648	8262648	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8262648delG								FBN3 (50267 upstream) : LASS4 (11569 downstream)																																			---	---	---	---
KANK3	256949	broad.mit.edu	37	19	8391692	8391693	+	Intron	INS	-	C	C	rs145593148		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8391692_8391693insC	uc010dwa.2	-							NM_198471	NP_940873			ankyrin repeat domain 47												0																		---	---	---	---
MYO1F	4542	broad.mit.edu	37	19	8586699	8586699	+	Intron	DEL	T	-	-	rs35658338		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8586699delT	uc002mkg.2	-							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	9093576	9093576	+	5'Flank	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9093576delA	uc002mkp.2	-							NM_024690	NP_078966			mucin 16						cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	9340107	9340107	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9340107delA								OR7D4 (14594 upstream) : OR7E24 (21613 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	9557042	9557057	+	IGR	DEL	ACACACACACACACAC	-	-	rs113974742		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9557042_9557057delACACACACACACACAC								ZNF266 (10808 upstream) : ZNF560 (19974 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	9612845	9612845	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9612845delA								ZNF560 (3566 upstream) : ZNF426 (25838 downstream)																																			---	---	---	---
ZNF121	7675	broad.mit.edu	37	19	9690981	9690981	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9690981delA	uc010xkp.1	-						ZNF121_uc010dwt.2_Intron|ZNF121_uc010xkq.1_Intron	NM_001008727	NP_001008727			zinc finger protein 121						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
ZNF562	54811	broad.mit.edu	37	19	9764669	9764670	+	Intron	DEL	TT	-	-	rs145922849		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9764669_9764670delTT	uc010xks.1	-						ZNF562_uc002mly.2_Intron|ZNF562_uc002mlx.2_Intron|ZNF562_uc010xkt.1_Intron|ZNF562_uc010xku.1_Intron|ZNF562_uc010xkv.1_Intron|ZNF562_uc010xkw.1_Intron	NM_001130032	NP_001123504			zinc finger protein 562 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
ZNF846	162993	broad.mit.edu	37	19	9867871	9867871	+	Intron	DEL	A	-	-	rs34789194		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9867871delA	uc010dww.2	-						ZNF846_uc010xky.1_Intron|ZNF846_uc010xkz.1_Intron	NM_001077624	NP_001071092			zinc finger protein 846						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
COL5A3	50509	broad.mit.edu	37	19	10070441	10070441	+	3'UTR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10070441delC	uc002mmq.1	-	67						NM_015719	NP_056534			collagen, type V, alpha 3 preproprotein						collagen fibril organization|skin development	collagen type V	collagen binding|extracellular matrix structural constituent			ovary(7)|lung(1)|central_nervous_system(1)|skin(1)	10			Epithelial(33;7.11e-05)															---	---	---	---
Unknown	0	broad.mit.edu	37	19	10136823	10136824	+	IGR	INS	-	AT	AT	rs143478112	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10136823_10136824insAT								RDH8 (3870 upstream) : C3P1 (15208 downstream)																																			---	---	---	---
C3P1	388503	broad.mit.edu	37	19	10160326	10160329	+	Intron	DEL	AGAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10160326_10160329delAGAA	uc010dwx.1	+							NR_027300				Synthetic construct DNA, clone: pF1KB7402, Homo sapiens LOC388503 gene, without stop codon, in Flexi system.												0																		---	---	---	---
MRPL4	51073	broad.mit.edu	37	19	10367123	10367123	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10367123delA	uc002mnm.2	+						MRPL4_uc002mnn.2_Intron|MRPL4_uc002mno.2_Intron	NM_146387	NP_666499			mitochondrial ribosomal protein L4 isoform a						translation	mitochondrion|ribosome	structural constituent of ribosome			ovary(1)	1		Renal(1328;0.0112)	OV - Ovarian serous cystadenocarcinoma(20;1.39e-09)|Epithelial(33;1.99e-06)|all cancers(31;4.81e-06)	Lung(535;0.00705)														---	---	---	---
RAVER1	125950	broad.mit.edu	37	19	10427729	10427729	+	3'UTR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10427729delA	uc002moa.2	-	13					FDX1L_uc002mnx.1_5'Flank|FDX1L_uc002mny.1_5'Flank|RAVER1_uc002mnz.2_3'UTR	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)															---	---	---	---
ATG4D	84971	broad.mit.edu	37	19	10657199	10657199	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10657199delT	uc002mov.2	+						ATG4D_uc010xlg.1_Intron|ATG4D_uc010xlh.1_Intron|ATG4D_uc010dxh.2_Intron|ATG4D_uc010dxi.2_Intron|ATG4D_uc010dxj.2_Intron	NM_032885	NP_116274			APG4 autophagy 4 homolog D						autophagy|protein transport	cytoplasm	cysteine-type endopeptidase activity				0			Epithelial(33;9.2e-06)|all cancers(31;3.9e-05)															---	---	---	---
SLC44A2	57153	broad.mit.edu	37	19	10753742	10753742	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10753742delG	uc002mpf.2	+						SLC44A2_uc002mpe.3_Intron|SLC44A2_uc002mpg.1_3'UTR|SLC44A2_uc002mph.2_Intron|SLC44A2_uc002mpi.2_Intron	NM_020428	NP_065161			solute carrier family 44, member 2 isoform 1						positive regulation of I-kappaB kinase/NF-kappaB cascade	integral to membrane|plasma membrane	choline transmembrane transporter activity|signal transducer activity			ovary(1)	1			Epithelial(33;8.7e-06)|all cancers(31;2.77e-05)		Choline(DB00122)													---	---	---	---
Unknown	0	broad.mit.edu	37	19	10808720	10808720	+	IGR	DEL	T	-	-	rs112749204		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10808720delT								ILF3 (5627 upstream) : QTRT1 (3392 downstream)																																			---	---	---	---
DNM2	1785	broad.mit.edu	37	19	10912585	10912585	+	Intron	DEL	A	-	-	rs34959391		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10912585delA	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	11144368	11144368	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11144368delT	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_uc010dxt.1_Intron|SMARCA4_uc002mqh.3_Intron|SMARCA4_uc002mqi.1_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				---	---	---	---
Unknown	0	broad.mit.edu	37	19	11395291	11395291	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11395291delT								DOCK6 (22134 upstream) : TSPAN16 (11533 downstream)																																			---	---	---	---
ECSIT	51295	broad.mit.edu	37	19	11637535	11637535	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11637535delT	uc002msb.2	-						ECSIT_uc010dyc.1_Intron|ECSIT_uc010dyd.2_Intron|ECSIT_uc010xma.1_Intron	NM_016581	NP_057665			evolutionarily conserved signaling intermediate						innate immune response|regulation of oxidoreductase activity	mitochondrion	oxidoreductase activity, acting on NADH or NADPH|protein binding			ovary(1)	1																		---	---	---	---
ZNF136	7695	broad.mit.edu	37	19	12284722	12284722	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12284722delT	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																		---	---	---	---
SYCE2	256126	broad.mit.edu	37	19	13024652	13024652	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13024652delT	uc002mvr.2	-							NM_001105578	NP_001099048			synaptonemal complex central element protein 2						cell division	central element					0																		---	---	---	---
GADD45GIP1	90480	broad.mit.edu	37	19	13070728	13070728	+	5'Flank	DEL	T	-	-	rs111543759		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13070728delT	uc002mwb.2	-							NM_052850	NP_443082			growth arrest and DNA-damage-inducible, gamma						cell cycle|interspecies interaction between organisms	nucleus	protein binding			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	14367223	14367226	+	IGR	DEL	TCCC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14367223_14367226delTCCC								LPHN1 (50226 upstream) : CD97 (124987 downstream)																																			---	---	---	---
EMR3	84658	broad.mit.edu	37	19	14732269	14732270	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14732269_14732270delAA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	14919755	14919755	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14919755delT								OR7C1 (8807 upstream) : OR7A5 (17385 downstream)																																			---	---	---	---
ILVBL	10994	broad.mit.edu	37	19	15238079	15238079	+	5'Flank	DEL	G	-	-	rs4494664	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15238079delG	uc002nam.2	-						ILVBL_uc010dzw.2_5'Flank|ILVBL_uc010dzx.1_5'Flank	NM_006844	NP_006835			ilvB (bacterial acetolactate synthase)-like							integral to membrane	magnesium ion binding|thiamine pyrophosphate binding|transferase activity			ovary(2)	2																		---	---	---	---
NOTCH3	4854	broad.mit.edu	37	19	15273581	15273584	+	Intron	DEL	TGTT	-	-	rs5827278		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15273581_15273584delTGTT	uc002nan.2	-							NM_000435	NP_000426			Notch homolog 3 precursor						Notch receptor processing|Notch signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane	calcium ion binding|protein binding|receptor activity			lung(8)|ovary(5)|skin(4)|prostate(2)|central_nervous_system(1)|breast(1)	21			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)															---	---	---	---
BRD4	23476	broad.mit.edu	37	19	15392831	15392834	+	5'Flank	DEL	AAAC	-	-	rs34560606		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15392831_15392834delAAAC	uc002nar.2	-						BRD4_uc002nas.2_5'Flank|BRD4_uc002nat.3_Intron|BRD4_uc002nau.3_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								---	---	---	---
PGLYRP2	114770	broad.mit.edu	37	19	15581119	15581119	+	Intron	DEL	C	-	-	rs112620863		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15581119delC	uc002nbf.3	-						PGLYRP2_uc002nbg.3_Intron	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	15658802	15658807	+	Intron	DEL	GAGAGG	-	-	rs36213762		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15658802_15658807delGAGAGG	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	15691836	15691837	+	IGR	INS	-	TCTT	TCTT	rs146876025	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15691836_15691837insTCTT								CYP4F22 (28709 upstream) : CYP4F8 (34192 downstream)																																			---	---	---	---
CYP4F2	8529	broad.mit.edu	37	19	15991138	15991139	+	Intron	DEL	AA	-	-	rs76756803		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15991138_15991139delAA	uc002nbs.1	-						CYP4F2_uc010xot.1_Intron	NM_001082	NP_001073			cytochrome P450, family 4, subfamily F,						leukotriene metabolic process|long-chain fatty acid metabolic process|very long-chain fatty acid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	alkane 1-monooxygenase activity|electron carrier activity|heme binding|leukotriene-B4 20-monooxygenase activity|oxygen binding|protein binding			ovary(1)|skin(1)	2																		---	---	---	---
CIB3	117286	broad.mit.edu	37	19	16283777	16283780	+	Intron	DEL	GAAG	-	-	rs3076228		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16283777_16283780delGAAG	uc002nds.2	-						CIB3_uc010eae.2_Intron|CIB3_uc010eaf.2_Intron|CIB3_uc010eag.2_Intron	NM_054113	NP_473454			DNA-dependent protein kinase catalytic								calcium ion binding			ovary(1)	1																		---	---	---	---
AP1M1	8907	broad.mit.edu	37	19	16320150	16320150	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16320150delT	uc002ndu.2	+						AP1M1_uc002ndv.2_Intron|AP1M1_uc010xpd.1_Intron	NM_032493	NP_115882			adaptor-related protein complex 1, mu 1 subunit						cellular membrane organization|endosome to melanosome transport|interspecies interaction between organisms|intracellular protein transport|melanosome organization|post-Golgi vesicle-mediated transport|regulation of defense response to virus by virus|viral reproduction	clathrin adaptor complex|clathrin coated vesicle membrane|cytosol|Golgi membrane|lysosomal membrane	protein binding			ovary(3)|breast(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	16371611	16371612	+	IGR	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16371611_16371612delAC								AP1M1 (25455 upstream) : KLF2 (64039 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	16418938	16418939	+	IGR	INS	-	A	A	rs35524958		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16418938_16418939insA								AP1M1 (72782 upstream) : KLF2 (16712 downstream)																																			---	---	---	---
CALR3	125972	broad.mit.edu	37	19	16594979	16594979	+	Intron	DEL	C	-	-	rs7252242	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16594979delC	uc002ned.2	-						MED26_uc002nee.2_Intron	NM_145046	NP_659483			calreticulin 3 precursor						protein folding	endoplasmic reticulum lumen	calcium ion binding|sugar binding|unfolded protein binding				0																		---	---	---	---
MED26	9441	broad.mit.edu	37	19	16734924	16734925	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16734924_16734925delAA	uc002nen.1	-						MED26_uc002nee.2_Intron	NM_004831	NP_004822			mediator complex subunit 26						regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	DNA binding|RNA polymerase II transcription cofactor activity|transcription coactivator activity			ovary(2)	2																		---	---	---	---
NWD1	284434	broad.mit.edu	37	19	16893673	16893676	+	Intron	DEL	TTCT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16893673_16893676delTTCT	uc002neu.3	+						NWD1_uc002net.3_Intron|NWD1_uc002nev.3_Intron					RecName: Full=NACHT and WD repeat domain-containing protein 1;								ATP binding			skin(3)|ovary(2)|pancreas(2)	7																		---	---	---	---
USHBP1	83878	broad.mit.edu	37	19	17363696	17363696	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17363696delA	uc002nfs.1	-						USHBP1_uc002nfr.1_Intron|USHBP1_uc002nft.1_Intron|USHBP1_uc010xpk.1_Intron	NM_031941	NP_114147			Usher syndrome 1C binding protein 1								PDZ domain binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	17454869	17454870	+	IGR	INS	-	AAAC	AAAC	rs141993407	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17454869_17454870insAAAC								GTPBP3 (1330 upstream) : PLVAP (7394 downstream)																																			---	---	---	---
GLT25D1	79709	broad.mit.edu	37	19	17675973	17675974	+	Intron	INS	-	C	C	rs3052537		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17675973_17675974insC	uc002nhc.1	+							NM_024656	NP_078932			glycosyltransferase 25 domain containing 1						lipopolysaccharide biosynthetic process	endoplasmic reticulum lumen	procollagen galactosyltransferase activity				0																		---	---	---	---
GLT25D1	79709	broad.mit.edu	37	19	17676880	17676880	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17676880delA	uc002nhc.1	+						GLT25D1_uc010eax.1_5'Flank	NM_024656	NP_078932			glycosyltransferase 25 domain containing 1						lipopolysaccharide biosynthetic process	endoplasmic reticulum lumen	procollagen galactosyltransferase activity				0																		---	---	---	---
SLC5A5	6528	broad.mit.edu	37	19	17994332	17994332	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17994332delG	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	18447926	18447927	+	IGR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18447926_18447927insA								LSM4 (13925 upstream) : PGPEP1 (3481 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	18493620	18493621	+	IGR	INS	-	A	A	rs142733081	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18493620_18493621insA								PGPEP1 (12857 upstream) : GDF15 (3347 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	18738165	18738166	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18738165_18738166delTT								TMEM59L (6322 upstream) : KLHL26 (9672 downstream)																																			---	---	---	---
SLC25A42	284439	broad.mit.edu	37	19	19194250	19194250	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19194250delC	uc002nlf.1	+							NM_178526	NP_848621			solute carrier family 25, member 42						transmembrane transport	integral to membrane|mitochondrial inner membrane	binding				0			OV - Ovarian serous cystadenocarcinoma(5;5.4e-06)|Epithelial(12;0.000497)															---	---	---	---
Unknown	0	broad.mit.edu	37	19	20780756	20780756	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:20780756delG								ZNF737 (32130 upstream) : ZNF626 (21989 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	21167223	21167224	+	IGR	INS	-	CTCTTCTTC	CTCTTCTTC	rs147984331	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21167223_21167224insCTCTTCTTC								ZNF85 (33722 upstream) : ZNF430 (36273 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	21427256	21427256	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21427256delT								ZNF431 (58451 upstream) : ZNF708 (46707 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	21672369	21672369	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21672369delT	uc002nqa.2	+						uc002nqb.2_Intron					Homo sapiens cDNA FLJ40062 fis, clone TESOP2000090.																														---	---	---	---
Unknown	0	broad.mit.edu	37	19	21753653	21753653	+	RNA	DEL	G	-	-	rs35864944		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21753653delG	uc002nqe.2	-	2		c.1070delC								full-length cDNA clone CS0DH004YH18 of T cells (Jurkat cell line) of Homo sapiens (human).																														---	---	---	---
Unknown	0	broad.mit.edu	37	19	21823322	21823322	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21823322delT								ZNF429 (84254 upstream) : ZNF100 (83522 downstream)																																			---	---	---	---
ZNF43	7594	broad.mit.edu	37	19	21989300	21989300	+	3'UTR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21989300delA	uc002nqj.2	-	4					ZNF43_uc010ecv.2_3'UTR|ZNF43_uc002nql.2_3'UTR|ZNF43_uc002nqm.2_3'UTR|ZNF43_uc002nqk.2_3'UTR	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)														---	---	---	---
ZNF91	7644	broad.mit.edu	37	19	23540842	23540842	+	3'UTR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:23540842delA	uc002nre.2	-	4					ZNF91_uc002nrd.2_Intron|ZNF91_uc010xrj.1_3'UTR	NM_003430	NP_003421			zinc finger protein 91							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		all_lung(12;0.0349)|Lung NSC(12;0.0538)|all_epithelial(12;0.0611)																---	---	---	---
ZNF91	7644	broad.mit.edu	37	19	23547734	23547737	+	Intron	DEL	AATT	-	-	rs71878350		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:23547734_23547737delAATT	uc002nre.2	-						ZNF91_uc010xrj.1_Intron	NM_003430	NP_003421			zinc finger protein 91							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		all_lung(12;0.0349)|Lung NSC(12;0.0538)|all_epithelial(12;0.0611)																---	---	---	---
Unknown	0	broad.mit.edu	37	19	23605096	23605097	+	IGR	INS	-	TTG	TTG	rs34982030		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:23605096_23605097insTTG								ZNF91 (26827 upstream) : ZNF675 (230612 downstream)																																			---	---	---	---
RPSAP58	388524	broad.mit.edu	37	19	23976368	23976368	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:23976368delT	uc002nrn.2	+							NM_002295	NP_002286			ribosomal protein SA												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	24156497	24156498	+	IGR	INS	-	AA	AA			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:24156497_24156498insAA								RPSAP58 (145580 upstream) : ZNF254 (59749 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	24549747	24549748	+	IGR	INS	-	GAGAA	GAGAA	rs113572148		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:24549747_24549748insGAGAA								LOC100101266 (203498 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	24587721	24587722	+	IGR	INS	-	T	T	rs148066182		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:24587721_24587722insT								LOC100101266 (241472 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	27879008	27879009	+	IGR	INS	-	AC	AC	rs145042475		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:27879008_27879009insAC								None (None upstream) : LOC148189 (402393 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	28266790	28266790	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:28266790delT								None (None upstream) : LOC148189 (14612 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	28547577	28547577	+	IGR	DEL	A	-	-	rs71575587		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:28547577delA								LOC148189 (262729 upstream) : LOC148145 (908463 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	29275425	29275425	+	IGR	DEL	T	-	-	rs113671556		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:29275425delT								LOC148189 (990577 upstream) : LOC148145 (180615 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	30085549	30085558	+	IGR	DEL	ACACACACAC	-	-	rs67400834		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30085549_30085558delACACACACAC								VSTM2B (30323 upstream) : POP4 (11612 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	30149471	30149472	+	IGR	DEL	AC	-	-	rs35098556		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30149471_30149472delAC								POP4 (41309 upstream) : PLEKHF1 (6855 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	30396171	30396172	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30396171_30396172insT								CCNE1 (80953 upstream) : C19orf2 (18379 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	30526649	30526650	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30526649_30526650delTT								C19orf2 (20038 upstream) : ZNF536 (336678 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	30649137	30649137	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30649137delC								C19orf2 (142526 upstream) : ZNF536 (214191 downstream)																																			---	---	---	---
ZNF536	9745	broad.mit.edu	37	19	30950262	30950263	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30950262_30950263delTT	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	31172375	31172375	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31172375delC								ZNF536 (123410 upstream) : DKFZp566F0947 (468408 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	31591933	31591933	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31591933delA								ZNF536 (542968 upstream) : DKFZp566F0947 (48850 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	31629650	31629651	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31629650_31629651delTT								ZNF536 (580685 upstream) : DKFZp566F0947 (11132 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	31846295	31846295	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31846295delA								TSHZ3 (6105 upstream) : ZNF507 (990219 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	32128618	32128618	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:32128618delG								TSHZ3 (288428 upstream) : ZNF507 (707896 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	32264326	32264326	+	IGR	DEL	A	-	-	rs35629292		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:32264326delA								TSHZ3 (424136 upstream) : ZNF507 (572188 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	32544651	32544652	+	IGR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:32544651_32544652insA								TSHZ3 (704461 upstream) : ZNF507 (291862 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	32760220	32760220	+	IGR	DEL	T	-	-	rs151292743	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:32760220delT								TSHZ3 (920030 upstream) : ZNF507 (76294 downstream)																																			---	---	---	---
GPATCH1	55094	broad.mit.edu	37	19	33587442	33587442	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33587442delT	uc002nug.1	+							NM_018025	NP_060495			G patch domain containing 1							catalytic step 2 spliceosome	nucleic acid binding			skin(1)	1	Esophageal squamous(110;0.137)																	---	---	---	---
PEPD	5184	broad.mit.edu	37	19	33945550	33945550	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33945550delA	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	34058545	34058546	+	IGR	INS	-	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34058545_34058546insC								PEPD (45744 upstream) : CHST8 (54315 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	34069813	34069813	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34069813delG								PEPD (57012 upstream) : CHST8 (43048 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	34362142	34362143	+	IGR	DEL	TC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34362142_34362143delTC								KCTD15 (55477 upstream) : LSM14A (301209 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	34528720	34528720	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34528720delA								KCTD15 (222055 upstream) : LSM14A (134632 downstream)																																			---	---	---	---
LSM14A	26065	broad.mit.edu	37	19	34707371	34707371	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34707371delT	uc002nvb.3	+						LSM14A_uc002nva.3_Intron|LSM14A_uc010xru.1_Intron|LSM14A_uc002nvc.3_Intron	NM_001114093	NP_001107565			LSM14 homolog A isoform a						cytoplasmic mRNA processing body assembly|multicellular organismal development|regulation of translation	cytoplasmic mRNA processing body|intracellular membrane-bounded organelle|stress granule				skin(1)	1	Esophageal squamous(110;0.162)																	---	---	---	---
UBA2	10054	broad.mit.edu	37	19	34924232	34924232	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34924232delT	uc002nvk.2	+						UBA2_uc010xrx.1_Intron|UBA2_uc002nvl.2_Intron	NM_005499	NP_005490			SUMO-1 activating enzyme subunit 2						protein sumoylation	nucleus	ATP binding|enzyme activator activity|ligase activity|metal ion binding|protein heterodimerization activity|SUMO activating enzyme activity			ovary(1)	1	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.211)															---	---	---	---
Unknown	0	broad.mit.edu	37	19	34962954	34962954	+	IGR	DEL	T	-	-	rs74177154		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34962954delT								UBA2 (2157 upstream) : WTIP (9926 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	35136445	35136446	+	Intron	DEL	AG	-	-	rs72337452		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35136445_35136446delAG	uc002nvo.1	-											Homo sapiens cDNA FLJ36176 fis, clone TESTI2026491.																														---	---	---	---
SCN1B	6324	broad.mit.edu	37	19	35522266	35522267	+	Intron	DEL	GA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35522266_35522267delGA	uc002nxp.2	+						SCN1B_uc002nxo.1_Intron|SCN1B_uc010xsg.1_Intron	NM_001037	NP_001028			sodium channel, voltage-gated, type I, beta						axon guidance|synaptic transmission	integral to membrane	voltage-gated sodium channel activity			ovary(1)|central_nervous_system(1)	2	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)															---	---	---	---
LSR	51599	broad.mit.edu	37	19	35751737	35751738	+	Intron	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35751737_35751738delAC	uc002nyl.2	+						LSR_uc002nym.2_Intron|LSR_uc002nyn.2_Intron|LSR_uc002nyo.2_Intron|LSR_uc010xsr.1_Intron|LSR_uc002nyp.2_Intron	NM_205834	NP_991403			lipolysis stimulated lipoprotein receptor						embryo development|liver development	chylomicron|integral to membrane|low-density lipoprotein particle|plasma membrane|very-low-density lipoprotein particle	receptor activity				0	all_lung(56;3.91e-09)|Lung NSC(56;5.64e-09)|Esophageal squamous(110;0.162)		Epithelial(14;1.33e-19)|OV - Ovarian serous cystadenocarcinoma(14;1.29e-18)|all cancers(14;7.11e-17)|LUSC - Lung squamous cell carcinoma(66;0.0417)															---	---	---	---
USF2	7392	broad.mit.edu	37	19	35761964	35761964	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35761964delT	uc002nyq.1	+						USF2_uc010xss.1_Intron|USF2_uc002nyr.1_Intron|USF2_uc002nys.1_Intron|USF2_uc002nyt.1_Intron|USF2_uc002nyu.1_Intron|USF2_uc002nyv.1_Intron	NM_003367	NP_003358			upstream stimulatory factor 2 isoform 1						lipid homeostasis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter by glucose	nucleus	bHLH transcription factor binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sequence-specific enhancer binding RNA polymerase II transcription factor activity				0	all_lung(56;2.37e-08)|Lung NSC(56;3.66e-08)|Esophageal squamous(110;0.162)		Epithelial(14;7.4e-20)|OV - Ovarian serous cystadenocarcinoma(14;6.47e-19)|all cancers(14;4.17e-17)|LUSC - Lung squamous cell carcinoma(66;0.0417)															---	---	---	---
CD22	933	broad.mit.edu	37	19	35822750	35822750	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35822750delA	uc010edt.2	+						CD22_uc010xst.1_Intron|CD22_uc010edu.2_Intron|CD22_uc010edv.2_Intron|CD22_uc002nzb.3_5'Flank	NM_001771	NP_001762			CD22 molecule precursor						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)													---	---	---	---
GAPDHS	26330	broad.mit.edu	37	19	36027481	36027481	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36027481delA	uc002oaf.1	+							NM_014364	NP_055179			glyceraldehyde-3-phosphate dehydrogenase,						gluconeogenesis|glycolysis|positive regulation of glycolysis|sperm motility	cytosol	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity|NAD binding|protein binding				0	all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)		NADH(DB00157)													---	---	---	---
KIRREL2	84063	broad.mit.edu	37	19	36354667	36354668	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36354667_36354668insT	uc002ocb.3	+						KIRREL2_uc002obz.3_Intron|KIRREL2_uc002oca.3_Intron|KIRREL2_uc002occ.3_Intron|KIRREL2_uc002ocd.3_Intron	NM_199180	NP_954649			kin of IRRE-like 2 isoform c						cell adhesion	integral to membrane|plasma membrane				ovary(1)|central_nervous_system(1)|skin(1)	3	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)															---	---	---	---
NFKBID	84807	broad.mit.edu	37	19	36388162	36388162	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36388162delT	uc002oci.1	-						NFKBID_uc002och.1_5'Flank|NFKBID_uc002ocj.1_Intron	NM_139239	NP_640332			nuclear factor of kappa light polypeptide gene						inflammatory response	nucleus					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	36406006	36406006	+	IGR	DEL	A	-	-	rs112345087		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36406006delA								TYROBP (6820 upstream) : LRFN3 (22016 downstream)																																			---	---	---	---
WDR62	284403	broad.mit.edu	37	19	36568508	36568508	+	Intron	DEL	T	-	-	rs111946488		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36568508delT	uc002odc.2	+						WDR62_uc002odd.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	36862888	36862889	+	Intron	INS	-	GGAG	GGAG	rs139062759	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36862888_36862889insGGAG	uc010eex.1	-							NM_020917	NP_065968			zinc finger protein 14-like						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	Esophageal squamous(110;0.162)																	---	---	---	---
Unknown	0	broad.mit.edu	37	19	36926963	36926963	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36926963delA								ZFP82 (17413 upstream) : ZNF566 (9059 downstream)																																			---	---	---	---
ZNF260	339324	broad.mit.edu	37	19	37008741	37008741	+	Intron	DEL	T	-	-	rs72252812		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37008741delT	uc002oee.1	-						ZNF260_uc002oed.1_Intron|ZNF260_uc010eey.1_Intron|ZNF260_uc002oef.1_Intron	NM_001012756	NP_001012774			zinc finger protein 260						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Esophageal squamous(110;0.162)																	---	---	---	---
Unknown	0	broad.mit.edu	37	19	37246595	37246595	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37246595delA	uc010efc.2	-						uc010xtm.1_Intron					Homo sapiens zinc finger protein 850 pseudogene, mRNA (cDNA clone IMAGE:6082150).																														---	---	---	---
ZNF829	374899	broad.mit.edu	37	19	37393068	37393071	+	Intron	DEL	AAAG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37393068_37393071delAAAG	uc002ofa.1	-						ZNF345_uc002oez.2_Intron	NM_001037232	NP_001032309			zinc finger protein 829						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)															---	---	---	---
ZNF568	374900	broad.mit.edu	37	19	37421116	37421117	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37421116_37421117delTT	uc002ofc.2	+						ZNF568_uc010efg.2_Intron|ZNF568_uc010xtn.1_Intron|ZNF568_uc002ofd.2_Intron|ZNF568_uc010efe.2_Intron|ZNF568_uc010eff.1_Intron	NM_198539	NP_940941			zinc finger protein 568						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)															---	---	---	---
Unknown	0	broad.mit.edu	37	19	37556304	37556305	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37556304_37556305insT								ZNF568 (67470 upstream) : ZNF420 (13077 downstream)																																			---	---	---	---
RYR1	6261	broad.mit.edu	37	19	39021450	39021450	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39021450delT	uc002oit.2	+						RYR1_uc002oiu.2_Intron|RYR1_uc002oiv.1_Intron|RYR1_uc010xuf.1_Intron	NM_000540	NP_000531			skeletal muscle ryanodine receptor isoform 1						muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia	cell cortex|cytosol|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna	calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(7)|pancreas(2)|breast(1)|central_nervous_system(1)|skin(1)	12	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Dantrolene(DB01219)													---	---	---	---
HNRNPL	3191	broad.mit.edu	37	19	39330959	39330959	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39330959delG	uc010xul.1	-	8	1021	c.1010delC	c.(1009-1011)CCAfs	p.P337fs	HNRNPL_uc010ege.1_5'UTR|HNRNPL_uc002ojj.1_5'UTR|HNRNPL_uc002ojo.1_5'Flank|HNRNPL_uc002ojk.2_5'UTR|HNRNPL_uc002ojl.2_5'UTR|HNRNPL_uc010xum.1_Frame_Shift_Del_p.P204fs|HNRNPL_uc002ojp.1_5'UTR|HNRNPL_uc010xun.1_Frame_Shift_Del_p.H45fs	NM_001533	NP_001524	P14866	HNRPL_HUMAN	heterogeneous nuclear ribonucleoprotein L	337	Pro-rich.				nuclear mRNA splicing, via spliceosome	cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm	nucleotide binding|protein binding|RNA binding|transcription regulatory region DNA binding				0	all_cancers(60;6.83e-06)|Ovarian(47;0.0454)		Lung(45;0.00342)|LUSC - Lung squamous cell carcinoma(53;0.00575)															---	---	---	---
PAK4	10298	broad.mit.edu	37	19	39648717	39648718	+	Intron	DEL	TG	-	-	rs146221522		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39648717_39648718delTG	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)															---	---	---	---
PAK4	10298	broad.mit.edu	37	19	39667515	39667516	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39667515_39667516delTT	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)															---	---	---	---
SNRPA	6626	broad.mit.edu	37	19	41267197	41267197	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41267197delT	uc002ooz.2	+						SNRPA_uc002opa.2_Intron	NM_004596	NP_004587			small nuclear ribonucleoprotein polypeptide A							nucleoplasm|spliceosomal complex	nucleotide binding|protein binding|RNA binding			skin(2)|ovary(1)|central_nervous_system(1)	4			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)															---	---	---	---
CYP2S1	29785	broad.mit.edu	37	19	41706982	41706983	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41706982_41706983delAA	uc002opw.2	+						CYP2F1_uc010xvw.1_Intron|CYP2S1_uc010xvx.1_Intron	NM_030622	NP_085125			cytochrome P450, family 2, subfamily S,						xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|retinoic acid 4-hydroxylase activity			skin(1)	1																		---	---	---	---
CYP2F1	1572	broad.mit.edu	37	19	41767896	41767897	+	Intron	DEL	AC	-	-	rs72262253		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41767896_41767897delAC	uc010xvw.1	+						HNRNPUL1_uc002opz.3_5'Flank|HNRNPUL1_uc002oqa.3_5'Flank|HNRNPUL1_uc002oqb.3_5'Flank|HNRNPUL1_uc010ehm.2_5'Flank|HNRNPUL1_uc002oqc.3_5'Flank|HNRNPUL1_uc002oqe.3_5'Flank|HNRNPUL1_uc002oqd.3_5'Flank|HNRNPUL1_uc010ehn.2_5'Flank|HNRNPUL1_uc010ehl.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																		---	---	---	---
CEACAM21	90273	broad.mit.edu	37	19	42083433	42083434	+	Intron	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42083433_42083434delAC	uc002ore.3	+						CEACAM21_uc002orc.1_Intron|CEACAM21_uc002ord.1_Intron|CEACAM21_uc002orf.2_Intron|CEACAM21_uc002org.3_Intron	NM_001098506	NP_001091976			carcinoembryonic antigen-related cell adhesion							integral to membrane				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	42337689	42337689	+	IGR	DEL	A	-	-	rs34089459		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42337689delA								CEACAM3 (22098 upstream) : LYPD4 (3461 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	42883580	42883580	+	IGR	DEL	T	-	-	rs111742016		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42883580delT								MEGF8 (660 upstream) : CNFN (7594 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	42968621	42968621	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42968621delT	uc010eif.1	+						uc002ott.1_Intron|uc010eig.1_Intron|uc010eih.1_Intron					Homo sapiens cDNA FLJ39530 fis, clone PUAEN2004400.																														---	---	---	---
Unknown	0	broad.mit.edu	37	19	43204290	43204290	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43204290delT								CEACAM8 (105208 upstream) : PSG3 (21505 downstream)																																			---	---	---	---
ZNF227	7770	broad.mit.edu	37	19	44720839	44720840	+	Intron	INS	-	T	T	rs138556162	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44720839_44720840insT	uc002oyu.2	+						ZNF227_uc010xwu.1_Intron|ZNF227_uc002oyv.2_Intron|ZNF227_uc010xwv.1_Intron|ZNF227_uc010xww.1_Intron|ZNF227_uc002oyw.2_Intron|ZNF227_uc010ejh.2_5'Flank	NM_182490	NP_872296			zinc finger protein 227						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Prostate(69;0.0435)																---	---	---	---
CEACAM22P	388550	broad.mit.edu	37	19	45045139	45045140	+	Intron	DEL	AG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45045139_45045140delAG	uc010ejr.1	-							NR_027754				Homo sapiens cDNA FLJ41856 fis, clone NT2RI3006171, weakly similar to Carcinoembryonic antigen-related celladhesion molecule 5 precursor.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	45069532	45069533	+	IGR	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45069532_45069533delAC								CEACAM22P (9382 upstream) : PVR (77565 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	45616486	45616487	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45616486_45616487insA	uc002pas.2	+											Homo sapiens leucine rich repeat containing 68, mRNA (cDNA clone IMAGE:5573062), partial cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	19	45749986	45749986	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45749986delA								EXOC3L2 (12517 upstream) : MARK4 (4856 downstream)																																			---	---	---	---
MARK4	57787	broad.mit.edu	37	19	45776392	45776393	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45776392_45776393delTT	uc002pbb.1	+						MARK4_uc002paz.1_Intron|MARK4_uc002pba.1_Intron|MARK4_uc002pbc.1_Intron					RecName: Full=MAP/microtubule affinity-regulating kinase 4;          EC=2.7.11.1; AltName: Full=MAP/microtubule affinity-regulating kinase-like 1;						microtubule bundle formation|nervous system development|positive regulation of programmed cell death	centrosome|neuron projection	ATP binding|gamma-tubulin binding|microtubule binding|protein serine/threonine kinase activity|tau-protein kinase activity|ubiquitin binding			central_nervous_system(2)|large_intestine(1)	3		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0102)														---	---	---	---
MARK4	57787	broad.mit.edu	37	19	45785020	45785020	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45785020delG	uc002pbb.1	+						MARK4_uc002pba.1_Intron|MARK4_uc002pbc.1_Intron					RecName: Full=MAP/microtubule affinity-regulating kinase 4;          EC=2.7.11.1; AltName: Full=MAP/microtubule affinity-regulating kinase-like 1;						microtubule bundle formation|nervous system development|positive regulation of programmed cell death	centrosome|neuron projection	ATP binding|gamma-tubulin binding|microtubule binding|protein serine/threonine kinase activity|tau-protein kinase activity|ubiquitin binding			central_nervous_system(2)|large_intestine(1)	3		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0102)														---	---	---	---
CKM	1158	broad.mit.edu	37	19	45814503	45814503	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45814503delT	uc002pbd.2	-							NM_001824	NP_001815			muscle creatine kinase						creatine metabolic process	cytosol	ATP binding|creatine kinase activity			skin(1)	1		Ovarian(192;0.0336)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;2.29e-44)|Epithelial(262;1.05e-38)|GBM - Glioblastoma multiforme(486;3.56e-07)	Creatine(DB00148)													---	---	---	---
CKM	1158	broad.mit.edu	37	19	45822685	45822685	+	Intron	DEL	C	-	-	rs68016783		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45822685delC	uc002pbd.2	-							NM_001824	NP_001815			muscle creatine kinase						creatine metabolic process	cytosol	ATP binding|creatine kinase activity			skin(1)	1		Ovarian(192;0.0336)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;2.29e-44)|Epithelial(262;1.05e-38)|GBM - Glioblastoma multiforme(486;3.56e-07)	Creatine(DB00148)													---	---	---	---
GIPR	2696	broad.mit.edu	37	19	46177864	46177864	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46177864delA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	46262231	46262232	+	IGR	INS	-	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46262231_46262232insC								FBXO46 (28080 upstream) : SIX5 (5812 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	46775805	46775805	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46775805delA								IGFL1 (41307 upstream) : HIF3A (24500 downstream)																																			---	---	---	---
PPP5C	5536	broad.mit.edu	37	19	46874297	46874298	+	Intron	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46874297_46874298delTG	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	46949610	46949610	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46949610delG								CCDC8 (32691 upstream) : PNMAL1 (20139 downstream)																																			---	---	---	---
ZC3H4	23211	broad.mit.edu	37	19	47581749	47581749	+	Intron	DEL	C	-	-	rs68180872		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47581749delC	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-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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)														---	---	---	---
CCDC9	26093	broad.mit.edu	37	19	47773232	47773232	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47773232delT	uc010xym.1	+							NM_015603	NP_056418			coiled-coil domain containing 9												0		all_cancers(25;0.0432)|all_epithelial(76;0.00812)|Medulloblastoma(540;0.0208)|all_neural(266;0.0416)|Hepatocellular(1079;0.114)		OV - Ovarian serous cystadenocarcinoma(262;8.51e-95)|Epithelial(262;1.15e-92)|all cancers(93;7.67e-84)|GBM - Glioblastoma multiforme(486;0.024)|STAD - Stomach adenocarcinoma(1328;0.183)														---	---	---	---
EHD2	30846	broad.mit.edu	37	19	48245534	48245535	+	3'UTR	INS	-	CTTT	CTTT	rs144890729	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48245534_48245535insCTTT	uc002phj.3	+	6					EHD2_uc010xyu.1_3'UTR|EHD2_uc010xyv.1_3'UTR	NM_014601	NP_055416			EH-domain containing 2						blood coagulation|endocytic recycling	nucleus|plasma membrane|recycling endosome membrane	ATP binding|calcium ion binding|GTP binding|GTPase activity|nucleic acid binding			ovary(1)|skin(1)	2		all_cancers(25;6.74e-07)|all_lung(116;2.02e-05)|Lung NSC(112;3.77e-05)|all_epithelial(76;4.89e-05)|all_neural(266;0.0332)|Ovarian(192;0.086)		OV - Ovarian serous cystadenocarcinoma(262;0.000336)|all cancers(93;0.000415)|Epithelial(262;0.0132)|GBM - Glioblastoma multiforme(486;0.0537)														---	---	---	---
ZNF114	163071	broad.mit.edu	37	19	48774019	48774022	+	Intron	DEL	AGAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48774019_48774022delAGAA	uc002pil.1	+						ZNF114_uc010elv.1_5'Flank|ZNF114_uc002pim.1_5'Flank	NM_153608	NP_705836			zinc finger protein 114						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_epithelial(76;8.01e-05)|all_lung(116;0.000112)|Lung NSC(112;0.000192)|Prostate(7;0.0187)|all_neural(266;0.0228)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;7.56e-05)|all cancers(93;0.000113)|Epithelial(262;0.00962)|GBM - Glioblastoma multiforme(486;0.0153)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	49024381	49024382	+	IGR	DEL	AC	-	-	rs71896746		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49024381_49024382delAC								LMTK3 (7935 upstream) : SULT2B1 (31047 downstream)																																			---	---	---	---
NTN5	126147	broad.mit.edu	37	19	49173894	49173894	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49173894delC	uc002pkb.2	-	2	446	c.350delG	c.(349-351)GGCfs	p.G117fs	SEC1_uc010xzv.1_Intron|SEC1_uc002pka.2_Intron|SEC1_uc010xzw.1_Intron|SEC1_uc010ema.2_Intron|NTN5_uc002pkc.2_Frame_Shift_Del_p.G117fs	NM_145807	NP_665806	Q8WTR8	NET5_HUMAN	netrin 5 precursor	117						extracellular region				large_intestine(1)|pancreas(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	49382827	49382829	+	IGR	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49382827_49382829delTTT								PPP1R15A (3509 upstream) : TULP2 (1393 downstream)																																			---	---	---	---
NUCB1	4924	broad.mit.edu	37	19	49404368	49404373	+	Intron	DEL	CTGACT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49404368_49404373delCTGACT	uc002plb.3	+						NUCB1_uc002pla.2_Intron|NUCB1_uc002plc.2_Intron|TULP2_uc002pkz.2_5'Flank	NM_006184	NP_006175			nucleobindin 1 precursor							ER-Golgi intermediate compartment|extracellular space|Golgi apparatus|membrane|microtubule cytoskeleton	calcium ion binding|DNA binding				0		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;8.64e-05)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000171)|all cancers(93;0.000333)|Epithelial(262;0.0174)|GBM - Glioblastoma multiforme(486;0.0244)														---	---	---	---
DHDH	27294	broad.mit.edu	37	19	49434630	49434631	+	5'Flank	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49434630_49434631delTT	uc002ple.1	+							NM_014475	NP_055290			dimeric dihydrodiol dehydrogenase						carbohydrate metabolic process		binding|D-xylose 1-dehydrogenase (NADP+) activity|electron carrier activity|NAD(P)+ transhydrogenase activity|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity				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)		OV - Ovarian serous cystadenocarcinoma(262;0.000158)|all cancers(93;0.000258)|Epithelial(262;0.0173)|GBM - Glioblastoma multiforme(486;0.0179)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	49524922	49524923	+	IGR	DEL	AG	-	-	rs71698135		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49524922_49524923delAG								LHB (4575 upstream) : CGB (1204 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	49715837	49715838	+	IGR	INS	-	CTTC	CTTC	rs76677262		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49715837_49715838insCTTC								TRPM4 (746 upstream) : SLC6A16 (77056 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	49723247	49723248	+	IGR	INS	-	T	T	rs144326236	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49723247_49723248insT								TRPM4 (8156 upstream) : SLC6A16 (69646 downstream)																																			---	---	---	---
TEAD2	8463	broad.mit.edu	37	19	49850473	49850473	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49850473delG	uc002pnj.2	-	9	974	c.883delC	c.(883-885)CATfs	p.H295fs	TEAD2_uc002png.2_Frame_Shift_Del_p.H298fs|TEAD2_uc002pnh.2_Frame_Shift_Del_p.H299fs|TEAD2_uc002pni.2_Frame_Shift_Del_p.H298fs|TEAD2_uc010yao.1_Frame_Shift_Del_p.H167fs|TEAD2_uc010emw.2_Frame_Shift_Del_p.H298fs	NM_003598	NP_003589	Q15562	TEAD2_HUMAN	TEA domain family member 2	295	Transcriptional activation (Potential).				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	49866661	49866664	+	5'Flank	DEL	GAGT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49866661_49866664delGAGT	uc002pnj.2	-						TEAD2_uc002png.2_5'Flank|TEAD2_uc002pnh.2_5'Flank|TEAD2_uc002pni.2_5'Flank|TEAD2_uc010yao.1_5'Flank|TEAD2_uc010emw.2_5'Flank|DKKL1_uc002pnk.2_5'Flank	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)														---	---	---	---
ALDH16A1	126133	broad.mit.edu	37	19	49960366	49960367	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49960366_49960367delAA	uc002pnt.2	+						ALDH16A1_uc010yar.1_Intron|ALDH16A1_uc010yas.1_Intron|ALDH16A1_uc010yat.1_Intron	NM_153329	NP_699160			aldehyde dehydrogenase 16 family, member A1								oxidoreductase activity|protein binding			skin(1)	1		all_lung(116;5.39e-06)|Lung NSC(112;1.97e-05)|all_neural(266;0.0966)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00156)|GBM - Glioblastoma multiforme(486;0.0251)														---	---	---	---
NOSIP	51070	broad.mit.edu	37	19	50079394	50079394	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50079394delA	uc002pok.2	-						NOSIP_uc002pol.2_Intron|NOSIP_uc010yay.1_Intron	NM_015953	NP_057037			nitric oxide synthase interacting protein						negative regulation of nitric-oxide synthase activity|nitric oxide metabolic process	cytosol|nucleus	protein binding			skin(1)	1		all_lung(116;7.84e-06)|Lung NSC(112;2.8e-05)|all_neural(266;0.0966)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00321)|GBM - Glioblastoma multiforme(134;0.0133)														---	---	---	---
VRK3	51231	broad.mit.edu	37	19	50488237	50488238	+	Intron	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50488237_50488238delTG	uc002prg.2	-						VRK3_uc002prh.1_Intron|VRK3_uc002pri.1_Intron|VRK3_uc010ens.2_Intron|VRK3_uc010ybl.1_Intron|VRK3_uc010ybm.1_Intron|VRK3_uc002prj.1_Intron|VRK3_uc002prk.1_Intron	NM_016440	NP_057524			vaccinia related kinase 3 isoform 1							nucleus	ATP binding|protein kinase activity			stomach(1)|skin(1)	2		all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00166)|OV - Ovarian serous cystadenocarcinoma(262;0.00652)														---	---	---	---
MYH14	79784	broad.mit.edu	37	19	50806911	50806912	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50806911_50806912insT	uc002prr.1	+						MYH14_uc010enu.1_Intron|MYH14_uc002prq.1_Intron|MYH14_uc010ycb.1_Intron|MYH14_uc002prs.1_Intron	NM_024729	NP_079005			myosin, heavy chain 14 isoform 2						axon guidance|regulation of cell shape	myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			central_nervous_system(1)	1		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)														---	---	---	---
NAPSB	256236	broad.mit.edu	37	19	50847032	50847035	+	Intron	DEL	AAAC	-	-	rs138720423		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50847032_50847035delAAAC	uc002prw.2	-						NR1H2_uc002prv.3_Intron	NR_002798				Homo sapiens napsin B pseudogene, mRNA sequence.											central_nervous_system(1)	1																		---	---	---	---
NR1H2	7376	broad.mit.edu	37	19	50879050	50879050	+	5'Flank	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50879050delA	uc010enw.2	+						NR1H2_uc002prv.3_Intron|NR1H2_uc002prz.3_5'Flank|NR1H2_uc002psa.3_5'Flank	NM_007121	NP_009052			nuclear receptor subfamily 1, group H, member 2						negative regulation of cholesterol storage|negative regulation of interferon-gamma-mediated signaling pathway|negative regulation of lipid transport|negative regulation of pinocytosis|negative regulation of transcription, DNA-dependent|positive regulation of cellular protein metabolic process|positive regulation of cholesterol efflux|positive regulation of fatty acid biosynthetic process|positive regulation of lipoprotein lipase activity|positive regulation of transcription from RNA polymerase II promoter|positive regulation of triglyceride biosynthetic process|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	cytoplasm|nucleoplasm	sequence-specific DNA binding|steroid hormone receptor activity|zinc ion binding				0		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00757)|GBM - Glioblastoma multiforme(134;0.0186)														---	---	---	---
NR1H2	7376	broad.mit.edu	37	19	50880753	50880753	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50880753delA	uc010enw.2	+						NR1H2_uc002prv.3_Intron|NR1H2_uc002prz.3_Intron|NR1H2_uc002psa.3_Intron	NM_007121	NP_009052			nuclear receptor subfamily 1, group H, member 2						negative regulation of cholesterol storage|negative regulation of interferon-gamma-mediated signaling pathway|negative regulation of lipid transport|negative regulation of pinocytosis|negative regulation of transcription, DNA-dependent|positive regulation of cellular protein metabolic process|positive regulation of cholesterol efflux|positive regulation of fatty acid biosynthetic process|positive regulation of lipoprotein lipase activity|positive regulation of transcription from RNA polymerase II promoter|positive regulation of triglyceride biosynthetic process|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	cytoplasm|nucleoplasm	sequence-specific DNA binding|steroid hormone receptor activity|zinc ion binding				0		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00757)|GBM - Glioblastoma multiforme(134;0.0186)														---	---	---	---
MYBPC2	4606	broad.mit.edu	37	19	50962861	50962861	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50962861delG	uc002psf.2	+							NM_004533	NP_004524			myosin binding protein C, fast type						cell adhesion|muscle filament sliding	cytosol|myosin filament	actin binding|structural constituent of muscle			breast(1)	1		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.0079)|GBM - Glioblastoma multiforme(134;0.0144)														---	---	---	---
C19orf48	84798	broad.mit.edu	37	19	51302732	51302732	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51302732delG	uc002ptf.2	-						C19orf48_uc002pte.2_Intron|C19orf48_uc002ptg.2_Intron|SNORD88B_uc010eoc.1_5'Flank|SNORD88A_uc002pth.1_RNA	NM_199249	NP_954857			multidrug resistance-related protein											ovary(1)	1		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00531)|GBM - Glioblastoma multiforme(134;0.0145)														---	---	---	---
ETFB	2109	broad.mit.edu	37	19	51863274	51863274	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51863274delA	uc002pwh.2	-							NM_001985	NP_001976			electron-transfer-flavoprotein, beta polypeptide						respiratory electron transport chain|transport	mitochondrial matrix	electron carrier activity				0		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000226)|OV - Ovarian serous cystadenocarcinoma(262;0.00661)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	51973328	51973328	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51973328delT								SIGLEC8 (11620 upstream) : CEACAM18 (6510 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	52166483	52166483	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52166483delT								SIGLEC14 (16351 upstream) : MIR99B (29382 downstream)																																			---	---	---	---
ZNF766	90321	broad.mit.edu	37	19	52786701	52786703	+	Intron	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52786701_52786703delTTT	uc002pyr.1	+						ZNF766_uc002pys.1_Intron|ZNF766_uc002pyt.1_Intron	NM_001010851	NP_001010851			zinc finger protein 766						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				GBM - Glioblastoma multiforme(134;0.00236)|OV - Ovarian serous cystadenocarcinoma(262;0.00871)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	52796874	52796877	+	IGR	DEL	TTTG	-	-	rs112083187		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52796874_52796877delTTTG								ZNF766 (897 upstream) : ZNF480 (3549 downstream)																																			---	---	---	---
ZNF83	55769	broad.mit.edu	37	19	53151407	53151407	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53151407delT	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)														---	---	---	---
ZNF28	7576	broad.mit.edu	37	19	53323916	53323919	+	Intron	DEL	CTCA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53323916_53323919delCTCA	uc002qad.2	-						ZNF28_uc002qac.2_Intron|ZNF28_uc010eqe.2_Intron	NM_006969	NP_008900			zinc finger protein 28						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1				GBM - Glioblastoma multiforme(134;0.0386)|Lung(386;0.145)														---	---	---	---
ZNF320	162967	broad.mit.edu	37	19	53388538	53388538	+	Intron	DEL	A	-	-	rs149114517		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53388538delA	uc002qag.2	-						ZNF320_uc010eqi.1_Intron|ZNF320_uc002qah.2_Intron|ZNF320_uc002qai.2_Intron	NM_207333	NP_997216			zinc finger protein 320						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				GBM - Glioblastoma multiforme(134;0.0534)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	53526566	53526566	+	IGR	DEL	A	-	-	rs115744457	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53526566delA								ZNF702P (29782 upstream) : ZNF160 (43302 downstream)																																			---	---	---	---
ZNF347	84671	broad.mit.edu	37	19	53658197	53658197	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53658197delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	53733329	53733330	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53733329_53733330delTT								ZNF665 (36710 upstream) : ZNF677 (5308 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	53737573	53737573	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53737573delT								ZNF665 (40954 upstream) : ZNF677 (1065 downstream)																																			---	---	---	---
ZNF765	91661	broad.mit.edu	37	19	53878838	53878838	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53878838delA	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)														---	---	---	---
DPRX	503834	broad.mit.edu	37	19	54133904	54133904	+	5'Flank	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54133904delA	uc002qcf.1	+							NM_001012728	NP_001012746			divergent-paired related homeobox							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.013)														---	---	---	---
VSTM1	284415	broad.mit.edu	37	19	54547141	54547142	+	Intron	INS	-	GAGGGGAGAA	GAGGGGAGAA			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54547141_54547142insGAGGGGAGAA	uc002qcw.3	-						VSTM1_uc010erb.2_Intron|VSTM1_uc002qcx.3_Intron	NM_198481	NP_940883			V-set and transmembrane domain containing 1							integral to membrane					0	all_cancers(19;0.0128)|all_epithelial(19;0.00564)|all_lung(19;0.031)|Lung NSC(19;0.0358)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.165)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	54920169	54920170	+	IGR	INS	-	AAGG	AAGG	rs149859402	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54920169_54920170insAAGG								LAIR1 (38005 upstream) : TTYH1 (6465 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	55211511	55211512	+	IGR	INS	-	GT	GT	rs147726175	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55211511_55211512insGT								LILRB4 (31667 upstream) : LILRP2 (8089 downstream)																																			---	---	---	---
NLRP2	55655	broad.mit.edu	37	19	55479286	55479289	+	Intron	DEL	TTTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55479286_55479289delTTTT	uc002qij.2	+						NLRP7_uc010esl.2_5'Flank|NLRP2_uc010yfp.1_Intron|NLRP2_uc010esn.2_Intron|NLRP2_uc010eso.2_Intron|NLRP2_uc010esp.2_Intron	NM_017852	NP_060322			NLR family, pyrin domain containing 2						apoptosis|positive regulation of caspase activity|positive regulation of interleukin-1 beta secretion	cytoplasm	ATP binding|Pyrin domain binding			ovary(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(297;0.163)	GBM - Glioblastoma multiforme(193;0.028)														---	---	---	---
NLRP2	55655	broad.mit.edu	37	19	55505987	55505987	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55505987delT	uc002qij.2	+						NLRP2_uc010yfp.1_Intron|NLRP2_uc010esn.2_Intron|NLRP2_uc010eso.2_Intron|NLRP2_uc010esp.2_Intron	NM_017852	NP_060322			NLR family, pyrin domain containing 2						apoptosis|positive regulation of caspase activity|positive regulation of interleukin-1 beta secretion	cytoplasm	ATP binding|Pyrin domain binding			ovary(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(297;0.163)	GBM - Glioblastoma multiforme(193;0.028)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	55633620	55633620	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55633620delT								PPP1R12C (4693 upstream) : TNNT1 (10542 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	56582167	56582167	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56582167delT								NLRP5 (8995 upstream) : ZNF787 (16565 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	56999702	56999703	+	Intron	INS	-	T	T	rs140466729	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56999702_56999703insT	uc002qnf.2	+						uc002qng.2_Intron					Homo sapiens cDNA clone IMAGE:5753168.																														---	---	---	---
Unknown	0	broad.mit.edu	37	19	57221367	57221368	+	Intron	DEL	GT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57221367_57221368delGT	uc010ygp.1	+											Homo sapiens cDNA clone IMAGE:4793694.																														---	---	---	---
Unknown	0	broad.mit.edu	37	19	57240569	57240570	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57240569_57240570delAA	uc010ygp.1	+											Homo sapiens cDNA clone IMAGE:4793694.																														---	---	---	---
Unknown	0	broad.mit.edu	37	19	57556925	57556925	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57556925delA								MIMT1 (197003 upstream) : USP29 (74584 downstream)																																			---	---	---	---
ZNF264	9422	broad.mit.edu	37	19	57731580	57731580	+	3'UTR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57731580delT	uc002qob.2	+	4						NM_003417	NP_003408			zinc finger protein 264						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0135)														---	---	---	---
ZNF304	57343	broad.mit.edu	37	19	57864600	57864601	+	Intron	INS	-	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57864600_57864601insG	uc010ygw.1	+						ZNF304_uc010etw.2_Intron|ZNF304_uc010etx.2_Intron	NM_020657	NP_065708			zinc finger protein 304						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;0.0265)														---	---	---	---
ZNF547	284306	broad.mit.edu	37	19	58058212	58058212	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58058212delA	uc002qpm.3	+						ZNF549_uc010eud.1_Intron|ZNF550_uc002qpc.2_RNA|ZNF550_uc010eue.1_RNA|ZNF550_uc002qpd.2_RNA					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)														---	---	---	---
ZNF211	10520	broad.mit.edu	37	19	58144695	58144695	+	5'UTR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58144695delA	uc002qpq.2	+	1					ZNF211_uc010yhb.1_Intron|ZNF211_uc002qpp.2_5'UTR|ZNF211_uc002qpr.2_5'UTR|ZNF211_uc002qps.2_5'UTR|ZNF211_uc002qpt.2_5'UTR|ZNF211_uc010yhc.1_5'UTR|ZNF211_uc010yhd.1_Intron|ZNF211_uc010yhe.1_Intron	NM_198855	NP_942152			zinc finger protein 211 isoform 2							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)														---	---	---	---
ZNF776	284309	broad.mit.edu	37	19	58201812	58201813	+	Intron	DEL	TA	-	-	rs141081497		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58201812_58201813delTA	uc002qpx.2	+							NM_173632	NP_775903			zinc finger protein 776						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0256)														---	---	---	---
ZNF274	10782	broad.mit.edu	37	19	58723422	58723422	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58723422delA	uc002qrq.1	+						ZNF274_uc002qrr.1_Intron|ZNF274_uc002qrs.1_Intron|ZNF274_uc010eum.1_Intron	NM_133502	NP_598009			zinc finger protein 274 isoform c						viral reproduction	centrosome|nucleolus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			ovary(1)	1		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Ovarian(87;0.0443)|Breast(46;0.0889)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)|Lung(386;0.215)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	58936839	58936840	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58936839_58936840insT								ZNF584 (7149 upstream) : ZNF132 (7342 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	63549	63549	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:63549delT								None (None upstream) : DEFB125 (4802 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	298602	298603	+	IGR	INS	-	A	A	rs113919209		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:298602_298603insA								ZCCHC3 (17641 upstream) : SOX12 (7636 downstream)																																			---	---	---	---
RBCK1	10616	broad.mit.edu	37	20	390111	390114	+	Intron	DEL	TTTT	-	-	rs11475730		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:390111_390114delTTTT	uc002wdp.3	+						RBCK1_uc010zpl.1_Intron|RBCK1_uc010zpm.1_Intron|RBCK1_uc002wdq.3_Intron|RBCK1_uc010fzy.2_Intron|RBCK1_uc002wdr.3_Intron|RBCK1_uc002wdo.2_Intron	NM_031229	NP_112506			RanBP-type and C3HC4-type zinc finger containing						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)																---	---	---	---
RBCK1	10616	broad.mit.edu	37	20	399354	399354	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:399354delT	uc002wdp.3	+						RBCK1_uc010zpl.1_Intron|RBCK1_uc010zpm.1_Intron|RBCK1_uc002wdq.3_Intron|RBCK1_uc010fzy.2_Intron|RBCK1_uc002wdr.3_Intron	NM_031229	NP_112506			RanBP-type and C3HC4-type zinc finger containing						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)																---	---	---	---
RBCK1	10616	broad.mit.edu	37	20	405057	405058	+	Intron	INS	-	C	C	rs146810443	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:405057_405058insC	uc002wdp.3	+						RBCK1_uc010zpm.1_Intron|RBCK1_uc002wdq.3_Intron|RBCK1_uc010fzy.2_Intron|RBCK1_uc002wdr.3_Intron	NM_031229	NP_112506			RanBP-type and C3HC4-type zinc finger containing						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	541117	541117	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:541117delA								CSNK2A1 (16635 upstream) : TCF15 (43522 downstream)																																			---	---	---	---
SCRT2	85508	broad.mit.edu	37	20	654835	654836	+	Intron	DEL	CT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:654835_654836delCT	uc002wec.2	-						SRXN1_uc002web.2_Intron	NM_033129	NP_149120			scratch 2 protein						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	1078485	1078486	+	IGR	DEL	GA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1078485_1078486delGA								RSPO4 (95581 upstream) : PSMF1 (15420 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	1173752	1173752	+	IGR	DEL	A	-	-	rs112398472		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1173752delA								C20orf46 (8635 upstream) : C20orf202 (10346 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	1192938	1192938	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1192938delT								C20orf202 (4022 upstream) : RAD21L1 (13826 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	1510591	1510591	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1510591delT								SIRPB2 (38358 upstream) : SIRPD (4308 downstream)																																			---	---	---	---
SIRPA	140885	broad.mit.edu	37	20	1912066	1912066	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1912066delC	uc002wfq.2	+						SIRPA_uc010zps.1_Intron|SIRPA_uc002wfr.2_Intron|SIRPA_uc002wfs.2_Intron|SIRPA_uc002wft.2_Intron	NM_001040022	NP_001035111			signal-regulatory protein alpha precursor						blood coagulation|cell adhesion|cell junction assembly|leukocyte migration	integral to membrane|plasma membrane	SH3 domain binding			ovary(1)	1				Colorectal(46;0.018)|READ - Rectum adenocarcinoma(1;0.0556)														---	---	---	---
TGM3	7053	broad.mit.edu	37	20	2279457	2279458	+	Intron	DEL	CT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2279457_2279458delCT	uc002wfx.3	+							NM_003245	NP_003236			transglutaminase 3 precursor						cell envelope organization|hair follicle morphogenesis|keratinization|peptide cross-linking|protein tetramerization	cytoplasm|extrinsic to internal side of plasma membrane	acyltransferase activity|calcium ion binding|GDP binding|GTP binding|GTPase activity|magnesium ion binding|protein-glutamine gamma-glutamyltransferase activity			large_intestine(4)|ovary(3)|breast(1)|skin(1)	9					L-Glutamine(DB00130)													---	---	---	---
ZNF343	79175	broad.mit.edu	37	20	2504044	2504045	+	Intron	DEL	TT	-	-	rs6036830	byFrequency;by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2504044_2504045delTT	uc010gao.1	-							NM_024325	NP_077301			zinc finger protein 343						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
PTPRA	5786	broad.mit.edu	37	20	2925688	2925688	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2925688delT	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|PTPRA_uc002whn.2_Intron					SubName: Full=cDNA FLJ60525, highly similar to Receptor-type tyrosine-protein phosphatase alpha (EC 3.1.3.48);						axon guidance|protein phosphorylation	integral to plasma membrane	transmembrane receptor protein tyrosine phosphatase activity			upper_aerodigestive_tract(1)	1																		---	---	---	---
C20orf194	25943	broad.mit.edu	37	20	3263409	3263409	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3263409delC	uc002wii.2	-						C20orf194_uc002wij.3_Intron|C20orf194_uc002wik.2_Intron	NM_001009984	NP_001009984			hypothetical protein LOC25943												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	3444636	3444636	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3444636delA								C20orf194 (56049 upstream) : ATRN (7029 downstream)																																			---	---	---	---
ATRN	8455	broad.mit.edu	37	20	3520851	3520851	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3520851delT	uc002wim.2	+						ATRN_uc002wil.2_Intron	NM_139321	NP_647537			attractin isoform 1						inflammatory response	extracellular space|integral to plasma membrane	receptor activity|sugar binding			ovary(1)|breast(1)	2																		---	---	---	---
ATRN	8455	broad.mit.edu	37	20	3600801	3600801	+	Intron	DEL	T	-	-	rs147111966		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3600801delT	uc002wim.2	+							NM_139321	NP_647537			attractin isoform 1						inflammatory response	extracellular space|integral to plasma membrane	receptor activity|sugar binding			ovary(1)|breast(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	3705111	3705112	+	IGR	INS	-	AGAG	AGAG	rs138353743	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3705111_3705112insAGAG								SIGLEC1 (17336 upstream) : HSPA12B (8244 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	4008764	4008783	+	IGR	DEL	CTTCCTTCTTTCCTTCCTTC	-	-	rs71195879		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4008764_4008783delCTTCCTTCTTTCCTTCCTTC								RNF24 (12548 upstream) : SMOX (120667 downstream)																																			---	---	---	---
RASSF2	9770	broad.mit.edu	37	20	4798258	4798258	+	5'Flank	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4798258delA	uc002wld.2	-						RASSF2_uc002wle.2_Intron|RASSF2_uc002wlf.2_Intron	NM_170774	NP_739580			Ras association domain family 2						cell cycle|signal transduction	nucleus	protein binding			ovary(3)|lung(2)|large_intestine(1)	6																		---	---	---	---
SLC23A2	9962	broad.mit.edu	37	20	4853411	4853411	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4853411delT	uc002wlg.1	-						SLC23A2_uc010zqr.1_Intron|SLC23A2_uc002wlh.1_Intron|SLC23A2_uc002wli.2_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																		---	---	---	---
SLC23A2	9962	broad.mit.edu	37	20	4873717	4873719	+	Intron	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4873717_4873719delTTT	uc002wlg.1	-						SLC23A2_uc010zqr.1_Intron|SLC23A2_uc002wlh.1_Intron|SLC23A2_uc002wli.2_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	5215581	5215581	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5215581delT								CDS2 (43594 upstream) : PROKR2 (67106 downstream)																																			---	---	---	---
C20orf196	149840	broad.mit.edu	37	20	5784535	5784535	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5784535delA	uc002wmf.2	+							NM_152504	NP_689717			hypothetical protein LOC149840												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	5885206	5885207	+	IGR	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5885206_5885207delTG								C20orf196 (40650 upstream) : CHGB (6767 downstream)																																			---	---	---	---
CRLS1	54675	broad.mit.edu	37	20	5997614	5997614	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5997614delT	uc002wmn.3	+						CRLS1_uc010gbq.2_Intron|CRLS1_uc010gbr.2_Intron	NM_019095	NP_061968			cardiolipin synthase 1 isoform 1						phospholipid biosynthetic process	integral to membrane|mitochondrial inner membrane	phosphotransferase activity, for other substituted phosphate groups				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	6382520	6382520	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:6382520delT								FERMT1 (278329 upstream) : BMP2 (366225 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	6468165	6468165	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:6468165delA								FERMT1 (363974 upstream) : BMP2 (280580 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	7081435	7081437	+	IGR	DEL	AAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:7081435_7081437delAAA								BMP2 (320525 upstream) : HAO1 (782194 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	7115008	7115009	+	IGR	DEL	AA	-	-	rs11476305		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:7115008_7115009delAA								BMP2 (354098 upstream) : HAO1 (748622 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	7186921	7186922	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:7186921_7186922insT								BMP2 (426011 upstream) : HAO1 (676709 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	7434531	7434531	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:7434531delA								BMP2 (673621 upstream) : HAO1 (429100 downstream)																																			---	---	---	---
PLCB1	23236	broad.mit.edu	37	20	8099250	8099250	+	Intron	DEL	G	-	-	rs72323796		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:8099250delG	uc010zrb.1	+							NM_182734	NP_877398			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	8255129	8255129	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:8255129delT	uc002wnb.2	+						PLCB1_uc010zrb.1_Intron|PLCB1_uc010gbv.1_Intron|PLCB1_uc002wmz.1_Intron|PLCB1_uc002wna.2_Intron	NM_015192	NP_056007			phosphoinositide-specific phospholipase C beta 1						activation of meiosis involved in egg activation|CD24 biosynthetic process|cerebral cortex development|G1 phase|G2/M transition of mitotic cell cycle|glutamate signaling pathway|insulin-like growth factor receptor signaling pathway|interleukin-1-mediated signaling pathway|interleukin-12-mediated signaling pathway|interleukin-15-mediated signaling pathway|intracellular signal transduction|lipid catabolic process|memory|muscarinic acetylcholine receptor signaling pathway|negative regulation of monocyte extravasation|negative regulation of transcription, DNA-dependent|phosphatidylinositol metabolic process|positive regulation of acrosome reaction|positive regulation of developmental growth|positive regulation of embryonic development|positive regulation of interleukin-12 production|positive regulation of JNK cascade|positive regulation of myoblast differentiation|positive regulation of transcription, DNA-dependent|regulation of fertilization|regulation of G-protein coupled receptor protein signaling pathway|synaptic transmission	cytosol|nuclear chromatin|nuclear speck	calcium ion binding|calmodulin binding|enzyme binding|GTPase activator activity|phosphatidylinositol phospholipase C activity|phosphatidylinositol-4,5-bisphosphate binding|protein homodimerization activity|signal transducer activity			ovary(4)|breast(3)|upper_aerodigestive_tract(2)|skin(2)|lung(1)	12																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	9042357	9042358	+	IGR	INS	-	TTCT	TTCT	rs142004450	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9042357_9042358insTTCT								PLCB1 (176812 upstream) : PLCB4 (7343 downstream)																																			---	---	---	---
PLCB4	5332	broad.mit.edu	37	20	9384151	9384151	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9384151delA	uc002wnf.2	+						PLCB4_uc010gbw.1_Intron|PLCB4_uc010gbx.2_Intron|PLCB4_uc002wne.2_Intron|PLCB4_uc002wnh.2_Intron	NM_182797	NP_877949			phospholipase C beta 4 isoform b						intracellular signal transduction|lipid catabolic process	cytosol	calcium ion binding|phosphatidylinositol phospholipase C activity|protein binding|signal transducer activity			skin(11)|ovary(3)|pancreas(1)	15																		---	---	---	---
PAK7	57144	broad.mit.edu	37	20	9812163	9812163	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9812163delT	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	9947170	9947170	+	IGR	DEL	T	-	-	rs112851723		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9947170delT								PAK7 (127483 upstream) : ANKRD5 (68527 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	10341604	10341604	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10341604delG								SNAP25 (53539 upstream) : MKKS (44229 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	10676850	10676850	+	IGR	DEL	T	-	-	rs67862973		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10676850delT								JAG1 (22156 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	10969788	10969788	+	IGR	DEL	T	-	-	rs150698914		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10969788delT								JAG1 (315094 upstream) : BTBD3 (901689 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	11248228	11248228	+	RNA	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:11248228delT	uc002wnx.2	-	2		c.1350delA								Homo sapiens hypothetical protein LOC339593, mRNA (cDNA clone IMAGE:5166493), partial cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	20	11508170	11508171	+	IGR	DEL	AA	-	-	rs72426531		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:11508170_11508171delAA								JAG1 (853476 upstream) : BTBD3 (363306 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	11651899	11651900	+	IGR	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:11651899_11651900delTG								JAG1 (997205 upstream) : BTBD3 (219577 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	12830200	12830200	+	IGR	DEL	A	-	-	rs66896011		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:12830200delA								BTBD3 (922958 upstream) : SPTLC3 (159427 downstream)																																			---	---	---	---
ISM1	140862	broad.mit.edu	37	20	13269439	13269440	+	Intron	DEL	TT	-	-	rs66516088		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13269439_13269440delTT	uc010gce.1	+						TASP1_uc010zri.1_Intron	NM_080826	NP_543016			isthmin 1 homolog precursor							extracellular region					0																		---	---	---	---
TASP1	55617	broad.mit.edu	37	20	13345568	13345568	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13345568delT	uc010zri.1	-											Homo sapiens cDNA FLJ20212 fis, clone COLF1860.						asparagine catabolic process via L-aspartate|positive regulation of transcription, DNA-dependent|protein maturation		threonine-type endopeptidase activity				0																		---	---	---	---
TASP1	55617	broad.mit.edu	37	20	13364432	13364432	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13364432delA	uc010zri.1	-											Homo sapiens cDNA FLJ20212 fis, clone COLF1860.						asparagine catabolic process via L-aspartate|positive regulation of transcription, DNA-dependent|protein maturation		threonine-type endopeptidase activity				0																		---	---	---	---
TASP1	55617	broad.mit.edu	37	20	13530087	13530088	+	Intron	INS	-	TG	TG			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13530087_13530088insTG	uc002woi.2	-						TASP1_uc010zri.1_Intron|TASP1_uc002woh.2_Intron|TASP1_uc010zrj.1_Intron	NM_017714	NP_060184			taspase 1 precursor						asparagine catabolic process via L-aspartate|positive regulation of transcription, DNA-dependent|protein maturation		threonine-type endopeptidase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	13653193	13653193	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13653193delA								TASP1 (33610 upstream) : ESF1 (41777 downstream)																																			---	---	---	---
SEL1L2	80343	broad.mit.edu	37	20	13895708	13895708	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13895708delA	uc010gcf.2	-						SEL1L2_uc002woq.3_Intron|SEL1L2_uc010zrl.1_Intron|SEL1L2_uc002wor.2_Intron	NM_025229	NP_079505			sel-1 suppressor of lin-12-like 2 precursor							integral to membrane	binding			ovary(2)	2																		---	---	---	---
MACROD2	140733	broad.mit.edu	37	20	14321612	14321612	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:14321612delA	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	14369366	14369366	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:14369366delT	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	14441602	14441602	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:14441602delC	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	14566890	14566891	+	Intron	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:14566890_14566891delTG	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	14824843	14824843	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:14824843delT	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	14893303	14893303	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:14893303delG	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	15202657	15202657	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:15202657delG	uc002wou.2	+						MACROD2_uc002wot.2_Intron|MACROD2_uc002woz.2_Intron	NM_080676	NP_542407			MACRO domain containing 2 isoform 1												0		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)																---	---	---	---
MACROD2	140733	broad.mit.edu	37	20	15342655	15342658	+	Intron	DEL	TTTT	-	-	rs148365713		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:15342655_15342658delTTTT	uc002wou.2	+						MACROD2_uc002wot.2_Intron|MACROD2_uc002woz.2_Intron	NM_080676	NP_542407			MACRO domain containing 2 isoform 1												0		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)																---	---	---	---
MACROD2	140733	broad.mit.edu	37	20	15488034	15488035	+	Intron	INS	-	TCCT	TCCT	rs148622293	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:15488034_15488035insTCCT	uc002wou.2	+						MACROD2_uc002wot.2_Intron|MACROD2_uc002woz.2_Intron	NM_080676	NP_542407			MACRO domain containing 2 isoform 1												0		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)																---	---	---	---
MACROD2	140733	broad.mit.edu	37	20	15739361	15739362	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:15739361_15739362insT	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)																---	---	---	---
KIF16B	55614	broad.mit.edu	37	20	16261487	16261490	+	Intron	DEL	GTGT	-	-	rs71966852	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16261487_16261490delGTGT	uc002wpg.1	-						KIF16B_uc002wpe.1_Intron|KIF16B_uc002wpf.1_Intron|KIF16B_uc010gch.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																		---	---	---	---
KIF16B	55614	broad.mit.edu	37	20	16412388	16412388	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16412388delG	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																		---	---	---	---
KIF16B	55614	broad.mit.edu	37	20	16429892	16429892	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16429892delA	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																		---	---	---	---
KIF16B	55614	broad.mit.edu	37	20	16467897	16467897	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16467897delA	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																		---	---	---	---
KIF16B	55614	broad.mit.edu	37	20	16468817	16468817	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16468817delA	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	16775589	16775590	+	IGR	INS	-	T	T	rs111545202		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16775589_16775590insT								OTOR (42781 upstream) : PCSK2 (431162 downstream)																																			---	---	---	---
PCSK2	5126	broad.mit.edu	37	20	17299069	17299069	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17299069delA	uc002wpm.2	+						PCSK2_uc002wpl.2_Intron|PCSK2_uc010zrm.1_Intron	NM_002594	NP_002585			proprotein convertase subtilisin/kexin type 2						enkephalin processing|insulin processing|islet amyloid polypeptide processing	extracellular space|membrane|soluble fraction|transport vesicle	serine-type endopeptidase activity			ovary(3)|central_nervous_system(2)|large_intestine(1)|pancreas(1)	7					Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)													---	---	---	---
BFSP1	631	broad.mit.edu	37	20	17482822	17482823	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17482822_17482823delAA	uc002wpo.2	-						BFSP1_uc002wpp.2_Intron|BFSP1_uc010zrn.1_Intron|BFSP1_uc010zro.1_Intron	NM_001195	NP_001186			filensin isoform 1							cytoplasm|intermediate filament|membrane	structural constituent of cytoskeleton|structural constituent of eye lens			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	17730492	17730493	+	IGR	INS	-	T	T	rs144575212	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17730492_17730493insT								BANF2 (13975 upstream) : SNX5 (191753 downstream)																																			---	---	---	---
CSRP2BP	57325	broad.mit.edu	37	20	18156323	18156323	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18156323delT	uc002wqj.2	+						CSRP2BP_uc002wqk.2_Intron|CSRP2BP_uc010zru.1_Intron	NM_020536	NP_065397			CSRP2 binding protein						histone H3 acetylation	Ada2/Gcn5/Ada3 transcription activator complex|cytoplasm	LIM domain binding|N-acetyltransferase activity			lung(3)|ovary(2)|skin(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	18262356	18262356	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18262356delA								CSRP2BP (93341 upstream) : ZNF133 (6765 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	18303900	18303900	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18303900delA	uc002wqn.2	-											Homo sapiens cDNA clone IMAGE:5296922.																														---	---	---	---
RBBP9	10741	broad.mit.edu	37	20	18470643	18470643	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18470643delA	uc002wqy.2	-							NM_006606	NP_006597			retinoblastoma binding protein 9							cytoplasm|nucleus	hydrolase activity			haematopoietic_and_lymphoid_tissue(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	18913288	18913288	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18913288delT								C20orf79 (118255 upstream) : SLC24A3 (280002 downstream)																																			---	---	---	---
NAA20	51126	broad.mit.edu	37	20	20009306	20009307	+	Intron	INS	-	AT	AT			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20009306_20009307insAT	uc002wrp.2	+						NAA20_uc002wrq.2_Intron|NAA20_uc002wrr.2_Intron	NM_016100	NP_057184			N-acetyltransferase 5 isoform a							cytoplasm|nucleus	peptide alpha-N-acetyltransferase activity				0																		---	---	---	---
CRNKL1	51340	broad.mit.edu	37	20	20017073	20017073	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20017073delT	uc002wrs.2	-							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	20046261	20046262	+	Intron	DEL	AA	-	-	rs146412705		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20046261_20046262delAA	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	20102579	20102579	+	Intron	DEL	T	-	-	rs74931934		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20102579delT	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	20220605	20220605	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20220605delA	uc002wru.2	+						C20orf26_uc010zse.1_Intron|C20orf26_uc002wrw.2_Intron|C20orf26_uc002wrv.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	20343894	20343894	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20343894delG								C20orf26 (2545 upstream) : INSM1 (4871 downstream)																																			---	---	---	---
RALGAPA2	57186	broad.mit.edu	37	20	20498706	20498706	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20498706delT	uc002wrz.2	-						RALGAPA2_uc010gcx.2_Intron|RALGAPA2_uc010zsg.1_Intron|RALGAPA2_uc002wsa.1_Intron	NM_020343	NP_065076			akt substrate AS250						activation of Ral GTPase activity	cytosol|nucleus	protein heterodimerization activity|Ral GTPase activator activity			ovary(1)	1																		---	---	---	---
RALGAPA2	57186	broad.mit.edu	37	20	20527127	20527129	+	Intron	DEL	ATG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20527127_20527129delATG	uc002wrz.2	-						RALGAPA2_uc010gcx.2_Intron|RALGAPA2_uc010zsg.1_Intron	NM_020343	NP_065076			akt substrate AS250						activation of Ral GTPase activity	cytosol|nucleus	protein heterodimerization activity|Ral GTPase activator activity			ovary(1)	1																		---	---	---	---
PLK1S1	55857	broad.mit.edu	37	20	21187948	21187948	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21187948delT	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	21880812	21880812	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21880812delG								PAX1 (184192 upstream) : LOC284788 (500159 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	22339917	22339917	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:22339917delA								PAX1 (643297 upstream) : LOC284788 (41054 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	22350311	22350311	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:22350311delT								PAX1 (653691 upstream) : LOC284788 (30660 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	22472367	22472368	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:22472367_22472368delTT								LOC284788 (71086 upstream) : C20orf56 (68826 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	22781881	22781881	+	IGR	DEL	T	-	-	rs79836617		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:22781881delT								FOXA2 (215780 upstream) : SSTR4 (234176 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	22994898	22994898	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:22994898delA	uc002wsq.1	-											Homo sapiens cDNA clone IMAGE:5271939.																														---	---	---	---
Unknown	0	broad.mit.edu	37	20	23438749	23438750	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23438749_23438750delAA								CST11 (5267 upstream) : CST8 (33016 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	23832616	23832616	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23832616delT								CST2 (25304 upstream) : CST5 (23956 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	24416222	24416229	+	IGR	DEL	TGTGTGTG	-	-	rs66472844		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:24416222_24416229delTGTGTGTG								GGTLC1 (446806 upstream) : TMEM90B (33606 downstream)																																			---	---	---	---
TMEM90B	79953	broad.mit.edu	37	20	24634889	24634890	+	Intron	DEL	AA	-	-	rs72149664		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:24634889_24634890delAA	uc002wtw.1	+							NM_024893	NP_079169			transmembrane protein 90B						response to biotic stimulus	early endosome membrane|integral to membrane|plasma membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	25158911	25158913	+	IGR	DEL	GAG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25158911_25158913delGAG								LOC284798 (29485 upstream) : ENTPD6 (17426 downstream)																																			---	---	---	---
PYGB	5834	broad.mit.edu	37	20	25270292	25270292	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25270292delA	uc002wup.2	+						uc010gdm.1_5'Flank	NM_002862	NP_002853			brain glycogen phosphorylase						glucose metabolic process|glycogen catabolic process	cytoplasm	glycogen phosphorylase activity|pyridoxal phosphate binding			central_nervous_system(1)|skin(1)	2					Pyridoxal Phosphate(DB00114)													---	---	---	---
ABHD12	26090	broad.mit.edu	37	20	25282736	25282737	+	Intron	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25282736_25282737delTG	uc002wus.1	-						ABHD12_uc002wuq.2_Intron|ABHD12_uc002wur.2_Intron|ABHD12_uc002wut.1_Intron|ABHD12_uc002wuu.1_Intron	NM_001042472	NP_001035937			abhydrolase domain containing 12 isoform a							integral to membrane	acylglycerol lipase activity			skin(1)	1																		---	---	---	---
NANP	140838	broad.mit.edu	37	20	25595619	25595620	+	3'UTR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25595619_25595620delAA	uc002wuy.2	-	2						NM_152667	NP_689880			N-acetylneuraminic acid phosphatase						N-acetylneuraminate biosynthetic process		N-acylneuraminate-9-phosphatase activity|phosphoglycolate phosphatase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	25867976	25867976	+	IGR	DEL	G	-	-	rs111513763		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25867976delG								FAM182B (19190 upstream) : LOC100134868 (122459 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	25912775	25912775	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25912775delT								FAM182B (63989 upstream) : LOC100134868 (77660 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	25968471	25968472	+	IGR	DEL	CT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25968471_25968472delCT								FAM182B (119685 upstream) : LOC100134868 (21963 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	25977318	25977319	+	IGR	DEL	CA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25977318_25977319delCA								FAM182B (128532 upstream) : LOC100134868 (13116 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	26141744	26141745	+	IGR	DEL	AG	-	-	rs75593323		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26141744_26141745delAG								C20orf191 (47067 upstream) : MIR663 (47077 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	26142245	26142250	+	IGR	DEL	TTTTCT	-	-	rs75244022		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26142245_26142250delTTTTCT								C20orf191 (47568 upstream) : MIR663 (46572 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	26142535	26142536	+	IGR	INS	-	T	T	rs112408405		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26142535_26142536insT								C20orf191 (47858 upstream) : MIR663 (46286 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	26145851	26145851	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26145851delA								C20orf191 (51174 upstream) : MIR663 (42971 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	26213033	26213036	+	IGR	DEL	AAGA	-	-	rs139976989		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26213033_26213036delAAGA								MIR663 (24119 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	26252429	26252430	+	IGR	DEL	TA	-	-	rs148238331	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26252429_26252430delTA								MIR663 (63515 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	29421541	29421542	+	IGR	DEL	TT	-	-	rs113835826		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29421541_29421542delTT								None (None upstream) : FRG1B (190337 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	29429611	29429611	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29429611delG								None (None upstream) : FRG1B (182268 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	29453483	29453484	+	IGR	INS	-	CTGT	CTGT	rs149191907	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29453483_29453484insCTGT								None (None upstream) : FRG1B (158395 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	29583616	29583617	+	IGR	INS	-	A	A	rs147019354		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29583616_29583617insA								None (None upstream) : FRG1B (28262 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	29588739	29588740	+	IGR	INS	-	C	C	rs149163760		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29588739_29588740insC								None (None upstream) : FRG1B (23139 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	29930733	29930733	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29930733delT								DEFB116 (34345 upstream) : DEFB118 (25695 downstream)																																			---	---	---	---
BCL2L1	598	broad.mit.edu	37	20	30277240	30277241	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30277240_30277241delAA	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)															---	---	---	---
TPX2	22974	broad.mit.edu	37	20	30352764	30352764	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30352764delT	uc002wwp.1	+						TPX2_uc010gdv.1_Intron	NM_012112	NP_036244			TPX2, microtubule-associated protein homolog						activation of protein kinase activity|apoptosis|cell division|cell proliferation|mitosis|regulation of mitotic spindle organization	cytoplasm|microtubule|nucleus|spindle pole	ATP binding|GTP binding|protein kinase binding			large_intestine(1)|ovary(1)	2			Epithelial(4;0.000771)|Colorectal(19;0.00306)|all cancers(5;0.004)|COAD - Colon adenocarcinoma(19;0.0347)|OV - Ovarian serous cystadenocarcinoma(3;0.0656)															---	---	---	---
TPX2	22974	broad.mit.edu	37	20	30364331	30364332	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30364331_30364332delTT	uc002wwp.1	+						TPX2_uc010gdv.1_Intron	NM_012112	NP_036244			TPX2, microtubule-associated protein homolog						activation of protein kinase activity|apoptosis|cell division|cell proliferation|mitosis|regulation of mitotic spindle organization	cytoplasm|microtubule|nucleus|spindle pole	ATP binding|GTP binding|protein kinase binding			large_intestine(1)|ovary(1)	2			Epithelial(4;0.000771)|Colorectal(19;0.00306)|all cancers(5;0.004)|COAD - Colon adenocarcinoma(19;0.0347)|OV - Ovarian serous cystadenocarcinoma(3;0.0656)															---	---	---	---
TTLL9	164395	broad.mit.edu	37	20	30462850	30462853	+	Intron	DEL	TTTG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30462850_30462853delTTTG	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)															---	---	---	---
XKR7	343702	broad.mit.edu	37	20	30579257	30579257	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30579257delC	uc002wxe.2	+							NM_001011718	NP_001011718			XK, Kell blood group complex subunit-related							integral to membrane				ovary(1)|breast(1)|skin(1)	3			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)															---	---	---	---
TM9SF4	9777	broad.mit.edu	37	20	30720342	30720344	+	Intron	DEL	GAG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30720342_30720344delGAG	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	30775152	30775152	+	IGR	DEL	A	-	-	rs113899517		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30775152delA								TM9SF4 (20091 upstream) : TSPYL3 (1797 downstream)																																			---	---	---	---
ASXL1	171023	broad.mit.edu	37	20	30972658	30972658	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30972658delT	uc002wxs.2	+						ASXL1_uc002wxr.1_Intron|ASXL1_uc010geb.2_Intron	NM_015338	NP_056153			additional sex combs like 1 isoform 1						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	PR-DUB complex	metal ion binding|protein binding			haematopoietic_and_lymphoid_tissue(239)|large_intestine(6)|central_nervous_system(2)|ovary(1)	248								F|N|Mis		MDS|CMML								---	---	---	---
Unknown	0	broad.mit.edu	37	20	31613530	31613545	+	IGR	DEL	TCCGTCCGTCCGTCCG	-	-	rs71842653	by1000genomes;by1000genomes;by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31613530_31613545delTCCGTCCGTCCGTCCG								BPIL1 (2016 upstream) : BPIL3 (5909 downstream)																																			---	---	---	---
C20orf185	359710	broad.mit.edu	37	20	31659294	31659295	+	Intron	DEL	GA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31659294_31659295delGA	uc002wym.1	+							NM_182658	NP_872599			antimicrobial peptide RYA3 precursor						innate immune response	cytoplasm|extracellular region	lipid binding|protein binding			ovary(4)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	31776104	31776104	+	IGR	DEL	T	-	-	rs67745079		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31776104delT								C20orf70 (6881 upstream) : BASE (5307 downstream)																																			---	---	---	---
CDK5RAP1	51654	broad.mit.edu	37	20	31956944	31956945	+	Intron	INS	-	A	A	rs74721387		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31956944_31956945insA	uc010gek.2	-						CDK5RAP1_uc002wyy.2_Intron|CDK5RAP1_uc002wyz.2_Intron|CDK5RAP1_uc002wza.2_Intron|CDK5RAP1_uc010gel.2_Intron|CDK5RAP1_uc010gem.2_Intron|CDK5RAP1_uc002wzc.1_Intron|CDK5RAP1_uc002wzb.1_Intron	NM_016408	NP_057492			CDK5 regulatory subunit associated protein 1						brain development|negative regulation of cyclin-dependent protein kinase activity|regulation of neuron differentiation|tRNA modification	cytoplasm	4 iron, 4 sulfur cluster binding|metal ion binding|neuronal Cdc2-like kinase binding|transferase activity			ovary(2)|skin(2)|lung(1)	5																		---	---	---	---
CBFA2T2	9139	broad.mit.edu	37	20	32211761	32211763	+	Intron	DEL	AAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32211761_32211763delAAA	uc002wzg.1	+						CBFA2T2_uc010zug.1_Intron|CBFA2T2_uc002wze.1_Intron|CBFA2T2_uc002wzf.1_Intron|CBFA2T2_uc002wzh.1_Intron|CBFA2T2_uc002wzi.1_Intron|CBFA2T2_uc002wzj.1_Intron	NM_005093	NP_005084			core-binding factor, runt domain, alpha subunit							nucleus	protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			pancreas(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	32312579	32312580	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32312579_32312580delTT								PXMP4 (4443 upstream) : ZNF341 (7228 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	32468681	32468681	+	IGR	DEL	T	-	-	rs140749264		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32468681delT								CHMP4B (26512 upstream) : RALY (113051 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	32534757	32534758	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32534757_32534758insT								CHMP4B (92588 upstream) : RALY (46974 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	32534862	32534868	+	IGR	DEL	TTTTTTT	-	-	rs138131919		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32534862_32534868delTTTTTTT								CHMP4B (92693 upstream) : RALY (46864 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	32857443	32857443	+	IGR	DEL	A	-	-	rs61652884	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32857443delA								ASIP (295 upstream) : AHCY (10630 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	32933748	32933748	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32933748delA								AHCY (34140 upstream) : ITCH (17314 downstream)																																			---	---	---	---
ITCH	83737	broad.mit.edu	37	20	32988345	32988345	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32988345delA	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																		---	---	---	---
GGT7	2686	broad.mit.edu	37	20	33458589	33458590	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33458589_33458590insT	uc002xay.2	-						GGT7_uc002xaz.1_Intron|GGT7_uc002xba.1_Intron	NM_178026	NP_821158			gamma-glutamyltransferase 7						glutathione biosynthetic process	integral to membrane	acyltransferase activity|gamma-glutamyltransferase activity			ovary(1)	1																		---	---	---	---
TRPC4AP	26133	broad.mit.edu	37	20	33669159	33669159	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33669159delA	uc002xbk.2	-						TRPC4AP_uc002xbl.2_Intron|TRPC4AP_uc010zur.1_Intron|TRPC4AP_uc002xbm.1_Intron	NM_015638	NP_056453			TRPC4-associated protein isoform a						protein ubiquitination|ubiquitin-dependent protein catabolic process	Cul4A-RING ubiquitin ligase complex	protein binding			central_nervous_system(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(18;0.00936)															---	---	---	---
TRPC4AP	26133	broad.mit.edu	37	20	33672072	33672073	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33672072_33672073delAA	uc002xbk.2	-						TRPC4AP_uc002xbl.2_Intron|TRPC4AP_uc010zur.1_Intron|TRPC4AP_uc002xbm.1_Intron	NM_015638	NP_056453			TRPC4-associated protein isoform a						protein ubiquitination|ubiquitin-dependent protein catabolic process	Cul4A-RING ubiquitin ligase complex	protein binding			central_nervous_system(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(18;0.00936)															---	---	---	---
EDEM2	55741	broad.mit.edu	37	20	33736028	33736028	+	5'Flank	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33736028delT	uc002xbo.2	-						EDEM2_uc010zuv.1_Intron|EDEM2_uc002xbq.2_5'Flank|EDEM2_uc010zut.1_5'Flank|EDEM2_uc002xbp.2_5'Flank|EDEM2_uc002xbn.2_5'Flank|EDEM2_uc002xbr.2_5'Flank|EDEM2_uc010zuu.1_5'Flank	NM_018217	NP_060687			ER degradation enhancer, mannosidase alpha-like						post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine|response to unfolded protein	endoplasmic reticulum lumen|endoplasmic reticulum membrane|extracellular region	calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity|misfolded protein binding				0			BRCA - Breast invasive adenocarcinoma(18;0.00936)															---	---	---	---
GDF5	8200	broad.mit.edu	37	20	33935201	33935201	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33935201delT	uc010gfc.1	-						UQCC_uc010zuy.1_Intron|UQCC_uc002xcd.2_Intron|UQCC_uc010zuz.1_Intron|UQCC_uc010zva.1_Intron|UQCC_uc002xce.2_Intron|UQCC_uc002xcg.2_Intron|UQCC_uc010gfb.2_Intron|UQCC_uc010zvb.1_Intron|UQCC_uc002xcf.2_Intron|UQCC_uc002xci.1_Intron|UQCC_uc010gfd.1_Intron	NM_000557	NP_000548			growth differentiation factor 5 preproprotein						cartilage development|cell-cell signaling|growth|transforming growth factor beta receptor signaling pathway	extracellular space	cytokine activity|growth factor activity				0	Lung NSC(9;0.00642)|all_lung(11;0.0094)		BRCA - Breast invasive adenocarcinoma(18;0.00663)															---	---	---	---
GDF5	8200	broad.mit.edu	37	20	33969913	33969913	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33969913delT	uc010gfc.1	-						UQCC_uc010zuy.1_Intron|UQCC_uc002xcd.2_Intron|UQCC_uc010zuz.1_Intron|UQCC_uc010zva.1_Intron|UQCC_uc002xce.2_Intron|UQCC_uc002xcg.2_Intron|UQCC_uc010gfb.2_Intron|UQCC_uc010zvb.1_Intron|UQCC_uc002xcf.2_Intron|UQCC_uc002xci.1_Intron|UQCC_uc010gfd.1_Intron	NM_000557	NP_000548			growth differentiation factor 5 preproprotein						cartilage development|cell-cell signaling|growth|transforming growth factor beta receptor signaling pathway	extracellular space	cytokine activity|growth factor activity				0	Lung NSC(9;0.00642)|all_lung(11;0.0094)		BRCA - Breast invasive adenocarcinoma(18;0.00663)															---	---	---	---
C20orf173	140873	broad.mit.edu	37	20	34113381	34113381	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34113381delA	uc010gff.2	-							NM_001145350				hypothetical protein LOC140873												0																		---	---	---	---
FER1L4	80307	broad.mit.edu	37	20	34180575	34180575	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34180575delG	uc002xcy.3	-							NR_024377				Homo sapiens clone PP3795 unknown mRNA.												0																		---	---	---	---
NFS1	9054	broad.mit.edu	37	20	34284029	34284029	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34284029delA	uc002xdw.1	-						NFS1_uc002xdt.1_Intron|NFS1_uc002xdu.1_Intron|NFS1_uc002xdv.1_Intron|NFS1_uc010zvk.1_Intron|NFS1_uc010zvl.1_Intron|NFS1_uc002xdx.2_Intron	NM_021100	NP_066923			NFS1 nitrogen fixation 1 precursor						cysteine metabolic process|iron incorporation into metallo-sulfur cluster|Mo-molybdopterin cofactor biosynthetic process|protein complex assembly|water-soluble vitamin metabolic process	cytosol|mitochondrial matrix|nucleus	cysteine desulfurase activity|protein homodimerization activity|pyridoxal phosphate binding			ovary(1)|skin(1)	2	Lung NSC(9;0.00608)|all_lung(11;0.00918)		BRCA - Breast invasive adenocarcinoma(18;0.0886)		L-Alanine(DB00160)|L-Cysteine(DB00151)|Pyridoxal Phosphate(DB00114)													---	---	---	---
PHF20	51230	broad.mit.edu	37	20	34435403	34435403	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34435403delG	uc002xek.1	+						PHF20_uc002xei.1_Intron|PHF20_uc010gfo.1_Intron|PHF20_uc002xej.1_Intron|PHF20_uc002xel.1_Intron	NM_016436	NP_057520			PHD finger protein 20						regulation of transcription, DNA-dependent|transcription, DNA-dependent	MLL1 complex	DNA binding|zinc ion binding			ovary(1)	1	Breast(12;0.00631)|all_lung(11;0.0145)																	---	---	---	---
EPB41L1	2036	broad.mit.edu	37	20	34779621	34779621	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34779621delG	uc002xfb.2	+						EPB41L1_uc002xeu.2_Intron|EPB41L1_uc010zvo.1_Intron|EPB41L1_uc002xev.2_Intron|EPB41L1_uc002xew.2_Intron|EPB41L1_uc002xex.2_Intron|EPB41L1_uc002xey.2_Intron|EPB41L1_uc002xez.2_Intron	NM_012156	NP_036288			erythrocyte membrane protein band 4.1-like 1						cortical actin cytoskeleton organization|synaptic transmission	cytoskeleton|cytosol|extrinsic to membrane|plasma membrane	actin binding|structural molecule activity			ovary(2)|pancreas(1)	3	Breast(12;0.0239)																	---	---	---	---
Unknown	0	broad.mit.edu	37	20	34882036	34882039	+	IGR	DEL	TTTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34882036_34882039delTTTT								C20orf4 (23196 upstream) : DLGAP4 (12264 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	35189744	35189745	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35189744_35189745delAA	uc002xfk.3	-											Homo sapiens, clone IMAGE:5165100, mRNA.																														---	---	---	---
SLA2	84174	broad.mit.edu	37	20	35257128	35257129	+	Intron	DEL	TT	-	-	rs116535713	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35257128_35257129delTT	uc002xfv.2	-						SLA2_uc002xfu.2_Intron	NM_032214	NP_115590			Src-like-adaptor 2 isoform a						antigen receptor-mediated signaling pathway|B cell mediated immunity|intracellular receptor mediated signaling pathway|negative regulation of B cell activation|negative regulation of calcium-mediated signaling|negative regulation of transcription from RNA polymerase II promoter|T cell activation	cytoplasmic membrane-bounded vesicle|endosome membrane|plasma membrane	protein N-terminus binding|SH3/SH2 adaptor activity				0	Breast(12;0.114)	Myeloproliferative disorder(115;0.00878)																---	---	---	---
NDRG3	57446	broad.mit.edu	37	20	35288834	35288834	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35288834delA	uc002xfw.2	-						NDRG3_uc002xfx.2_Intron|NDRG3_uc010zvq.1_Intron|NDRG3_uc010zvr.1_Intron	NM_032013	NP_114402			N-myc downstream regulated gene 3 isoform a						cell differentiation|negative regulation of cell growth|spermatogenesis	cytoplasm				ovary(1)	1		Myeloproliferative disorder(115;0.00878)																---	---	---	---
C20orf117	140710	broad.mit.edu	37	20	35473414	35473417	+	Intron	DEL	AAAA	-	-	rs67403323		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35473414_35473417delAAAA	uc002xgd.1	-							NM_199181	NP_954650			hypothetical protein LOC140710 isoform 2												0		Myeloproliferative disorder(115;0.00874)																---	---	---	---
Unknown	0	broad.mit.edu	37	20	35498846	35498846	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35498846delA								C20orf117 (10570 upstream) : C20orf118 (5724 downstream)																																			---	---	---	---
RPN2	6185	broad.mit.edu	37	20	35861473	35861473	+	Intron	DEL	A	-	-	rs4810452	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35861473delA	uc002xgp.2	+						RPN2_uc002xgq.2_Intron	NM_002951	NP_002942			ribophorin II isoform 1 precursor						post-translational protein modification|protein N-linked glycosylation via asparagine	integral to membrane|nucleus|oligosaccharyltransferase complex	dolichyl-diphosphooligosaccharide-protein glycotransferase activity|protein binding			ovary(2)|skin(1)	3		Myeloproliferative disorder(115;0.00878)																---	---	---	---
CTNNBL1	56259	broad.mit.edu	37	20	36484603	36484603	+	Intron	DEL	A	-	-	rs72145244		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36484603delA	uc010zvw.1	+						CTNNBL1_uc002xhh.2_Intron|CTNNBL1_uc002xhi.2_Intron|CTNNBL1_uc002xhj.2_Intron	NM_030877	NP_110517			beta catenin-like 1						apoptosis|positive regulation of apoptosis|somatic diversification of immunoglobulins	nucleus	enzyme binding			ovary(2)	2		Myeloproliferative disorder(115;0.00878)																---	---	---	---
KIAA0406	9675	broad.mit.edu	37	20	36625458	36625458	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36625458delA	uc002xhl.2	-						KIAA0406_uc002xhm.2_Intron	NM_014657	NP_055472			hypothetical protein LOC9675								binding				0		Myeloproliferative disorder(115;0.00874)																---	---	---	---
RPRD1B	58490	broad.mit.edu	37	20	36683853	36683854	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36683853_36683854delTT	uc002xho.3	+							NM_021215	NP_067038			Regulation of nuclear pre-mRNA domain containing											pancreas(1)	1																		---	---	---	---
RALGAPB	57148	broad.mit.edu	37	20	37108627	37108629	+	Intron	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37108627_37108629delTTT	uc002xiw.2	+						RALGAPB_uc010zvz.1_Intron|RALGAPB_uc002xix.2_Intron	NM_020336	NP_065069			Ral GTPase activating protein, beta subunit						activation of Ral GTPase activity	intracellular	protein heterodimerization activity|Ral GTPase activator activity			pancreas(1)|skin(1)	2																		---	---	---	---
RALGAPB	57148	broad.mit.edu	37	20	37169993	37169993	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37169993delT	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																		---	---	---	---
RALGAPB	57148	broad.mit.edu	37	20	37183732	37183732	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37183732delA	uc002xiw.2	+						RALGAPB_uc002xix.2_Intron|RALGAPB_uc002xiy.1_Intron|RALGAPB_uc002xiz.2_Intron	NM_020336	NP_065069			Ral GTPase activating protein, beta subunit						activation of Ral GTPase activity	intracellular	protein heterodimerization activity|Ral GTPase activator activity			pancreas(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	37281795	37281797	+	IGR	DEL	ATG	-	-	rs112245163		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37281795_37281797delATG								ADIG (64691 upstream) : SLC32A1 (71308 downstream)																																			---	---	---	---
ACTR5	79913	broad.mit.edu	37	20	37389489	37389489	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37389489delT	uc002xjd.2	+							NM_024855	NP_079131			ARP5 actin-related protein 5 homolog						DNA recombination|double-strand break repair|regulation of transcription, DNA-dependent|transcription, DNA-dependent|UV-damage excision repair	cytoplasm|Ino80 complex	ATP binding|protein binding				0		Myeloproliferative disorder(115;0.00878)																---	---	---	---
PPP1R16B	26051	broad.mit.edu	37	20	37520868	37520868	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37520868delT	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	37698663	37698663	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37698663delG								DHX35 (30300 upstream) : LOC339568 (143761 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	37704682	37704682	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37704682delT								DHX35 (36319 upstream) : LOC339568 (137742 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	37740367	37740380	+	IGR	DEL	GGGAGGAGGAAAAG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37740367_37740380delGGGAGGAGGAAAAG								DHX35 (72004 upstream) : LOC339568 (102044 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	37841871	37841871	+	IGR	DEL	T	-	-	rs73622065		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37841871delT								DHX35 (173508 upstream) : LOC339568 (553 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	38702213	38702215	+	IGR	DEL	TTT	-	-	rs11476728		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:38702213_38702215delTTT								LOC339568 (848822 upstream) : MAFB (612304 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	39764986	39764986	+	Intron	DEL	G	-	-	rs35990648		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39764986delG	uc002xjn.1	-						PLCG1_uc002xjo.1_5'Flank|PLCG1_uc002xjp.1_5'Flank					Homo sapiens cDNA clone IMAGE:5260583.																														---	---	---	---
CHD6	84181	broad.mit.edu	37	20	40045114	40045114	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40045114delA	uc002xka.1	-						CHD6_uc002xjz.1_5'Flank	NM_032221	NP_115597			chromodomain helicase DNA binding protein 6						chromatin remodeling|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding			ovary(6)|skin(5)|lung(2)|central_nervous_system(1)	14		Myeloproliferative disorder(115;0.00425)																---	---	---	---
Unknown	0	broad.mit.edu	37	20	40336943	40336943	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40336943delT								CHD6 (89810 upstream) : PTPRT (364450 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	40603434	40603434	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40603434delG								CHD6 (356301 upstream) : PTPRT (97959 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	40668721	40668721	+	IGR	DEL	C	-	-	rs6029940	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40668721delC								CHD6 (421588 upstream) : PTPRT (32672 downstream)																																			---	---	---	---
PTPRT	11122	broad.mit.edu	37	20	40747539	40747539	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40747539delG	uc002xkg.2	-						PTPRT_uc010ggj.2_Intron|PTPRT_uc010ggi.2_Intron	NM_007050	NP_008981			protein tyrosine phosphatase, receptor type, T						homophilic cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway	cell surface|integral to membrane|plasma membrane	alpha-catenin binding|beta-catenin binding|cadherin binding|delta-catenin binding|gamma-catenin binding|protein tyrosine phosphatase activity|receptor activity			skin(8)|ovary(7)|lung(5)	20		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)																---	---	---	---
PTPRT	11122	broad.mit.edu	37	20	40767754	40767755	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40767754_40767755insT	uc002xkg.2	-						PTPRT_uc010ggj.2_Intron|PTPRT_uc010ggi.2_Intron	NM_007050	NP_008981			protein tyrosine phosphatase, receptor type, T						homophilic cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway	cell surface|integral to membrane|plasma membrane	alpha-catenin binding|beta-catenin binding|cadherin binding|delta-catenin binding|gamma-catenin binding|protein tyrosine phosphatase activity|receptor activity			skin(8)|ovary(7)|lung(5)	20		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)																---	---	---	---
PTPRT	11122	broad.mit.edu	37	20	40930102	40930102	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40930102delT	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	40934268	40934269	+	Intron	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40934268_40934269delTG	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	40979754	40979755	+	Intron	DEL	TT	-	-	rs147817365		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40979754_40979755delTT	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	41625880	41625880	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:41625880delC	uc002xkg.2	-						PTPRT_uc010ggj.2_Intron	NM_007050	NP_008981			protein tyrosine phosphatase, receptor type, T						homophilic cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway	cell surface|integral to membrane|plasma membrane	alpha-catenin binding|beta-catenin binding|cadherin binding|delta-catenin binding|gamma-catenin binding|protein tyrosine phosphatase activity|receptor activity			skin(8)|ovary(7)|lung(5)	20		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)																---	---	---	---
Unknown	0	broad.mit.edu	37	20	42043712	42043713	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42043712_42043713delAA								PTPRT (225155 upstream) : SFRS6 (42791 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	42127535	42127536	+	IGR	DEL	AA	-	-	rs76634015		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42127535_42127536delAA								SFRS6 (35293 upstream) : L3MBTL (8814 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	42477603	42477603	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42477603delT								GTSF1L (121961 upstream) : TOX2 (65889 downstream)																																			---	---	---	---
TTPAL	79183	broad.mit.edu	37	20	43104740	43104741	+	Intron	INS	-	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43104740_43104741insG	uc002xmc.1	+						TTPAL_uc002xmd.1_Intron	NM_024331	NP_077307			tocopherol (alpha) transfer protein-like							intracellular	transporter activity			breast(1)	1																		---	---	---	---
WISP2	8839	broad.mit.edu	37	20	43343738	43343739	+	5'UTR	DEL	CA	-	-	rs35689383		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43343738_43343739delCA	uc002xmn.2	+	1					uc002xml.1_Intron|uc002xmm.1_Intron|WISP2_uc002xmo.1_5'Flank|WISP2_uc002xmp.2_5'Flank|WISP2_uc002xmq.2_5'Flank	NM_003881	NP_003872			WNT1 inducible signaling pathway protein 2						cell adhesion|cell-cell signaling|signal transduction	extracellular region|soluble fraction	insulin-like growth factor binding			skin(1)	1		Myeloproliferative disorder(115;0.0122)																---	---	---	---
Unknown	0	broad.mit.edu	37	20	43714776	43714776	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43714776delA								STK4 (6185 upstream) : KCNS1 (6175 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	43910273	43910274	+	IGR	INS	-	A	A	rs77395668		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43910273_43910274insA								SLPI (27067 upstream) : MATN4 (11813 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	44624529	44624532	+	IGR	DEL	CTTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44624529_44624532delCTTT								ZNF335 (23696 upstream) : MMP9 (13015 downstream)																																			---	---	---	---
CDH22	64405	broad.mit.edu	37	20	44894669	44894670	+	Intron	DEL	TC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44894669_44894670delTC	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)																---	---	---	---
ELMO2	63916	broad.mit.edu	37	20	45007640	45007640	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45007640delT	uc002xrt.1	-						ELMO2_uc010zxq.1_5'Flank|ELMO2_uc002xrs.1_Intron|ELMO2_uc002xru.1_Intron|ELMO2_uc010zxr.1_Intron|ELMO2_uc010zxs.1_Intron|ELMO2_uc002xrw.2_Intron|ELMO2_uc002xrx.1_Intron	NM_133171	NP_573403			engulfment and cell motility 2						apoptosis|cell chemotaxis|phagocytosis	cytoskeleton|cytosol|membrane	lyase activity|receptor tyrosine kinase binding|SH3 domain binding			ovary(1)	1		Myeloproliferative disorder(115;0.0122)																---	---	---	---
ELMO2	63916	broad.mit.edu	37	20	45060180	45060181	+	Intron	DEL	CA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45060180_45060181delCA	uc010zxs.1	-						uc002xry.2_Intron					SubName: Full=ELMO2 protein; SubName: Full=Engulfment and cell motility 2;						apoptosis|cell chemotaxis|phagocytosis	cytoskeleton|cytosol|membrane	lyase activity|receptor tyrosine kinase binding|SH3 domain binding			ovary(1)	1		Myeloproliferative disorder(115;0.0122)																---	---	---	---
SLC13A3	64849	broad.mit.edu	37	20	45308253	45308254	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45308253_45308254delAA	uc002xsg.1	-						SLC13A3_uc010gho.1_Intron	NM_001011554	NP_001011554			solute carrier family 13 member 3 isoform b							integral to membrane|plasma membrane	high affinity sodium:dicarboxylate symporter activity			ovary(1)	1		Myeloproliferative disorder(115;0.0122)			Succinic acid(DB00139)													---	---	---	---
ZMYND8	23613	broad.mit.edu	37	20	45967173	45967174	+	Intron	DEL	AA	-	-	rs67835508		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45967173_45967174delAA	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_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)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	46030963	46030964	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46030963_46030964delAA								ZMYND8 (45489 upstream) : NCOA3 (99693 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	46042399	46042401	+	IGR	DEL	AAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46042399_46042401delAAA								ZMYND8 (56925 upstream) : NCOA3 (88256 downstream)																																			---	---	---	---
NCOA3	8202	broad.mit.edu	37	20	46191283	46191284	+	Intron	DEL	TT	-	-	rs75850932		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46191283_46191284delTT	uc002xtk.2	+						NCOA3_uc010ght.1_Intron|NCOA3_uc002xtl.2_Intron|NCOA3_uc002xtm.2_Intron|NCOA3_uc002xtn.2_Intron	NM_181659	NP_858045			nuclear receptor coactivator 3 isoform a						androgen receptor signaling pathway|cellular lipid metabolic process|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleoplasm	androgen receptor binding|histone acetyltransferase activity|ligand-dependent nuclear receptor binding|protein N-terminus binding|signal transducer activity|thyroid hormone receptor binding			ovary(3)|lung(1)|skin(1)	5																		---	---	---	---
NCOA3	8202	broad.mit.edu	37	20	46281062	46281063	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46281062_46281063delAA	uc002xtk.2	+						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																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	46494022	46494022	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46494022delG								SULF2 (78662 upstream) : LOC284749 (494632 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	46576760	46576760	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46576760delA								SULF2 (161400 upstream) : LOC284749 (411894 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	46601328	46601328	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46601328delT								SULF2 (185968 upstream) : LOC284749 (387326 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	46757846	46757849	+	IGR	DEL	AAAA	-	-	rs11364717		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46757846_46757849delAAAA								SULF2 (342486 upstream) : LOC284749 (230805 downstream)																																			---	---	---	---
PREX1	57580	broad.mit.edu	37	20	47293920	47293921	+	Intron	INS	-	G	G	rs148772668	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47293920_47293921insG	uc002xtw.1	-							NM_020820	NP_065871			phosphatidylinositol-3,4,						actin filament polymerization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|neutrophil activation|small GTPase mediated signal transduction|superoxide metabolic process	cytosol|plasma membrane	enzyme binding|phospholipid binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|ovary(2)|pancreas(1)	6			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)															---	---	---	---
CSE1L	1434	broad.mit.edu	37	20	47674643	47674643	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47674643delT	uc002xty.2	+						CSE1L_uc010zyg.1_Intron|CSE1L_uc010ghx.2_5'Flank	NM_001316	NP_001307			CSE1 chromosome segregation 1-like protein						apoptosis|cell proliferation|intracellular protein transport	cytoplasm|nucleus	importin-alpha export receptor activity			large_intestine(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(12;0.000491)|Colorectal(8;0.198)															---	---	---	---
CSE1L	1434	broad.mit.edu	37	20	47676417	47676417	+	Intron	DEL	A	-	-	rs111872809		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47676417delA	uc002xty.2	+						CSE1L_uc010zyg.1_Intron|CSE1L_uc010ghx.2_Intron	NM_001316	NP_001307			CSE1 chromosome segregation 1-like protein						apoptosis|cell proliferation|intracellular protein transport	cytoplasm|nucleus	importin-alpha export receptor activity			large_intestine(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(12;0.000491)|Colorectal(8;0.198)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	47817138	47817138	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47817138delA								STAU1 (11850 upstream) : DDX27 (18694 downstream)																																			---	---	---	---
DDX27	55661	broad.mit.edu	37	20	47838273	47838273	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47838273delA	uc002xuh.2	+							NM_017895	NP_060365			DEAD (Asp-Glu-Ala-Asp) box polypeptide 27							nucleus	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			kidney(2)	2			BRCA - Breast invasive adenocarcinoma(12;0.000899)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)															---	---	---	---
DDX27	55661	broad.mit.edu	37	20	47840583	47840583	+	Intron	DEL	T	-	-	rs79452818		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47840583delT	uc002xuh.2	+							NM_017895	NP_060365			DEAD (Asp-Glu-Ala-Asp) box polypeptide 27							nucleus	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			kidney(2)	2			BRCA - Breast invasive adenocarcinoma(12;0.000899)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)															---	---	---	---
B4GALT5	9334	broad.mit.edu	37	20	48252783	48252783	+	3'UTR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48252783delA	uc002xuu.3	-	9						NM_004776	NP_004767			UDP-Gal:betaGlcNAc beta 1,4-						post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi cisterna membrane|integral to membrane	galactosyltransferase activity|metal ion binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(9;2.51e-06)															---	---	---	---
B4GALT5	9334	broad.mit.edu	37	20	48289090	48289093	+	Intron	DEL	GACA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48289090_48289093delGACA	uc002xuu.3	-							NM_004776	NP_004767			UDP-Gal:betaGlcNAc beta 1,4-						post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi cisterna membrane|integral to membrane	galactosyltransferase activity|metal ion binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(9;2.51e-06)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	48584081	48584081	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48584081delA								RNF114 (13661 upstream) : SNAI1 (15446 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	48584999	48585000	+	IGR	DEL	GA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48584999_48585000delGA								RNF114 (14579 upstream) : SNAI1 (14527 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	48678461	48678462	+	IGR	INS	-	T	T	rs146790269	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48678461_48678462insT								SNAI1 (73043 upstream) : TMEM189-UBE2V1 (19201 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	48976468	48976468	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48976468delA								CEBPB (167256 upstream) : PTPN1 (150423 downstream)																																			---	---	---	---
FAM65C	140876	broad.mit.edu	37	20	49259283	49259283	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49259283delA	uc010zyt.1	-						FAM65C_uc010zyu.1_Intron	NM_080829	NP_543019			hypothetical protein LOC140876											ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	49664338	49664339	+	IGR	INS	-	TTT	TTT	rs146898252	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49664338_49664339insTTT								KCNG1 (24663 upstream) : NFATC2 (343427 downstream)																																			---	---	---	---
ATP9A	10079	broad.mit.edu	37	20	50349919	50349919	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50349919delT	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	50399314	50399314	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50399314delA								ATP9A (14406 upstream) : SALL4 (1271 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	50482669	50482669	+	IGR	DEL	T	-	-	rs7344657		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50482669delT								SALL4 (63621 upstream) : ZFP64 (217882 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	50632140	50632141	+	IGR	INS	-	TA	TA	rs151267588	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50632140_50632141insTA								SALL4 (213092 upstream) : ZFP64 (68410 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	50883089	50883089	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50883089delT								ZFP64 (74565 upstream) : TSHZ2 (705788 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	51022944	51022944	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51022944delT								ZFP64 (214420 upstream) : TSHZ2 (565933 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	51185532	51185532	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51185532delT								ZFP64 (377008 upstream) : TSHZ2 (403345 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	51488667	51488668	+	IGR	DEL	CA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51488667_51488668delCA								ZFP64 (680143 upstream) : TSHZ2 (100209 downstream)																																			---	---	---	---
TSHZ2	128553	broad.mit.edu	37	20	52032362	52032363	+	Intron	DEL	CA	-	-	rs73625474		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52032362_52032363delCA	uc002xwo.2	+						uc002xwp.1_Intron	NM_173485	NP_775756			teashirt zinc finger homeobox 2						multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|haematopoietic_and_lymphoid_tissue(1)	6			STAD - Stomach adenocarcinoma(23;0.1)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	52138579	52138586	+	IGR	DEL	GAAGGAGG	-	-	rs74179204		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52138579_52138586delGAAGGAGG								TSHZ2 (34614 upstream) : ZNF217 (45026 downstream)																																			---	---	---	---
ZNF217	7764	broad.mit.edu	37	20	52211455	52211455	+	5'Flank	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52211455delT	uc010gij.1	-							NM_006526	NP_006517			zinc finger protein 217						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	52558356	52558357	+	IGR	DEL	AC	-	-	rs34045663		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52558356_52558357delAC								SUMO1P1 (66108 upstream) : BCAS1 (1722 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	52999960	52999960	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52999960delT								PFDN4 (163469 upstream) : DOK5 (92297 downstream)																																			---	---	---	---
DOK5	55816	broad.mit.edu	37	20	53260332	53260332	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:53260332delG	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	54422339	54422339	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:54422339delT								None (None upstream) : CBLN4 (150158 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	54528351	54528351	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:54528351delA								None (None upstream) : CBLN4 (44146 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	54875470	54875470	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:54875470delG								MC3R (50599 upstream) : C20orf108 (58513 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	55449774	55449775	+	IGR	INS	-	AG	AG	rs139223336	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55449774_55449775insAG								TFAP2C (235438 upstream) : BMP7 (294034 downstream)																																			---	---	---	---
BMP7	655	broad.mit.edu	37	20	55748105	55748105	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55748105delT	uc010gip.1	-						BMP7_uc010giq.1_Intron|BMP7_uc002xyc.2_3'UTR	NM_001719	NP_001710			bone morphogenetic protein 7 precursor						BMP signaling pathway|cartilage development|cellular response to hypoxia|epithelial to mesenchymal transition|growth|mesonephros development|negative regulation of glomerular mesangial cell proliferation|negative regulation of MAP kinase activity|negative regulation of mitosis|negative regulation of neuron differentiation|negative regulation of NF-kappaB import into nucleus|negative regulation of NF-kappaB transcription factor activity|negative regulation of phosphorylation|negative regulation of striated muscle cell apoptosis|negative regulation of transcription, DNA-dependent|ossification|pathway-restricted SMAD protein phosphorylation|positive regulation of bone mineralization|positive regulation of osteoblast differentiation|positive regulation of pathway-restricted SMAD protein phosphorylation|protein localization to nucleus|regulation of removal of superoxide radicals|SMAD protein signal transduction|steroid hormone mediated signaling pathway|ureteric bud development	extracellular space	cytokine activity|growth factor activity			skin(1)	1	all_lung(29;0.0133)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(4;2.49e-13)|Epithelial(14;1.74e-08)|all cancers(14;2.05e-07)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	56358736	56358736	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56358736delC								PMEPA1 (72195 upstream) : C20orf85 (367247 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	56469595	56469596	+	IGR	INS	-	AGGAAGGGAGGA	AGGAAGGGAGGA	rs148209557	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56469595_56469596insAGGAAGGGAGGA								PMEPA1 (183054 upstream) : C20orf85 (256387 downstream)																																			---	---	---	---
PPP4R1L	55370	broad.mit.edu	37	20	56835701	56835701	+	Intron	DEL	T	-	-	rs10710910		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56835701delT	uc002xyy.1	-						PPP4R1L_uc010gjn.1_Intron					SubName: Full=cDNA FLJ50842, moderately similar to Serine/threonine-protein phosphatase 4regulatory subunit 1;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	57154449	57154449	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57154449delA	uc002xzg.1	+											Homo sapiens cDNA FLJ30075 fis, clone BGGI11000285.																														---	---	---	---
GNAS	2778	broad.mit.edu	37	20	57447591	57447591	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57447591delT	uc002xzw.2	+						GNAS_uc002xzt.2_Intron|GNAS_uc002xzu.3_Intron|GNAS_uc010gjq.2_Intron|GNAS_uc002xzv.2_Intron	NM_080425	NP_536350			GNAS complex locus XLas						activation of adenylate cyclase activity|cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|intracellular transport|platelet activation|regulation of insulin secretion|sensory perception of smell|transmembrane transport|water transport	heterotrimeric G-protein complex|intrinsic to membrane|trans-Golgi network membrane	adenylate cyclase activity|GTP binding|GTPase activity|guanyl-nucleotide exchange factor activity|identical protein binding|signal transducer activity			pituitary(201)|thyroid(35)|ovary(15)|adrenal_gland(9)|liver(7)|large_intestine(5)|parathyroid(5)|kidney(5)|haematopoietic_and_lymphoid_tissue(3)|lung(2)|testis(1)|stomach(1)|small_intestine(1)|autonomic_ganglia(1)|pancreas(1)	292	all_lung(29;0.0104)		BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109)					Mis		pituitary adenoma		McCune-Albright syndrome; pseudohypoparathyroidism|type IA		3-Methylglutaconic_Aciduria_and_Myelodysplasia|McCune-Albright_syndrome|Mazabraud_syndrome	TSP Lung(22;0.16)			---	---	---	---
TUBB1	81027	broad.mit.edu	37	20	57598532	57598532	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57598532delT	uc002yak.2	+							NM_030773	NP_110400			beta tubulin 1, class VI						'de novo' posttranslational protein folding|microtubule-based movement|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity			ovary(1)	1	all_lung(29;0.00711)		Colorectal(105;0.109)		Colchicine(DB01394)|Docetaxel(DB01248)|Paclitaxel(DB01229)|Vindesine(DB00309)													---	---	---	---
TUBB1	81027	broad.mit.edu	37	20	57598688	57598688	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57598688delG	uc002yak.2	+							NM_030773	NP_110400			beta tubulin 1, class VI						'de novo' posttranslational protein folding|microtubule-based movement|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity			ovary(1)	1	all_lung(29;0.00711)		Colorectal(105;0.109)		Colchicine(DB01394)|Docetaxel(DB01248)|Paclitaxel(DB01229)|Vindesine(DB00309)													---	---	---	---
Unknown	0	broad.mit.edu	37	20	57849926	57849926	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57849926delT								ZNF831 (15761 upstream) : EDN3 (25573 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	58140845	58140846	+	IGR	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58140845_58140846delAC								EDN3 (239799 upstream) : PHACTR3 (11718 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	58143149	58143150	+	IGR	DEL	GT	-	-	rs147026973	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58143149_58143150delGT								EDN3 (242103 upstream) : PHACTR3 (9414 downstream)																																			---	---	---	---
PHACTR3	116154	broad.mit.edu	37	20	58257416	58257416	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58257416delA	uc002yau.2	+						PHACTR3_uc002yat.2_Intron|PHACTR3_uc010zzw.1_Intron|PHACTR3_uc002yav.2_Intron	NM_080672	NP_542403			phosphatase and actin regulator 3 isoform 1							nuclear matrix	actin binding|protein phosphatase inhibitor activity			ovary(2)|pancreas(1)	3	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;2.76e-09)															---	---	---	---
PHACTR3	116154	broad.mit.edu	37	20	58261778	58261780	+	Intron	DEL	TTA	-	-	rs7409727		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58261778_58261780delTTA	uc002yau.2	+						PHACTR3_uc002yat.2_Intron|PHACTR3_uc010zzw.1_Intron|PHACTR3_uc002yav.2_Intron	NM_080672	NP_542403			phosphatase and actin regulator 3 isoform 1							nuclear matrix	actin binding|protein phosphatase inhibitor activity			ovary(2)|pancreas(1)	3	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;2.76e-09)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	59205609	59205609	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59205609delT	uc010gjw.1	+											Homo sapiens cDNA FLJ35486 fis, clone SMINT2008491.																														---	---	---	---
Unknown	0	broad.mit.edu	37	20	59477028	59477029	+	IGR	DEL	CT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59477028_59477029delCT								MIR646 (593403 upstream) : CDH4 (350530 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	59532740	59532748	+	IGR	DEL	CCCTGGAGG	-	-	rs71906649		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59532740_59532748delCCCTGGAGG								MIR646 (649115 upstream) : CDH4 (294811 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	59767379	59767379	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59767379delT								MIR646 (883754 upstream) : CDH4 (60180 downstream)																																			---	---	---	---
CDH4	1002	broad.mit.edu	37	20	59919280	59919280	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59919280delT	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	59925770	59925771	+	Intron	DEL	CC	-	-	rs10534860		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59925770_59925771delCC	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	60557699	60557700	+	Intron	INS	-	A	A	rs147634297	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60557699_60557700insA	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)															---	---	---	---
LAMA5	3911	broad.mit.edu	37	20	60916348	60916348	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60916348delA	uc002ycq.2	-							NM_005560	NP_005551			laminin alpha 5 precursor						angiogenesis|cell proliferation|cell recognition|cytoskeleton organization|endothelial cell differentiation|focal adhesion assembly|integrin-mediated signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-11 complex	integrin binding			ovary(1)|pancreas(1)|skin(1)	3	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)		Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
Unknown	0	broad.mit.edu	37	20	61177950	61177950	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61177950delC								C20orf166 (9980 upstream) : SLCO4A1 (95847 downstream)																																			---	---	---	---
C20orf20	55257	broad.mit.edu	37	20	61425672	61425677	+	5'Flank	DEL	GAGGCA	-	-	rs74264393		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61425672_61425677delGAGGCA	uc002ydi.2	+							NM_018270	NP_060740			MRG-binding protein						chromatin modification|regulation of growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	H4/H2A histone acetyltransferase complex					0	Breast(26;3.65e-08)																	---	---	---	---
TCFL5	10732	broad.mit.edu	37	20	61491080	61491080	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61491080delT	uc002ydp.2	-						TCFL5_uc002ydo.2_Intron|TCFL5_uc002ydq.2_Intron	NM_006602	NP_006593			transcription factor-like 5 protein						cell differentiation|multicellular organismal development|regulation of cell differentiation|regulation of cell proliferation|spermatogenesis|transcription from RNA polymerase II promoter		DNA binding|sequence-specific DNA binding transcription factor activity			large_intestine(1)	1	Breast(26;5.68e-08)																	---	---	---	---
KCNQ2	3785	broad.mit.edu	37	20	62055336	62055336	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62055336delG	uc002yey.1	-						KCNQ2_uc002yez.1_Intron|KCNQ2_uc002yfa.1_Intron|KCNQ2_uc002yfb.1_Intron|KCNQ2_uc011aax.1_3'UTR	NM_172107	NP_742105			potassium voltage-gated channel KQT-like protein						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)													---	---	---	---
RTEL1	51750	broad.mit.edu	37	20	62288493	62288494	+	5'Flank	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62288493_62288494insA	uc002yfu.1	+						RTEL1_uc011abc.1_5'Flank|RTEL1_uc002yft.1_5'Flank|RTEL1_uc011abd.1_5'Flank|RTEL1_uc002yfv.2_5'Flank|RTEL1_uc011abe.1_5'Flank|RTEL1_uc002yfw.2_5'Flank	NM_016434	NP_057518			regulator of telomere elongation helicase 1						DNA repair|regulation of double-strand break repair via homologous recombination|telomere maintenance	nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding|iron-sulfur cluster binding|metal ion binding				0	all_cancers(38;6.47e-12)|all_epithelial(29;3.75e-13)		Epithelial(9;1.25e-09)|all cancers(9;5.13e-09)|BRCA - Breast invasive adenocarcinoma(10;7.26e-05)|OV - Ovarian serous cystadenocarcinoma(5;0.00223)|Colorectal(105;0.107)															---	---	---	---
ZBTB46	140685	broad.mit.edu	37	20	62433773	62433773	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62433773delA	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)																	---	---	---	---
ZBTB46	140685	broad.mit.edu	37	20	62441315	62441315	+	Intron	DEL	A	-	-	rs72442208		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62441315delA	uc002ygu.2	-						uc002ygw.2_Intron	NM_025224				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)																	---	---	---	---
PRPF6	24148	broad.mit.edu	37	20	62625036	62625037	+	Intron	INS	-	G	G	rs138342962	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62625036_62625037insG	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)																	---	---	---	---
MYT1	4661	broad.mit.edu	37	20	62799760	62799760	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62799760delT	uc002yii.2	+						MYT1_uc002yih.2_Intron	NM_004535	NP_004526			myelin transcription factor 1						cell differentiation|nervous system development	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2	all_cancers(38;1.82e-11)|all_epithelial(29;3.3e-13)|Lung NSC(23;5.21e-10)|all_lung(23;1.92e-09)																	---	---	---	---
Unknown	0	broad.mit.edu	37	21	9476416	9476416	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9476416delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	10409966	10409966	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10409966delA								None (None upstream) : TPTE (496777 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	10415826	10415826	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10415826delT								None (None upstream) : TPTE (490917 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	10583485	10583485	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10583485delT	uc011abv.1	-											Homo sapiens cDNA, FLJ18615.																														---	---	---	---
Unknown	0	broad.mit.edu	37	21	10607791	10607791	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10607791delT								None (None upstream) : TPTE (298952 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	10626449	10626449	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10626449delA								None (None upstream) : TPTE (280294 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	10782298	10782312	+	IGR	DEL	TGGAATGGAATTGAA	-	-	rs111968915		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10782298_10782312delTGGAATGGAATTGAA								None (None upstream) : TPTE (124431 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	10806893	10806922	+	IGR	DEL	AATGGAATGGACTCGAATGGAATGGACTCG	-	-	rs55638432		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10806893_10806922delAATGGAATGGACTCGAATGGAATGGACTCG								None (None upstream) : TPTE (99821 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	10858073	10858077	+	IGR	DEL	AATGT	-	-	rs60527052		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10858073_10858077delAATGT								None (None upstream) : TPTE (48666 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	10873042	10873044	+	IGR	DEL	TTG	-	-	rs111484177		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10873042_10873044delTTG								None (None upstream) : TPTE (33699 downstream)																																			---	---	---	---
BAGE2	85319	broad.mit.edu	37	21	11037537	11037537	+	Intron	DEL	T	-	-	rs57142183		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11037537delT	uc002yit.1	-						TPTE_uc002yis.1_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	14381877	14381878	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14381877_14381878insT								None (None upstream) : C21orf99 (28609 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	14612928	14612928	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14612928delG								C21orf99 (122359 upstream) : POTED (369570 downstream)																																			---	---	---	---
ABCC13	150000	broad.mit.edu	37	21	15680961	15680961	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:15680961delT	uc002yjs.2	+											Homo sapiens ATP-binding cassette protein C13 (ABCC13) mRNA, complete cds.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	16445270	16445271	+	IGR	DEL	TG	-	-	rs139828992		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:16445270_16445271delTG								NRIP1 (8144 upstream) : USP25 (657225 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	16470417	16470417	+	IGR	DEL	T	-	-	rs5842514		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:16470417delT								NRIP1 (33291 upstream) : USP25 (632079 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	16719209	16719209	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:16719209delA								NRIP1 (282083 upstream) : USP25 (383287 downstream)																																			---	---	---	---
USP25	29761	broad.mit.edu	37	21	17124548	17124548	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:17124548delT	uc002yjy.1	+						USP25_uc011aby.1_Intron|USP25_uc002yjz.1_Intron|USP25_uc010gla.1_Intron	NM_013396	NP_037528			ubiquitin specific peptidase 25						protein modification process|ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(3)|liver(2)	5				Epithelial(23;7.55e-05)|all cancers(11;0.000429)|COAD - Colon adenocarcinoma(22;0.00543)|OV - Ovarian serous cystadenocarcinoma(11;0.00743)|Colorectal(24;0.0116)|Lung(58;0.0853)|LUSC - Lung squamous cell carcinoma(23;0.0889)														---	---	---	---
USP25	29761	broad.mit.edu	37	21	17171033	17171033	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:17171033delT	uc002yjy.1	+						USP25_uc011aby.1_Intron|USP25_uc002yjz.1_Intron|USP25_uc010gla.1_Intron	NM_013396	NP_037528			ubiquitin specific peptidase 25						protein modification process|ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(3)|liver(2)	5				Epithelial(23;7.55e-05)|all cancers(11;0.000429)|COAD - Colon adenocarcinoma(22;0.00543)|OV - Ovarian serous cystadenocarcinoma(11;0.00743)|Colorectal(24;0.0116)|Lung(58;0.0853)|LUSC - Lung squamous cell carcinoma(23;0.0889)														---	---	---	---
USP25	29761	broad.mit.edu	37	21	17250089	17250089	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:17250089delT	uc002yjy.1	+						USP25_uc011aby.1_Intron|USP25_uc002yjz.1_Intron|USP25_uc010gla.1_Intron	NM_013396	NP_037528			ubiquitin specific peptidase 25						protein modification process|ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(3)|liver(2)	5				Epithelial(23;7.55e-05)|all cancers(11;0.000429)|COAD - Colon adenocarcinoma(22;0.00543)|OV - Ovarian serous cystadenocarcinoma(11;0.00743)|Colorectal(24;0.0116)|Lung(58;0.0853)|LUSC - Lung squamous cell carcinoma(23;0.0889)														---	---	---	---
Unknown	0	broad.mit.edu	37	21	18165269	18165269	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:18165269delT								C21orf34 (183175 upstream) : CXADR (720061 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	18191985	18191985	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:18191985delA								C21orf34 (209891 upstream) : CXADR (693345 downstream)																																			---	---	---	---
NCRNA00157	54075	broad.mit.edu	37	21	19254403	19254403	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:19254403delA	uc011aca.1	-							NR_024354				Homo sapiens non-protein coding RNA 157 (NCRNA00157), non-coding RNA.												0																		---	---	---	---
CHODL	140578	broad.mit.edu	37	21	19384983	19384983	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:19384983delA	uc002ykt.2	+						CHODL_uc002ykr.2_Intron|CHODL_uc002yks.2_Intron|CHODL_uc002yku.2_Intron					RecName: Full=Chondrolectin; AltName: Full=Transmembrane protein MT75; Flags: Precursor;						muscle organ development	integral to membrane|perinuclear region of cytoplasm	sugar binding			upper_aerodigestive_tract(1)	1		all_epithelial(11;0.21)		Epithelial(23;0.000191)|all cancers(11;0.000827)|LUSC - Lung squamous cell carcinoma(23;0.00646)|Lung(58;0.0129)|OV - Ovarian serous cystadenocarcinoma(11;0.017)|COAD - Colon adenocarcinoma(22;0.03)|Colorectal(24;0.0917)														---	---	---	---
Unknown	0	broad.mit.edu	37	21	20214333	20214333	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:20214333delA								TMPRSS15 (438363 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	20811098	20811099	+	IGR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:20811098_20811099insA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	20895832	20895832	+	IGR	DEL	T	-	-	rs71780776		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:20895832delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	21762521	21762521	+	IGR	DEL	A	-	-	rs113862959		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:21762521delA								None (None upstream) : C21orf131 (352393 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	22041164	22041164	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:22041164delT								None (None upstream) : C21orf131 (73750 downstream)																																			---	---	---	---
C21orf131	387486	broad.mit.edu	37	21	22170720	22170720	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:22170720delC	uc002ykz.3	-						C21orf131_uc002yky.3_Intron|C21orf131_uc002yla.3_Intron|C21orf131_uc002ylb.3_Intron|C21orf131_uc002ylc.3_Intron	NR_024090				Homo sapiens cDNA FLJ37207 fis, clone BRALZ2007576.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	23129247	23129248	+	Intron	INS	-	A	A	rs144467690	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:23129247_23129248insA	uc002yle.2	+											Homo sapiens, clone IMAGE:5547749, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	21	23129253	23129254	+	Intron	INS	-	G	G	rs59536780		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:23129253_23129254insG	uc002yle.2	+											Homo sapiens, clone IMAGE:5547749, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	21	23988243	23988245	+	IGR	DEL	AAA	-	-	rs112269699		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:23988243_23988245delAAA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	24948742	24948742	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:24948742delC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	25972423	25972424	+	IGR	INS	-	A	A	rs140572633	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:25972423_25972424insA								None (None upstream) : NCRNA00158 (785710 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	26036727	26036727	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:26036727delT								None (None upstream) : NCRNA00158 (721407 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	26355246	26355246	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:26355246delT								None (None upstream) : NCRNA00158 (402888 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	26366802	26366805	+	IGR	DEL	AAAA	-	-	rs112906253		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:26366802_26366805delAAAA								None (None upstream) : NCRNA00158 (391329 downstream)																																			---	---	---	---
NCRNA00158	54072	broad.mit.edu	37	21	26802950	26802953	+	Intron	DEL	TTTT	-	-	rs76814316		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:26802950_26802953delTTTT	uc002ylk.2	-						NCRNA00158_uc010glg.2_Intron	NR_024027				Homo sapiens C21orf42 protein mRNA, complete cds, alternatively spliced.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	26998585	26998585	+	IGR	DEL	A	-	-	rs112353023		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:26998585delA								MRPL39 (18784 upstream) : JAM2 (13004 downstream)																																			---	---	---	---
APP	351	broad.mit.edu	37	21	27482045	27482046	+	Intron	DEL	TG	-	-	rs139590528	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27482045_27482046delTG	uc002ylz.2	-						APP_uc010glk.2_Intron|APP_uc002yma.2_Intron|APP_uc011ach.1_Intron|APP_uc002ymb.2_Intron|APP_uc010glj.2_Intron|APP_uc011aci.1_Intron|APP_uc011acj.1_Intron	NM_000484	NP_000475			amyloid beta A4 protein isoform a precursor						adult locomotory behavior|axon cargo transport|axon midline choice point recognition|cell adhesion|cellular copper ion homeostasis|collateral sprouting in absence of injury|dendrite development|endocytosis|extracellular matrix organization|G2 phase of mitotic cell cycle|innate immune response|ionotropic glutamate receptor signaling pathway|mating behavior|mRNA polyadenylation|neuron apoptosis|neuron remodeling|Notch signaling pathway|platelet activation|platelet degranulation|positive regulation of mitotic cell cycle|protein phosphorylation|regulation of epidermal growth factor receptor activity|regulation of multicellular organism growth|regulation of synapse structure and activity|regulation of translation|visual learning	axon|cell surface|coated pit|dendritic shaft|dendritic spine|extracellular region|Golgi apparatus|integral to plasma membrane|platelet alpha granule lumen	acetylcholine receptor binding|DNA binding|heparin binding|identical protein binding|metal ion binding|protein binding|protein binding|PTB domain binding|serine-type endopeptidase inhibitor activity			ovary(1)	1		Breast(209;0.00295)																---	---	---	---
Unknown	0	broad.mit.edu	37	21	27748484	27748484	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27748484delA								APP (205038 upstream) : CYYR1 (90045 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	27987497	27987497	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27987497delA								CYYR1 (41916 upstream) : ADAMTS1 (221111 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	27995098	27995099	+	IGR	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27995098_27995099delTG								CYYR1 (49517 upstream) : ADAMTS1 (213509 downstream)																																			---	---	---	---
ADAMTS5	11096	broad.mit.edu	37	21	28304600	28304600	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:28304600delT	uc002ymg.2	-							NM_007038	NP_008969			ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	integrin binding|metalloendopeptidase activity|zinc ion binding			upper_aerodigestive_tract(2)|ovary(1)|pancreas(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	28409247	28409247	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:28409247delC								ADAMTS5 (69808 upstream) : NCRNA00113 (685451 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	28649549	28649549	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:28649549delT								ADAMTS5 (310110 upstream) : NCRNA00113 (445149 downstream)																																			---	---	---	---
RNF160	26046	broad.mit.edu	37	21	30319939	30319939	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30319939delA	uc002ymr.2	-							NM_015565	NP_056380			zinc finger protein 294								ligase activity|zinc ion binding				0																		---	---	---	---
USP16	10600	broad.mit.edu	37	21	30417886	30417886	+	Intron	DEL	T	-	-	rs78869864		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30417886delT	uc002ymy.2	+						USP16_uc002ymx.2_Intron|USP16_uc002ymw.2_Intron|USP16_uc011acm.1_Intron|USP16_uc011acn.1_Intron|USP16_uc011aco.1_Intron	NM_006447	NP_006438			ubiquitin specific protease 16 isoform a						cell division|histone deubiquitination|mitosis|positive regulation of transcription, DNA-dependent|protein homotetramerization|transcription, DNA-dependent|ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	cysteine-type endopeptidase activity|histone binding|transcription coactivator activity|ubiquitin binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			ovary(2)|breast(1)|pancreas(1)	4																		---	---	---	---
GRIK1	2897	broad.mit.edu	37	21	31052487	31052487	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31052487delA	uc002yno.1	-						GRIK1_uc002ynn.2_Intron|GRIK1_uc011acs.1_Intron|GRIK1_uc011act.1_Intron|GRIK1_uc010glq.1_Intron|GRIK1_uc002ynr.2_Intron	NM_000830	NP_000821			glutamate receptor, ionotropic, kainate 1						central nervous system development|synaptic transmission	cell junction|postsynaptic membrane	kainate selective glutamate receptor activity			large_intestine(1)|ovary(1)|skin(1)	3					L-Glutamic Acid(DB00142)|Topiramate(DB00273)													---	---	---	---
GRIK1	2897	broad.mit.edu	37	21	31283195	31283195	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31283195delT	uc002yno.1	-						GRIK1_uc002ynn.2_Intron|GRIK1_uc011acs.1_Intron|GRIK1_uc011act.1_Intron|GRIK1_uc010glq.1_Intron|GRIK1_uc002ynr.2_Intron	NM_000830	NP_000821			glutamate receptor, ionotropic, kainate 1						central nervous system development|synaptic transmission	cell junction|postsynaptic membrane	kainate selective glutamate receptor activity			large_intestine(1)|ovary(1)|skin(1)	3					L-Glutamic Acid(DB00142)|Topiramate(DB00273)													---	---	---	---
Unknown	0	broad.mit.edu	37	21	31407667	31407667	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31407667delA								GRIK1 (95385 upstream) : CLDN17 (130596 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	31588374	31588376	+	IGR	DEL	AAT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31588374_31588376delAAT								CLDN8 (56 upstream) : KRTAP24-1 (65253 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	32179200	32179201	+	IGR	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:32179200_32179201delAA								KRTAP21-1 (51504 upstream) : KRTAP8-1 (5815 downstream)																																			---	---	---	---
TIAM1	7074	broad.mit.edu	37	21	32866239	32866239	+	Intron	DEL	A	-	-	rs66591105		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:32866239delA	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																		---	---	---	---
HUNK	30811	broad.mit.edu	37	21	33324337	33324338	+	Intron	INS	-	TT	TT	rs139355141	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33324337_33324338insTT	uc002yph.2	+							NM_014586	NP_055401			hormonally upregulated Neu-associated kinase						multicellular organismal development|signal transduction		ATP binding|protein serine/threonine kinase activity			stomach(1)|skin(1)	2																		---	---	---	---
MRAP	56246	broad.mit.edu	37	21	33661536	33661536	+	5'Flank	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33661536delA	uc002ypj.2	+						MRAP_uc002ypk.2_5'Flank|MRAP_uc011ado.1_5'Flank	NM_178817	NP_848932			melanocortin 2 receptor accessory protein						positive regulation of cAMP biosynthetic process|protein localization at cell surface	endoplasmic reticulum|integral to membrane|perinuclear region of cytoplasm|plasma membrane	corticotropin hormone receptor binding|type 1 melanocortin receptor binding|type 3 melanocortin receptor binding|type 4 melanocortin receptor binding|type 5 melanocortin receptor binding				0																		---	---	---	---
MRAP	56246	broad.mit.edu	37	21	33682649	33682650	+	Intron	DEL	GG	-	-	rs113685676		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33682649_33682650delGG	uc002ypj.2	+						MRAP_uc002ypk.2_Intron|MRAP_uc011ado.1_Intron|MRAP_uc002ypl.2_Intron|uc002ypm.2_5'Flank	NM_178817	NP_848932			melanocortin 2 receptor accessory protein						positive regulation of cAMP biosynthetic process|protein localization at cell surface	endoplasmic reticulum|integral to membrane|perinuclear region of cytoplasm|plasma membrane	corticotropin hormone receptor binding|type 1 melanocortin receptor binding|type 3 melanocortin receptor binding|type 4 melanocortin receptor binding|type 5 melanocortin receptor binding				0																		---	---	---	---
GCFC1	94104	broad.mit.edu	37	21	34133202	34133205	+	Intron	DEL	GTGC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34133202_34133205delGTGC	uc002yqn.2	-						GCFC1_uc002yqo.2_Intron|GCFC1_uc002yqp.2_Intron|GCFC1_uc002yqr.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	34213398	34213398	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34213398delT								C21orf62 (27345 upstream) : OLIG2 (184841 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	34273870	34273870	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34273870delA								C21orf62 (87817 upstream) : OLIG2 (124369 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	34304410	34304417	+	IGR	DEL	CAAGGTCT	-	-	rs113956482		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34304410_34304417delCAAGGTCT								C21orf62 (118357 upstream) : OLIG2 (93822 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	34424137	34424137	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34424137delT								OLIG2 (22637 upstream) : OLIG1 (18313 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	34490155	34490156	+	IGR	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34490155_34490156delAC								OLIG1 (45428 upstream) : C21orf54 (47621 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	34575540	34575541	+	IGR	DEL	AT	-	-	rs138580212	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34575540_34575541delAT								C21orf54 (32999 upstream) : IFNAR2 (26690 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	34597271	34597272	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34597271_34597272delTT								C21orf54 (54730 upstream) : IFNAR2 (4959 downstream)																																			---	---	---	---
TMEM50B	757	broad.mit.edu	37	21	34818093	34818094	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34818093_34818094insA	uc002yrs.1	-							NM_006134				transmembrane protein 50B							endoplasmic reticulum|integral to membrane|plasma membrane				ovary(1)|skin(1)	2																		---	---	---	---
DNAJC28	54943	broad.mit.edu	37	21	34861875	34861880	+	Intron	DEL	TTTTTT	-	-	rs77181674		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34861875_34861880delTTTTTT	uc002yrv.2	-						DNAJC28_uc002yrw.2_Intron	NM_017833	NP_060303			DnaJ (Hsp40) homolog, subfamily C, member 28								heat shock protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	35370503	35370504	+	IGR	INS	-	T	T	rs75079454		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35370503_35370504insT								ATP5O (82345 upstream) : MRPS6 (75319 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	35377737	35377737	+	IGR	DEL	T	-	-	rs72448873		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35377737delT								ATP5O (89579 upstream) : MRPS6 (68086 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	35888211	35888211	+	IGR	DEL	A	-	-	rs34738893		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35888211delA								KCNE1 (3638 upstream) : RCAN1 (575 downstream)																																			---	---	---	---
RUNX1	861	broad.mit.edu	37	21	36786007	36786009	+	Intron	DEL	AAA	-	-	rs113236714		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:36786007_36786009delAAA	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	37081522	37081522	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37081522delT	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	37236105	37236105	+	Intron	DEL	C	-	-	rs73902105		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37236105delC	uc002yut.1	-											Synthetic construct DNA, clone: pF1KB4846, Homo sapiens RUNX1 gene for runt-related transcription factor 1, complete cds, without stop codon, in Flexi system.						myeloid cell differentiation|negative regulation of granulocyte differentiation|positive regulation of angiogenesis|positive regulation of granulocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent	nucleus|nucleus	ATP binding|calcium ion binding|DNA binding|DNA binding|protein binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding			haematopoietic_and_lymphoid_tissue(383)|lung(2)|ovary(1)|central_nervous_system(1)	387								T	RPL22|MDS1|EVI1|CBFA2T3|CBFA2T1|ETV6|LAF4	AML|preB- ALL|T-ALL				Platelet_disorder_associated_with_Myeloid_Malignancies				---	---	---	---
Unknown	0	broad.mit.edu	37	21	37368477	37368477	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37368477delC								RUNX1 (11430 upstream) : SETD4 (38363 downstream)																																			---	---	---	---
MORC3	23515	broad.mit.edu	37	21	37745998	37745998	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37745998delA	uc002yvi.2	+							NM_015358	NP_056173			MORC family CW-type zinc finger 3						cell aging|maintenance of protein location in nucleus|negative regulation of fibroblast proliferation|peptidyl-serine phosphorylation|protein stabilization	aggresome|intermediate filament cytoskeleton|PML body	ATP binding|zinc ion binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	37958211	37958218	+	IGR	DEL	CCTTCCTC	-	-	rs34097871		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37958211_37958218delCCTTCCTC								CLDN14 (9344 upstream) : SIM2 (113773 downstream)																																			---	---	---	---
SIM2	6493	broad.mit.edu	37	21	38116611	38116612	+	Intron	INS	-	C	C	rs35690458		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38116611_38116612insC	uc002yvr.2	+						SIM2_uc002yvq.2_Intron	NM_005069	NP_005060			single-minded homolog 2 long isoform						cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			central_nervous_system(1)	1																		---	---	---	---
HLCS	3141	broad.mit.edu	37	21	38335608	38335608	+	5'Flank	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38335608delC	uc010gnb.2	-						HLCS_uc002yvs.2_Intron|HLCS_uc010gnc.1_Intron	NM_000411	NP_000402			holocarboxylase synthetase						cell proliferation|histone biotinylation|response to biotin	chromatin|cytosol|mitochondrion|nuclear lamina|nuclear matrix	ATP binding|biotin binding|biotin-[acetyl-CoA-carboxylase] ligase activity|biotin-[methylcrotonoyl-CoA-carboxylase] ligase activity|biotin-[methylmalonyl-CoA-carboxytransferase] ligase activity|biotin-[propionyl-CoA-carboxylase (ATP-hydrolyzing)] ligase activity|enzyme binding			ovary(2)|breast(1)|kidney(1)|liver(1)	5		Myeloproliferative disorder(46;0.0422)			Biotin(DB00121)													---	---	---	---
DSCR3	10311	broad.mit.edu	37	21	38635070	38635072	+	Intron	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38635070_38635072delTTT	uc002ywf.1	-						DSCR3_uc010gnm.1_Intron|DSCR3_uc010gnn.1_Intron|DSCR3_uc010gnl.2_Intron|DSCR3_uc011aeg.1_Intron|DSCR3_uc011aeh.1_Intron	NM_006052	NP_006043			Down syndrome critical region protein 3						vacuolar transport	nucleus|retromer complex					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	38703141	38703142	+	IGR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38703141_38703142insA								DSCR3 (63308 upstream) : DYRK1A (36717 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	38725573	38725573	+	IGR	DEL	A	-	-	rs68160529		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38725573delA								DSCR3 (85740 upstream) : DYRK1A (14286 downstream)																																			---	---	---	---
DYRK1A	1859	broad.mit.edu	37	21	38748799	38748799	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38748799delT	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																		---	---	---	---
KCNJ6	3763	broad.mit.edu	37	21	39237678	39237679	+	Intron	DEL	TG	-	-	rs146629438	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39237678_39237679delTG	uc011aej.1	-						KCNJ6_uc002ywo.2_Intron	NM_002240	NP_002231			potassium inwardly-rectifying channel J6						synaptic transmission	Golgi apparatus|voltage-gated potassium channel complex	G-protein activated inward rectifier potassium channel activity|protein binding			skin(1)	1					Halothane(DB01159)													---	---	---	---
Unknown	0	broad.mit.edu	37	21	39359769	39359770	+	IGR	DEL	GT	-	-	rs28434095		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39359769_39359770delGT								KCNJ6 (71073 upstream) : DSCR4 (66544 downstream)																																			---	---	---	---
ERG	2078	broad.mit.edu	37	21	39941094	39941094	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39941094delC	uc010gnw.2	-						ERG_uc010gnv.2_Intron|ERG_uc010gnx.2_Intron|ERG_uc011ael.1_Intron|ERG_uc002yxb.2_Intron|ERG_uc002yxc.3_Intron|ERG_uc010gnz.2_Intron	NM_001136155	NP_001129627			ets-related isoform 4						cell proliferation|multicellular organismal development|protein phosphorylation	cytoplasm|nucleus|ribonucleoprotein complex	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity		TMPRSS2/ERG(2499)|FUS/ERG(163)|EWSR1/ERG(162)	prostate(2499)|bone(167)|haematopoietic_and_lymphoid_tissue(153)|soft_tissue(5)|lung(2)|skin(1)|ovary(1)	2828		Prostate(19;3.6e-06)																---	---	---	---
Unknown	0	broad.mit.edu	37	21	40169176	40169176	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40169176delT								NCRNA00114 (23775 upstream) : ETS2 (8055 downstream)																																			---	---	---	---
PSMG1	8624	broad.mit.edu	37	21	40555792	40555807	+	5'Flank	DEL	AGAGGGGCAGGGGGCG	-	-	rs111901809		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40555792_40555807delAGAGGGGCAGGGGGCG	uc002yxi.2	-						PSMG1_uc002yxj.2_5'Flank|PSMG1_uc010gob.2_5'Flank	NM_003720	NP_003711			Down syndrome critical region protein 2 isoform						proteasome assembly	endoplasmic reticulum	protein binding				0		Prostate(19;8.44e-08)														OREG0003859	type=REGULATORY REGION|Gene=DSCR2|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	---	---	---	---
WRB	7485	broad.mit.edu	37	21	40768975	40768975	+	3'UTR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40768975delT	uc002yxs.2	+	5					WRB_uc002yxt.3_3'UTR|WRB_uc010goj.2_RNA	NM_004627	NP_004618			tryptophan rich basic protein isoform 1							integral to membrane|nucleolus					0		Prostate(19;1.2e-06)																---	---	---	---
Unknown	0	broad.mit.edu	37	21	40771211	40771211	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40771211delT								WRB (1397 upstream) : LCA5L (6561 downstream)																																			---	---	---	---
SH3BGR	6450	broad.mit.edu	37	21	40830965	40830965	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40830965delT	uc002yya.2	+						SH3BGR_uc002yxz.2_Intron	NM_007341	NP_031367			SH3-binding domain and glutamic acid-rich						protein complex assembly	cytosol	SH3 domain binding|SH3/SH2 adaptor activity				0		all_cancers(19;1.16e-23)|all_epithelial(19;1.22e-20)|Prostate(19;2.55e-06)|Breast(209;0.0133)		STAD - Stomach adenocarcinoma(101;0.00151)														---	---	---	---
Unknown	0	broad.mit.edu	37	21	40887620	40887620	+	IGR	DEL	T	-	-	rs76379005		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40887620delT								SH3BGR (194 upstream) : B3GALT5 (40749 downstream)																																			---	---	---	---
B3GALT5	10317	broad.mit.edu	37	21	40974167	40974167	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40974167delC	uc002yyb.1	+						C21orf88_uc010gok.2_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)																---	---	---	---
IGSF5	150084	broad.mit.edu	37	21	41114708	41114709	+	5'Flank	INS	-	T	T	rs143381646	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41114708_41114709insT	uc002yyo.2	+							NM_001080444	NP_001073913			immunoglobulin superfamily 5 like							integral to membrane|tight junction					0		Prostate(19;5.35e-06)																---	---	---	---
DSCAM	1826	broad.mit.edu	37	21	41547736	41547737	+	Intron	INS	-	CACA	CACA			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41547736_41547737insCACA	uc002yyq.1	-						DSCAM_uc002yyr.1_Intron	NM_001389	NP_001380			Down syndrome cell adhesion molecule isoform						cell adhesion|dendrite self-avoidance|negative regulation of cell adhesion|positive regulation of axon extension involved in axon guidance|positive regulation of phosphorylation	axon|extracellular region|growth cone|integral to plasma membrane|membrane fraction	protein binding			ovary(6)|skin(4)|upper_aerodigestive_tract(1)	11		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)																---	---	---	---
DSCAM	1826	broad.mit.edu	37	21	42058276	42058277	+	Intron	DEL	CA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42058276_42058277delCA	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	42393072	42393073	+	IGR	INS	-	AAGA	AAGA	rs141309729	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42393072_42393073insAAGA								DSCAM (174033 upstream) : C21orf130 (120354 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	42422149	42422149	+	IGR	DEL	T	-	-	rs78733436		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42422149delT								DSCAM (203110 upstream) : C21orf130 (91278 downstream)																																			---	---	---	---
MX2	4600	broad.mit.edu	37	21	42763317	42763319	+	Intron	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42763317_42763319delTTT	uc002yzf.1	+						MX2_uc011aer.1_Intron|MX2_uc002yzg.1_Intron	NM_002463	NP_002454			myxovirus resistance protein 2						response to virus|type I interferon-mediated signaling pathway	cytoplasm|nucleus	GTP binding|GTPase activity			ovary(2)	2		Prostate(19;1.57e-07)|all_epithelial(19;0.0222)																---	---	---	---
Unknown	0	broad.mit.edu	37	21	42924835	42924835	+	IGR	DEL	T	-	-	rs67630125		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42924835delT								TMPRSS2 (21792 upstream) : NCRNA00111 (174627 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	43436563	43436563	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43436563delA								ZNF295 (6067 upstream) : C21orf121 (5550 downstream)																																			---	---	---	---
PKNOX1	5316	broad.mit.edu	37	21	44424348	44424348	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44424348delA	uc002zcq.1	+						PKNOX1_uc002zcp.1_Intron|PKNOX1_uc011aex.1_Intron|PKNOX1_uc002zcr.2_5'Flank	NM_004571	NP_004562			PBX/knotted 1 homeobox 1								sequence-specific DNA binding			large_intestine(2)	2																		---	---	---	---
PDXK	8566	broad.mit.edu	37	21	45170844	45170845	+	Intron	DEL	TG	-	-	rs72420203		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45170844_45170845delTG	uc002zdm.3	+						PDXK_uc010gpj.2_Intron|PDXK_uc002zdn.3_Intron|PDXK_uc002zdq.3_Intron	NM_003681	NP_003672			pyridoxal kinase						cell proliferation|pyridoxal 5'-phosphate salvage	cytosol	ATP binding|lithium ion binding|magnesium ion binding|potassium ion binding|protein homodimerization activity|pyridoxal kinase activity|pyridoxal phosphate binding|sodium ion binding|zinc ion binding				0				Colorectal(79;0.109)|READ - Rectum adenocarcinoma(84;0.161)|STAD - Stomach adenocarcinoma(101;0.18)	Pyridoxal(DB00147)|Pyridoxine(DB00165)													---	---	---	---
AGPAT3	56894	broad.mit.edu	37	21	45381023	45381025	+	Intron	DEL	AAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45381023_45381025delAAA	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	45499777	45499778	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45499777_45499778delAA	uc002zea.2	+						TRAPPC10_uc010gpo.2_Intron|TRAPPC10_uc011afa.1_5'Flank	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	45580124	45580129	+	IGR	DEL	TGTCCG	-	-	rs13048151		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45580124_45580129delTGTCCG								C21orf33 (14520 upstream) : ICOSLG (66595 downstream)																																			---	---	---	---
UBE2G2	7327	broad.mit.edu	37	21	46215674	46215675	+	Intron	INS	-	TGTT	TGTT	rs139873423	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46215674_46215675insTGTT	uc002zfy.2	-						UBE2G2_uc002zfx.2_Intron	NM_003343	NP_003334			ubiquitin-conjugating enzyme E2G 2 isoform 1						protein K48-linked ubiquitination	cytosol	ATP binding|protein binding|ubiquitin-protein ligase activity			breast(3)|central_nervous_system(1)	4				Colorectal(79;0.0638)														---	---	---	---
Unknown	0	broad.mit.edu	37	21	46269177	46269177	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46269177delG								SUMO3 (31133 upstream) : PTTG1IP (336 downstream)																																			---	---	---	---
COL18A1	80781	broad.mit.edu	37	21	46857168	46857169	+	Intron	INS	-	CT	CT	rs71921087		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46857168_46857169insCT	uc002zhg.2	+							NM_130445	NP_569712			alpha 1 type XVIII collagen isoform 2 precursor						cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception	collagen|extracellular space	extracellular matrix structural constituent|metal ion binding|protein binding			central_nervous_system(1)	1				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)														---	---	---	---
Unknown	0	broad.mit.edu	37	21	46983441	46983441	+	IGR	DEL	A	-	-	rs8132317	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46983441delA								SLC19A1 (19116 upstream) : PCBP3 (80242 downstream)																																			---	---	---	---
PCBP3	54039	broad.mit.edu	37	21	47125649	47125649	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47125649delT	uc010gqb.2	+							NM_020528	NP_065389			poly(rC) binding protein 3 isoform 1						mRNA metabolic process	cytosol|mitochondrion|nucleus|ribonucleoprotein complex	DNA binding|RNA binding			skin(1)	1	all_hematologic(128;0.24)			Colorectal(79;0.0411)|READ - Rectum adenocarcinoma(84;0.0649)														---	---	---	---
Unknown	0	broad.mit.edu	37	21	47488578	47488585	+	IGR	DEL	GCGTGTGC	-	-	rs72155199	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47488578_47488585delGCGTGTGC								COL6A1 (63615 upstream) : COL6A2 (29448 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	47875063	47875063	+	RNA	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47875063delT	uc002zjk.2	-	2		c.1366delA								full-length cDNA clone CS0DC003YA14 of Neuroblastoma Cot 25-normalized of Homo sapiens (human).																														---	---	---	---
CECR5	27440	broad.mit.edu	37	22	17648947	17648951	+	5'Flank	DEL	TTTTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17648947_17648951delTTTTT	uc002zmh.2	-							NM_017829	NP_060299			cat eye syndrome chromosome region, candidate 5								hydrolase activity				0		all_epithelial(15;0.0181)|Lung NSC(13;0.109)|all_lung(157;0.132)																---	---	---	---
CECR2	27443	broad.mit.edu	37	22	17861315	17861315	+	Intron	DEL	T	-	-	rs35721421		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17861315delT	uc010gqv.1	+							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)														---	---	---	---
MICAL3	57553	broad.mit.edu	37	22	18411205	18411205	+	Intron	DEL	A	-	-	rs35825903		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18411205delA	uc002zng.3	-						MICAL3_uc002znh.2_Intron|MICAL3_uc002znl.1_Intron|MICAL3_uc010grf.2_Intron|MICAL3_uc011agm.1_Intron	NM_015241	NP_056056			microtubule associated monoxygenase, calponin							cytoplasm|cytoskeleton	monooxygenase activity|zinc ion binding				0		all_epithelial(15;0.198)		Lung(27;0.0427)														---	---	---	---
DGCR2	9993	broad.mit.edu	37	22	19073996	19073996	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19073996delA	uc002zoq.1	-						DGCR2_uc002zor.1_Intron|DGCR2_uc011agr.1_Intron	NM_005137	NP_005128			integral membrane protein DGCR2 precursor						cell adhesion|organ morphogenesis	integral to membrane	receptor activity|sugar binding			large_intestine(1)	1	Colorectal(54;0.0993)																	---	---	---	---
Unknown	0	broad.mit.edu	37	22	19605556	19605557	+	IGR	INS	-	TTCT	TTCT	rs138229624	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19605556_19605557insTTCT								LOC150185 (51194 upstream) : SEPT5 (96430 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	19850245	19850248	+	IGR	DEL	AAAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19850245_19850248delAAAA								GNB1L (7783 upstream) : TXNRD2 (12792 downstream)																																			---	---	---	---
C22orf25	128989	broad.mit.edu	37	22	20033678	20033678	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20033678delT	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|C22orf25_uc010gry.1_Intron|C22orf25_uc002zrh.1_Intron	NM_152906	NP_690870			hypothetical protein LOC128989												0	Colorectal(54;0.0533)																	---	---	---	---
DGCR6L	85359	broad.mit.edu	37	22	20310493	20310494	+	5'Flank	INS	-	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20310493_20310494insG	uc002zrx.2	-						DGCR6L_uc010gsb.2_5'Flank|DGCR6L_uc010gsc.2_5'Flank	NM_033257	NP_150282			DiGeorge syndrome critical region gene 6 like							nucleus					0	Colorectal(54;0.0993)																	---	---	---	---
MED15	51586	broad.mit.edu	37	22	20917323	20917323	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20917323delA	uc002zsp.2	+						MED15_uc002zsn.1_Intron|MED15_uc002zso.2_Intron|MED15_uc002zsq.2_Intron|MED15_uc010gso.2_Intron|MED15_uc002zsr.2_Intron|MED15_uc011ahs.1_Intron|MED15_uc011aht.1_Intron|MED15_uc002zss.2_Intron	NM_001003891	NP_001003891			mediator complex subunit 15 isoform a						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	Golgi apparatus|mediator complex	protein binding			skin(1)	1	all_cancers(11;2.07e-24)|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)|Epithelial(17;0.209)															---	---	---	---
Unknown	0	broad.mit.edu	37	22	20967483	20967483	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20967483delG								MED15 (25565 upstream) : POM121L4P (76360 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	20973452	20973452	+	Intron	DEL	T	-	-	rs111447457		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20973452delT	uc002zsv.2	-											Homo sapiens, clone IMAGE:5171202, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	22	21253927	21253927	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21253927delT								SNAP29 (8428 upstream) : CRKL (17787 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	21479815	21479815	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21479815delA	uc010gsw.1	-						uc011aib.1_5'Flank					SubName: Full=HCG2019008, isoform CRA_d; SubName: Full=Putative uncharacterized protein ENSP00000324580;																														---	---	---	---
PPIL2	23759	broad.mit.edu	37	22	22049808	22049808	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22049808delG	uc010gtj.1	+						PPIL2_uc002zvh.3_Intron|PPIL2_uc002zvi.3_Intron|PPIL2_uc002zvg.3_3'UTR|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)																	---	---	---	---
MAPK1	5594	broad.mit.edu	37	22	22165686	22165686	+	Intron	DEL	A	-	-	rs148476960		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22165686delA	uc002zvn.2	-						MAPK1_uc002zvo.2_Intron|MAPK1_uc010gtk.1_Intron	NM_002745	NP_002736			mitogen-activated protein kinase 1						activation of MAPK activity|activation of MAPKK activity|axon guidance|cell cycle|epidermal growth factor receptor signaling pathway|ERK1 and ERK2 cascade|induction of apoptosis|innate immune response|insulin receptor signaling pathway|interspecies interaction between organisms|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|platelet activation|Ras protein signal transduction|regulation of sequence-specific DNA binding transcription factor activity|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|transcription, DNA-dependent	cytosol|nucleoplasm	ATP binding|DNA binding|MAP kinase activity|phosphatase binding|RNA polymerase II carboxy-terminal domain kinase activity			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3	Colorectal(54;0.105)	all_lung(157;3.89e-05)		READ - Rectum adenocarcinoma(21;0.0689)	Arsenic trioxide(DB01169)													---	---	---	---
LOC96610	96610	broad.mit.edu	37	22	22454503	22454503	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22454503delA	uc011aim.1	+											Parts of antibodies, mostly variable regions.												0																		---	---	---	---
LOC96610	96610	broad.mit.edu	37	22	23043815	23043815	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23043815delC	uc011aim.1	+											Parts of antibodies, mostly variable regions.												0																		---	---	---	---
LOC96610	96610	broad.mit.edu	37	22	23053801	23053802	+	Intron	DEL	CT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23053801_23053802delCT	uc011aim.1	+											Parts of antibodies, mostly variable regions.												0																OREG0026373	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
LOC96610	96610	broad.mit.edu	37	22	23229448	23229449	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23229448_23229449insA	uc011aim.1	+						uc011aiw.1_5'Flank|uc010gtu.1_5'Flank|uc002zws.2_5'Flank					Parts of antibodies, mostly variable regions.												0																		---	---	---	---
RAB36	9609	broad.mit.edu	37	22	23488568	23488568	+	Intron	DEL	G	-	-	rs147076751	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23488568delG	uc002zwv.1	+						RAB36_uc010gtw.1_Intron	NM_004914	NP_004905			RAB36, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	Golgi membrane	GTP binding			ovary(1)|central_nervous_system(1)	2	all_hematologic(9;0.0197)|Acute lymphoblastic leukemia(84;0.181)			READ - Rectum adenocarcinoma(21;0.155)														---	---	---	---
RAB36	9609	broad.mit.edu	37	22	23488570	23488570	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23488570delT	uc002zwv.1	+						RAB36_uc010gtw.1_Intron	NM_004914	NP_004905			RAB36, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	Golgi membrane	GTP binding			ovary(1)|central_nervous_system(1)	2	all_hematologic(9;0.0197)|Acute lymphoblastic leukemia(84;0.181)			READ - Rectum adenocarcinoma(21;0.155)														---	---	---	---
BCR	613	broad.mit.edu	37	22	23618979	23618982	+	Intron	DEL	AGAA	-	-	rs34936468		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23618979_23618982delAGAA	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								---	---	---	---
CYTSA	23384	broad.mit.edu	37	22	24747993	24747993	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24747993delT	uc002zzw.2	+						CYTSA_uc002zzv.3_Intron|CYTSA_uc011ajq.1_Intron	NM_015330	NP_056145			cytospin A						cell cycle|cell division						0																		---	---	---	---
GGT1	2678	broad.mit.edu	37	22	24994546	24994546	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24994546delT	uc003aan.1	+							NM_013430	NP_038347			gamma-glutamyltransferase 1 precursor						glutathione biosynthetic process	integral to membrane	acyltransferase activity|gamma-glutamyltransferase activity|protein binding				0					Glutathione(DB00143)													---	---	---	---
SGSM1	129049	broad.mit.edu	37	22	25225168	25225168	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25225168delA	uc003abg.2	+						SGSM1_uc003abh.2_Intron|SGSM1_uc010guu.1_Intron|SGSM1_uc003abj.2_Intron|SGSM1_uc003abf.2_Intron	NM_001039948	NP_001035037			RUN and TBC1 domain containing 2 isoform 1							Golgi apparatus	Rab GTPase activator activity			ovary(2)|central_nervous_system(2)|pancreas(1)	5																		---	---	---	---
MYO18B	84700	broad.mit.edu	37	22	26174254	26174255	+	Intron	INS	-	A	A	rs143540045	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26174254_26174255insA	uc003abz.1	+						MYO18B_uc003aca.1_Intron|MYO18B_uc010guy.1_Intron|MYO18B_uc010guz.1_Intron|MYO18B_uc011aka.1_Intron|MYO18B_uc011akb.1_Intron	NM_032608	NP_115997			myosin XVIIIB							nucleus|sarcomere|unconventional myosin complex	actin binding|ATP binding|motor activity			ovary(5)|central_nervous_system(3)|large_intestine(2)|breast(2)	12																		---	---	---	---
MYO18B	84700	broad.mit.edu	37	22	26258435	26258435	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26258435delA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	27256832	27256832	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27256832delT								MIAT (141883 upstream) : MN1 (887434 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	27311434	27311434	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27311434delT								MIAT (196485 upstream) : MN1 (832832 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	27781668	27781669	+	IGR	INS	-	C	C	rs139552925	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27781668_27781669insC								MIAT (666719 upstream) : MN1 (362597 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	27791724	27791725	+	IGR	DEL	CA	-	-	rs35220226		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27791724_27791725delCA								MIAT (676775 upstream) : MN1 (352541 downstream)																																			---	---	---	---
LOC284900	284900	broad.mit.edu	37	22	28332193	28332193	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:28332193delT	uc003ado.2	+							NR_026963				Homo sapiens mRNA for KIAA1648 protein, partial cds.												0																		---	---	---	---
TTC28	23331	broad.mit.edu	37	22	28520157	28520159	+	Intron	DEL	TTG	-	-	rs72306392		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:28520157_28520159delTTG	uc003adp.3	-							NM_001145418	NP_001138890			tetratricopeptide repeat domain 28								binding				0																		---	---	---	---
TTC28	23331	broad.mit.edu	37	22	28575315	28575315	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:28575315delT	uc003adp.3	-							NM_001145418	NP_001138890			tetratricopeptide repeat domain 28								binding				0																		---	---	---	---
TTC28	23331	broad.mit.edu	37	22	28686901	28686902	+	Intron	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:28686901_28686902delAC	uc003adp.3	-							NM_001145418	NP_001138890			tetratricopeptide repeat domain 28								binding				0																		---	---	---	---
ZNRF3	84133	broad.mit.edu	37	22	29367187	29367188	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29367187_29367188delTT	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	29427203	29427203	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29427203delA	uc003aeg.2	+						ZNRF3_uc003aeh.1_Intron	NM_032173	NP_115549			zinc and ring finger 3							integral to membrane	zinc ion binding			ovary(1)	1																		---	---	---	---
NIPSNAP1	8508	broad.mit.edu	37	22	29958680	29958681	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29958680_29958681insA	uc003afx.3	-						NIPSNAP1_uc011akp.1_Intron	NM_003634	NP_003625			nipsnap homolog 1									p.?(1)		skin(1)	1																		---	---	---	---
NIPSNAP1	8508	broad.mit.edu	37	22	29975069	29975069	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29975069delT	uc003afx.3	-						NIPSNAP1_uc011akp.1_Intron	NM_003634	NP_003625			nipsnap homolog 1									p.?(1)		skin(1)	1																		---	---	---	---
UQCR10	29796	broad.mit.edu	37	22	30165486	30165486	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30165486delA	uc003agq.1	+						ZMAT5_uc003agm.2_5'Flank|ZMAT5_uc003agn.2_5'Flank|ZMAT5_uc003ago.1_5'Flank|UQCR10_uc003agp.1_Intron	NM_013387	NP_037519			ubiquinol-cytochrome c reductase complex 7.2kDa						mitochondrial electron transport, ubiquinol to cytochrome c	mitochondrial inner membrane|respiratory chain	ubiquinol-cytochrome-c reductase activity			ovary(1)	1																		---	---	---	---
ASCC2	84164	broad.mit.edu	37	22	30218612	30218615	+	Intron	DEL	TTTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30218612_30218615delTTTT	uc003agr.2	-						ASCC2_uc003ags.2_Intron|ASCC2_uc003agt.2_Intron|ASCC2_uc011akr.1_Intron	NM_032204	NP_115580			activating signal cointegrator 1 complex subunit						regulation of transcription, DNA-dependent|transcription, DNA-dependent						0			OV - Ovarian serous cystadenocarcinoma(5;0.000103)|Epithelial(10;0.0169)|all cancers(5;0.0259)															---	---	---	---
ASCC2	84164	broad.mit.edu	37	22	30223796	30223797	+	Intron	INS	-	CTC	CTC	rs148580571	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30223796_30223797insCTC	uc003agr.2	-						ASCC2_uc003ags.2_Intron|ASCC2_uc003agt.2_Intron|ASCC2_uc011akr.1_Intron	NM_032204	NP_115580			activating signal cointegrator 1 complex subunit						regulation of transcription, DNA-dependent|transcription, DNA-dependent						0			OV - Ovarian serous cystadenocarcinoma(5;0.000103)|Epithelial(10;0.0169)|all cancers(5;0.0259)															---	---	---	---
ASCC2	84164	broad.mit.edu	37	22	30228002	30228003	+	Intron	INS	-	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30228002_30228003insG	uc003agr.2	-						ASCC2_uc003ags.2_Intron|ASCC2_uc003agt.2_Intron|ASCC2_uc011akr.1_Intron	NM_032204	NP_115580			activating signal cointegrator 1 complex subunit						regulation of transcription, DNA-dependent|transcription, DNA-dependent						0			OV - Ovarian serous cystadenocarcinoma(5;0.000103)|Epithelial(10;0.0169)|all cancers(5;0.0259)															---	---	---	---
MTMR3	8897	broad.mit.edu	37	22	30384736	30384738	+	Intron	DEL	TTT	-	-	rs5763672		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30384736_30384738delTTT	uc003agv.3	+						MTMR3_uc003agu.3_Intron|MTMR3_uc003agw.3_Intron	NM_021090	NP_066576			myotubularin-related protein 3 isoform c						phosphatidylinositol dephosphorylation	cytoplasm|membrane|membrane fraction|nucleus	metal ion binding|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity			breast(3)|ovary(1)|skin(1)	5			OV - Ovarian serous cystadenocarcinoma(5;0.00204)|Epithelial(10;0.06)|all cancers(5;0.107)															---	---	---	---
SEC14L4	284904	broad.mit.edu	37	22	30893511	30893512	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30893511_30893512insA	uc003aid.2	-						SEC14L4_uc011akz.1_Intron|SEC14L4_uc003aie.2_Intron|SEC14L4_uc003aif.2_Intron	NM_174977	NP_777637			SEC14p-like protein TAP3 isoform a							integral to membrane|intracellular	lipid binding|transporter activity			skin(1)	1					Vitamin E(DB00163)													---	---	---	---
OSBP2	23762	broad.mit.edu	37	22	31302452	31302452	+	3'UTR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31302452delT	uc003aiy.1	+	14					OSBP2_uc011ala.1_3'UTR|OSBP2_uc010gwc.1_3'UTR|OSBP2_uc011alb.1_3'UTR|OSBP2_uc003aiz.1_3'UTR|OSBP2_uc003aja.1_3'UTR|OSBP2_uc011alc.1_3'UTR|OSBP2_uc003ajb.2_3'UTR|OSBP2_uc011ald.1_3'UTR|OSBP2_uc010gwd.1_3'UTR	NM_030758	NP_110385			oxysterol binding protein 2 isoform a						lipid transport	membrane	lipid binding			breast(1)|skin(1)	2																		---	---	---	---
PIK3IP1	113791	broad.mit.edu	37	22	31679897	31679897	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31679897delT	uc003akm.2	-						PIK3IP1_uc003akl.2_Intron|PIK3IP1_uc011alo.1_Intron|PIK3IP1_uc003akn.2_Intron	NM_052880	NP_443112			HGFL protein isoform 1							integral to membrane				ovary(1)	1																		---	---	---	---
DEPDC5	9681	broad.mit.edu	37	22	32201493	32201493	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32201493delT	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	32356053	32356053	+	IGR	DEL	A	-	-	rs34758721		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32356053delA								YWHAH (2464 upstream) : SLC5A1 (82984 downstream)																																			---	---	---	---
SLC5A1	6523	broad.mit.edu	37	22	32469533	32469533	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32469533delT	uc003amc.2	+						SLC5A1_uc011alz.1_Intron	NM_000343	NP_000334			solute carrier family 5 (sodium/glucose						carbohydrate metabolic process	integral to plasma membrane	glucose:sodium symporter activity|protein binding			skin(1)	1																		---	---	---	---
SYN3	8224	broad.mit.edu	37	22	33372980	33372980	+	Intron	DEL	G	-	-	rs66561031		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:33372980delG	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																		---	---	---	---
LARGE	9215	broad.mit.edu	37	22	34057510	34057511	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:34057510_34057511delTT	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	34818015	34818015	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:34818015delA								LARGE (499431 upstream) : ISX (644114 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	35063550	35063550	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35063550delT								LARGE (744966 upstream) : ISX (398579 downstream)																																			---	---	---	---
TOM1	10043	broad.mit.edu	37	22	35726117	35726117	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35726117delA	uc003ann.2	+						TOM1_uc011ami.1_Intron|TOM1_uc011amj.1_Intron|TOM1_uc003ans.2_Intron|TOM1_uc011amk.1_Intron|TOM1_uc003anp.2_Intron|TOM1_uc011aml.1_Intron|TOM1_uc003ano.2_Intron|TOM1_uc003anq.2_Intron|TOM1_uc003anr.2_Intron	NM_005488	NP_005479			target of myb1 isoform 1						endocytosis|endosome transport|intracellular protein transport	cytosol|early endosome|membrane	protein binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	36082644	36082646	+	IGR	DEL	TCT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36082644_36082646delTCT								APOL6 (18189 upstream) : APOL5 (31273 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	36104243	36104243	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36104243delA								APOL6 (39788 upstream) : APOL5 (9676 downstream)																																			---	---	---	---
RBM9	23543	broad.mit.edu	37	22	36155026	36155026	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36155026delA	uc003aon.3	-						RBM9_uc003aog.3_Intron|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	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	36276199	36276200	+	Intron	DEL	AA	-	-	rs75514211		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36276199_36276200delAA	uc003aon.3	-						RBM9_uc010gwu.2_Intron|RBM9_uc003aoo.3_Intron	NM_001082578	NP_001076047			RNA binding motif protein 9 isoform 5						estrogen receptor signaling pathway|mRNA processing|negative regulation of transcription, DNA-dependent|regulation of cell proliferation|RNA splicing	cytoplasm|nucleus	nucleotide binding|RNA binding|transcription corepressor activity|transcription factor binding				0																		---	---	---	---
CACNG2	10369	broad.mit.edu	37	22	36997259	36997259	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36997259delT	uc003aps.1	-							NM_006078	NP_006069			voltage-dependent calcium channel gamma-2						membrane depolarization|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|endocytic vesicle membrane|voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity				0																		---	---	---	---
PVALB	5816	broad.mit.edu	37	22	37212087	37212088	+	Intron	DEL	TT	-	-	rs111360103		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37212087_37212088delTT	uc010gwz.2	-						PVALB_uc003apx.2_Intron	NM_002854	NP_002845			parvalbumin								calcium ion binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	37361062	37361062	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37361062delA								CSF2RB (24585 upstream) : C22orf33 (26099 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	37429961	37429961	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37429961delC								MPST (4099 upstream) : KCTD17 (17818 downstream)																																			---	---	---	---
TMPRSS6	164656	broad.mit.edu	37	22	37474823	37474825	+	Intron	DEL	AGA	-	-	rs71722051		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37474823_37474825delAGA	uc003aqs.1	-						TMPRSS6_uc003aqt.1_Intron	NM_153609	NP_705837			transmembrane protease, serine 6						angiogenesis|extracellular matrix organization|fibrinolysis|intracellular signal transduction|proteolysis	integral to membrane|intracellular|plasma membrane	serine-type endopeptidase activity			breast(4)|ovary(1)|skin(1)	6																		---	---	---	---
BAIAP2L2	80115	broad.mit.edu	37	22	38483897	38483898	+	Intron	INS	-	C	C	rs150241637	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38483897_38483898insC	uc003auw.2	-						BAIAP2L2_uc003auv.2_5'Flank	NM_025045	NP_079321			BAI1-associated protein 2-like 2						filopodium assembly|signal transduction		cytoskeletal adaptor activity|SH3 domain binding			pancreas(1)	1	Melanoma(58;0.045)																	---	---	---	---
TMEM184B	25829	broad.mit.edu	37	22	38670062	38670064	+	5'Flank	DEL	TTT	-	-	rs111708847		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38670062_38670064delTTT	uc003avf.1	-						TMEM184B_uc003avg.1_5'Flank|TMEM184B_uc003avh.1_5'Flank|TMEM184B_uc010gxl.1_5'Flank	NM_012264	NP_036396			transmembrane protein 184B							integral to membrane					0	Melanoma(58;0.045)																	---	---	---	---
DMC1	11144	broad.mit.edu	37	22	38954737	38954737	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38954737delA	uc003avz.1	-						DMC1_uc011anv.1_Intron|DMC1_uc003awa.1_Intron	NM_007068	NP_008999			DMC1 dosage suppressor of mck1 homolog						reciprocal meiotic recombination	condensed nuclear chromosome	ATP binding|DNA binding|DNA-dependent ATPase activity|protein binding			ovary(1)	1	Melanoma(58;0.0286)												Homologous_recombination					---	---	---	---
LOC646851	646851	broad.mit.edu	37	22	38993014	38993014	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38993014delA	uc011anw.1	-							NM_001013647	NP_001013669			hypothetical protein LOC646851												0																		---	---	---	---
LOC646851	646851	broad.mit.edu	37	22	39024946	39024946	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39024946delA	uc011anx.1	-						LOC646851_uc011anw.1_Intron					SubName: Full=Putative uncharacterized protein ENSP00000348086;												0																		---	---	---	---
CACNA1I	8911	broad.mit.edu	37	22	40005089	40005090	+	Intron	INS	-	CCT	CCT	rs150471436	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40005089_40005090insCCT	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)													---	---	---	---
ENTHD1	150350	broad.mit.edu	37	22	40172060	40172061	+	Intron	DEL	TT	-	-	rs112208046		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40172060_40172061delTT	uc003ayg.2	-							NM_152512	NP_689725			ENTH domain containing 1											ovary(2)|skin(1)	3	Melanoma(58;0.0749)																	---	---	---	---
ENTHD1	150350	broad.mit.edu	37	22	40220712	40220712	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40220712delA	uc003ayg.2	-							NM_152512	NP_689725			ENTH domain containing 1											ovary(2)|skin(1)	3	Melanoma(58;0.0749)																	---	---	---	---
MKL1	57591	broad.mit.edu	37	22	40822863	40822864	+	Intron	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40822863_40822864delTG	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								---	---	---	---
MKL1	57591	broad.mit.edu	37	22	40903625	40903625	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40903625delA	uc003ayw.1	-						MKL1_uc010gye.1_Intron|MKL1_uc010gyf.1_Intron|MKL1_uc003ayy.1_Intron	NM_020831	NP_065882			megakaryoblastic leukemia 1 protein						positive regulation of transcription from RNA polymerase II promoter|smooth muscle cell differentiation|transcription, DNA-dependent	cytoplasm|nucleus	actin monomer binding|leucine zipper domain binding|nucleic acid binding|transcription coactivator activity			ovary(2)|lung(1)|breast(1)|central_nervous_system(1)	5								T	RBM15	acute megakaryocytic leukemia								---	---	---	---
MKL1	57591	broad.mit.edu	37	22	40952858	40952858	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40952858delA	uc003ayw.1	-						MKL1_uc010gye.1_Intron|MKL1_uc010gyf.1_Intron|MKL1_uc003ayy.1_Intron	NM_020831	NP_065882			megakaryoblastic leukemia 1 protein						positive regulation of transcription from RNA polymerase II promoter|smooth muscle cell differentiation|transcription, DNA-dependent	cytoplasm|nucleus	actin monomer binding|leucine zipper domain binding|nucleic acid binding|transcription coactivator activity			ovary(2)|lung(1)|breast(1)|central_nervous_system(1)	5								T	RBM15	acute megakaryocytic leukemia								---	---	---	---
XPNPEP3	63929	broad.mit.edu	37	22	41318726	41318727	+	Intron	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41318726_41318727delAC	uc003azh.2	+						XPNPEP3_uc003azi.2_Intron|XPNPEP3_uc011aoy.1_Intron	NM_022098	NP_071381			X-prolyl aminopeptidase (aminopeptidase P) 3,						cellular process	mitochondrion	aminopeptidase activity|manganese ion binding|metallopeptidase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	41381588	41381588	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41381588delA								RBX1 (12922 upstream) : MIR1281 (106929 downstream)																																			---	---	---	---
ZC3H7B	23264	broad.mit.edu	37	22	41749841	41749841	+	Intron	DEL	T	-	-	rs60656030		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41749841delT	uc003azw.2	+						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																		---	---	---	---
TOB2	10766	broad.mit.edu	37	22	41832246	41832246	+	3'UTR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41832246delT	uc003azz.1	-	2						NM_016272	NP_057356			transducer of ERBB2, 2						female gamete generation|negative regulation of cell proliferation	cytoplasm|nucleus				ovary(1)	1																		---	---	---	---
ACO2	50	broad.mit.edu	37	22	41882109	41882110	+	Intron	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41882109_41882110delTG	uc003bac.2	+						ACO2_uc003bad.2_Intron	NM_001098	NP_001089			aconitase 2, mitochondrial precursor						citrate metabolic process|tricarboxylic acid cycle	mitochondrial matrix|nucleus	4 iron, 4 sulfur cluster binding|aconitate hydratase activity|citrate hydro-lyase (cis-aconitate-forming) activity|iron ion binding|isocitrate hydro-lyase (cis-aconitate-forming) activity			breast(2)|ovary(1)|lung(1)	4																		---	---	---	---
CSDC2	27254	broad.mit.edu	37	22	41967363	41967363	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41967363delA	uc003bak.1	+							NM_014460	NP_055275			RNA-binding protein pippin						histone mRNA 3'-end processing|regulation of transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein binding|RNA binding				0																		---	---	---	---
NHP2L1	4809	broad.mit.edu	37	22	42076082	42076082	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42076082delA	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	42143242	42143244	+	Intron	DEL	TTT	-	-	rs76274765		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42143242_42143244delTTT	uc003baz.1	+						WBP2NL_uc011ape.1_Intron|LOC339674_uc003bba.1_Intron|MEI1_uc011apd.1_Intron	NM_152513	NP_689726			meiosis defective 1								binding			central_nervous_system(1)|skin(1)	2																		---	---	---	---
FAM109B	150368	broad.mit.edu	37	22	42472306	42472306	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42472306delT	uc003bbz.2	+							NM_001002034	NP_001002034			hypothetical protein LOC150368						endosome organization|receptor recycling|retrograde transport, endosome to Golgi	clathrin-coated vesicle|early endosome|recycling endosome|trans-Golgi network	protein homodimerization activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	42495655	42495655	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42495655delT	uc003bcc.1	+						uc003bcd.1_Intron					Homo sapiens cDNA FLJ41636 fis, clone FEBRA1000022.																														---	---	---	---
Unknown	0	broad.mit.edu	37	22	42517679	42517679	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42517679delA	uc003bcc.1	+						uc003bcd.1_Intron					Homo sapiens cDNA FLJ41636 fis, clone FEBRA1000022.																														---	---	---	---
CYP2D7P1	1564	broad.mit.edu	37	22	42538264	42538265	+	Intron	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42538264_42538265delAC	uc003bci.2	-						CYP2D7P1_uc003bcg.2_5'Flank|CYP2D7P1_uc003bch.2_5'Flank|CYP2D7P1_uc010gyv.2_Intron|CYP2D7P1_uc010gyw.2_Intron|CYP2D7P1_uc010gyx.1_Intron	NR_002570				SubName: Full=Cytochrome P450 2D6;          EC=1.14.14.1;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	42881334	42881334	+	IGR	DEL	A	-	-	rs71844233		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42881334delA								NFAM1 (52933 upstream) : SERHL (15251 downstream)																																			---	---	---	---
PACSIN2	11252	broad.mit.edu	37	22	43306916	43306916	+	Intron	DEL	T	-	-	rs67845012		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43306916delT	uc010gzg.2	-						PACSIN2_uc003bdg.3_Intron|PACSIN2_uc003bde.3_Intron|PACSIN2_uc003bdf.3_Intron	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	43459641	43459642	+	Intron	DEL	TT	-	-	rs77325620		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43459641_43459642delTT	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)														---	---	---	---
EFCAB6	64800	broad.mit.edu	37	22	44166703	44166703	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44166703delA	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)																---	---	---	---
PARVB	29780	broad.mit.edu	37	22	44433382	44433382	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44433382delC	uc003ben.2	+						PARVB_uc003bem.2_Intron|PARVB_uc010gzn.2_Intron	NM_013327	NP_037459			parvin, beta isoform b						cell adhesion|cell junction assembly	cytoskeleton|cytosol|focal adhesion	actin binding				0		Ovarian(80;0.0246)|all_neural(38;0.0423)																---	---	---	---
PARVB	29780	broad.mit.edu	37	22	44505610	44505610	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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)																---	---	---	---
PRR5-ARHGAP8	553158	broad.mit.edu	37	22	45164720	45164721	+	Intron	INS	-	T	T	rs11704570		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45164720_45164721insT	uc003bfd.2	+						PRR5-ARHGAP8_uc003bfc.2_Intron|PRR5-ARHGAP8_uc011aqi.1_Intron|PRR5-ARHGAP8_uc011aqj.1_Intron|ARHGAP8_uc003bfi.2_Intron|ARHGAP8_uc010gzv.2_Intron|ARHGAP8_uc003bfj.2_Intron|ARHGAP8_uc003bfk.2_Intron|PRR5-ARHGAP8_uc003bfg.1_Intron	NM_181335	NP_851852			Rho GTPase activating protein 8 isoform 2											skin(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	45262333	45262333	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45262333delG								PRR5-ARHGAP8 (3671 upstream) : PHF21B (14712 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	46038942	46038942	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46038942delA								FBLN1 (40245 upstream) : ATXN10 (28745 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	48019240	48019241	+	Intron	INS	-	GA	GA			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:48019240_48019241insGA	uc003bii.2	-											Homo sapiens cDNA FLJ46257 fis, clone TESTI4024240.																														---	---	---	---
Unknown	0	broad.mit.edu	37	22	48077075	48077075	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:48077075delT	uc003bik.1	+											Homo sapiens cDNA FLJ35788 fis, clone TESTI2005683.																														---	---	---	---
Unknown	0	broad.mit.edu	37	22	48205589	48205590	+	Intron	DEL	GT	-	-	rs139955340	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:48205589_48205590delGT	uc003bik.1	+											Homo sapiens cDNA FLJ35788 fis, clone TESTI2005683.																														---	---	---	---
Unknown	0	broad.mit.edu	37	22	48366996	48366997	+	IGR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:48366996_48366997insA								TBC1D22A (797274 upstream) : FAM19A5 (518291 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	48656977	48656979	+	IGR	DEL	CAT	-	-	rs111747572		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:48656977_48656979delCAT								None (None upstream) : FAM19A5 (228309 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	49150200	49150207	+	IGR	DEL	ATGTACGG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49150200_49150207delATGTACGG								FAM19A5 (2458 upstream) : C22orf34 (657969 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	49547784	49547785	+	IGR	INS	-	CACAGCGGGGACACGGGCA	CACAGCGGGGACACGGGCA	rs145607058	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49547784_49547785insCACAGCGGGGACACGGGCA								FAM19A5 (400042 upstream) : C22orf34 (260391 downstream)																																			---	---	---	---
IL17REL	400935	broad.mit.edu	37	22	50445384	50445386	+	Intron	DEL	AAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50445384_50445386delAAA	uc003bje.1	-							NM_001001694	NP_001001694			interleukin 17 receptor E-like											pancreas(1)	1		all_cancers(38;5.53e-07)|all_epithelial(38;3.84e-06)|all_lung(38;0.00208)|Breast(42;0.0104)|Lung NSC(38;0.0199)|Ovarian(80;0.0907)|Lung SC(80;0.236)		BRCA - Breast invasive adenocarcinoma(115;0.2)|LUAD - Lung adenocarcinoma(64;0.247)														---	---	---	---
TUBGCP6	85378	broad.mit.edu	37	22	50681882	50681885	+	Intron	DEL	AAAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50681882_50681885delAAAA	uc003bkb.1	-						TUBGCP6_uc010har.1_Intron|TUBGCP6_uc010has.1_Intron|TUBGCP6_uc010hau.1_Intron	NM_020461	NP_065194			tubulin, gamma complex associated protein 6						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	50716447	50716447	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50716447delG	uc003bkv.3	-						PLXNB2_uc003bkt.1_Intron|PLXNB2_uc003bku.1_Intron	NM_012401	NP_036533			plexin B2 precursor						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	X	685596	685597	+	IGR	INS	-	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:685596_685597insC								SHOX (65451 upstream) : CRLF2 (629290 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	844406	844407	+	IGR	DEL	GA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:844406_844407delGA								SHOX (224261 upstream) : CRLF2 (470480 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	1253383	1253383	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1253383delA								SHOX (633238 upstream) : CRLF2 (61504 downstream)																																			---	---	---	---
CRLF2	64109	broad.mit.edu	37	X	1330062	1330065	+	Intron	DEL	ATGG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1330062_1330065delATGG	uc004cpm.1	-											Homo sapiens mRNA for IL-XR, complete cds.							extracellular region|integral to membrane|plasma membrane	receptor activity			haematopoietic_and_lymphoid_tissue(7)	7		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)						Mis|T	P2RY8|IGH@	B-ALL|Downs associated ALL								---	---	---	---
ASMTL	8623	broad.mit.edu	37	X	1543842	1543845	+	Intron	DEL	TCCA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1543842_1543845delTCCA	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	2013159	2013160	+	IGR	DEL	TC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2013159_2013160delTC								ASMT (251186 upstream) : DHRSX (124397 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	2516017	2516017	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2516017delT								DHRSX (97002 upstream) : CD99 (93211 downstream)																																			---	---	---	---
GYG2	8908	broad.mit.edu	37	X	2778180	2778180	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2778180delT	uc004cqs.1	+						GYG2_uc004cqt.1_Intron|GYG2_uc004cqu.1_Intron|GYG2_uc004cqv.1_Intron|GYG2_uc004cqw.1_Intron|GYG2_uc004cqx.1_Intron|GYG2_uc010ndc.1_Intron	NM_003918	NP_003909			glycogenin 2 isoform b						glucose metabolic process|glycogen biosynthetic process|glycogen catabolic process	cytosol|soluble fraction	glycogenin glucosyltransferase activity			ovary(1)|kidney(1)	2		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)																---	---	---	---
Unknown	0	broad.mit.edu	37	X	6426462	6426462	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:6426462delA								NLGN4X (279756 upstream) : VCX3A (25198 downstream)																																			---	---	---	---
STS	412	broad.mit.edu	37	X	7077156	7077156	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:7077156delT	uc004crw.2	+						STS_uc011mhp.1_Intron|STS_uc004crx.1_Intron					Homo sapiens cDNA, FLJ94694, highly similar to Homo sapiens steroid sulfatase (microsomal), arylsulfatase C,isozyme S (STS), mRNA.						female pregnancy|steroid catabolic process	endoplasmic reticulum membrane|endosome|Golgi apparatus|integral to membrane|lysosome|microsome|plasma membrane	metal ion binding|steryl-sulfatase activity			central_nervous_system(1)	1		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)			Estrone(DB00655)									Ichthyosis				---	---	---	---
Unknown	0	broad.mit.edu	37	X	7533815	7533815	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:7533815delT								STS (261135 upstream) : VCX (276488 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	8434873	8434875	+	IGR	DEL	GGT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:8434873_8434875delGGT								VCX3B (323 upstream) : KAL1 (62041 downstream)																																			---	---	---	---
MID1	4281	broad.mit.edu	37	X	10539930	10539930	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:10539930delA	uc004cte.3	-						MID1_uc004ctg.3_Intron|MID1_uc004cth.3_Intron|MID1_uc004ctk.3_Intron|MID1_uc004cti.3_Intron|MID1_uc004ctj.3_Intron|MID1_uc011mie.1_Intron|MID1_uc004cug.1_Intron	NM_033290	NP_150632			midline 1						microtubule cytoskeleton organization|pattern specification process|positive regulation of stress-activated MAPK cascade	cytoplasm|microtubule|microtubule associated complex|spindle	ligase activity|ubiquitin protein ligase binding|zinc ion binding			ovary(2)|pancreas(1)	3																		---	---	---	---
ARHGAP6	395	broad.mit.edu	37	X	11364089	11364091	+	Intron	DEL	TTT	-	-	rs113261353		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:11364089_11364091delTTT	uc004cup.1	-						ARHGAP6_uc004cuo.1_Intron|ARHGAP6_uc004cur.1_Intron|ARHGAP6_uc004cun.1_Intron|ARHGAP6_uc011mif.1_Intron	NM_013427	NP_038286			Rho GTPase activating protein 6 isoform 1						actin filament polymerization|activation of phospholipase C activity|negative regulation of focal adhesion assembly|negative regulation of stress fiber assembly|Rho protein signal transduction	actin filament|cytosol	phospholipase activator activity|phospholipase binding|Rho GTPase activator activity|SH3 domain binding|SH3/SH2 adaptor activity			urinary_tract(1)|lung(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	13296854	13296854	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:13296854delT								FAM9C (234054 upstream) : ATXN3L (39916 downstream)																																			---	---	---	---
TRAPPC2	6399	broad.mit.edu	37	X	13734502	13734502	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:13734502delA	uc010nek.1	-						TRAPPC2_uc010nej.1_5'Flank|TRAPPC2_uc010nel.1_Intron|TRAPPC2_uc010nem.1_3'UTR	NM_001011658	NP_001011658			trafficking protein particle complex 2 isoform						ER to Golgi vesicle-mediated transport	intracellular					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	14073838	14073838	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:14073838delT								GEMIN8 (25803 upstream) : GLRA2 (473582 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	14852768	14852768	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:14852768delT								GLRA2 (102837 upstream) : FANCB (8761 downstream)																																			---	---	---	---
MOSPD2	158747	broad.mit.edu	37	X	14900930	14900932	+	Intron	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:14900930_14900932delTTT	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	15358274	15358274	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:15358274delT								PIGA (4614 upstream) : FIGF (5444 downstream)																																			---	---	---	---
BMX	660	broad.mit.edu	37	X	15554697	15554697	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:15554697delA	uc004cww.2	+						BMX_uc004cwx.3_Intron|BMX_uc004cwy.3_Intron	NM_203281	NP_975010			BMX non-receptor tyrosine kinase						cellular component disassembly involved in apoptosis|intracellular signal transduction|mesoderm development	cytosol	ATP binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding|signal transducer activity			lung(3)|ovary(2)	5	Hepatocellular(33;0.183)																	---	---	---	---
RBBP7	5931	broad.mit.edu	37	X	16867569	16867569	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	16896692	16896692	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:16896692delT								RBBP7 (8158 upstream) : REPS2 (68122 downstream)																																			---	---	---	---
NHS	4810	broad.mit.edu	37	X	17551340	17551341	+	Intron	DEL	GT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:17551340_17551341delGT	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)																	---	---	---	---
SH3KBP1	30011	broad.mit.edu	37	X	19890931	19890932	+	Intron	DEL	TC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:19890931_19890932delTC	uc004czm.2	-							NM_031892	NP_114098			SH3-domain kinase binding protein 1 isoform a						apoptosis|cell-cell signaling|endocytosis|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway	cytoplasmic vesicle membrane|cytoskeleton|cytosol|focal adhesion|nucleus|synapse|synaptosome	SH3 domain binding				0																		---	---	---	---
RPS6KA3	6197	broad.mit.edu	37	X	20212653	20212653	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:20212653delA	uc004czu.2	-						RPS6KA3_uc011mjk.1_Intron|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	21043269	21043269	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:21043269delT								RPS6KA3 (757746 upstream) : CNKSR2 (349711 downstream)																																			---	---	---	---
SMS	6611	broad.mit.edu	37	X	21967720	21967720	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:21967720delT	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)													---	---	---	---
PHEX	5251	broad.mit.edu	37	X	22196327	22196328	+	Intron	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:22196327_22196328insT	uc004dah.2	+						PHEX_uc011mjr.1_Intron|PHEX_uc011mjs.1_Intron	NM_000444	NP_000435			phosphate-regulating neutral endopeptidase						biomineral tissue development|cell-cell signaling|protein modification process|proteolysis|skeletal system development	integral to plasma membrane	aminopeptidase activity|metalloendopeptidase activity|zinc ion binding			ovary(2)|lung(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	22664501	22664501	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:22664501delA								ZNF645 (371927 upstream) : DDX53 (353586 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	22968782	22968782	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:22968782delA								ZNF645 (676208 upstream) : DDX53 (49305 downstream)																																			---	---	---	---
PTCHD1	139411	broad.mit.edu	37	X	23371727	23371729	+	Intron	DEL	AAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:23371727_23371729delAAA	uc004dal.3	+						PTCHD1_uc010nfu.1_Intron	NM_173495	NP_775766			patched domain containing 1						cognition|smoothened signaling pathway	integral to membrane|plasma membrane	hedgehog receptor activity			ovary(4)|kidney(1)|skin(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	24360894	24360894	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24360894delA								FAM48B2 (29462 upstream) : FAM48B1 (19984 downstream)																																			---	---	---	---
PDK3	5165	broad.mit.edu	37	X	24517162	24517162	+	Intron	DEL	T	-	-	rs113531183		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24517162delT	uc004dbg.2	+						PDK3_uc004dbh.2_Intron	NM_005391	NP_005382			pyruvate dehydrogenase kinase 3 isoform 2						glucose metabolic process|peptidyl-histidine phosphorylation|pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix	ATP binding|protein binding|pyruvate dehydrogenase (acetyl-transferring) kinase activity|two-component sensor activity			lung(4)|upper_aerodigestive_tract(1)|ovary(1)	6																		---	---	---	---
PDK3	5165	broad.mit.edu	37	X	24541023	24541024	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24541023_24541024delAA	uc004dbg.2	+						PDK3_uc004dbh.2_Intron	NM_005391	NP_005382			pyruvate dehydrogenase kinase 3 isoform 2						glucose metabolic process|peptidyl-histidine phosphorylation|pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix	ATP binding|protein binding|pyruvate dehydrogenase (acetyl-transferring) kinase activity|two-component sensor activity			lung(4)|upper_aerodigestive_tract(1)|ovary(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	25117851	25117852	+	IGR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:25117851_25117852insA								ARX (83786 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	26451237	26451237	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:26451237delT								MAGEB6 (237475 upstream) : VENTXP1 (125217 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	26758534	26758535	+	IGR	DEL	AC	-	-	rs35017436		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:26758534_26758535delAC								VENTXP1 (179366 upstream) : SMEK3P (719793 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	26923631	26923631	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:26923631delA								VENTXP1 (344463 upstream) : SMEK3P (554697 downstream)																																			---	---	---	---
IL1RAPL1	11141	broad.mit.edu	37	X	28665054	28665054	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:28665054delT	uc004dby.2	+							NM_014271	NP_055086			interleukin 1 receptor accessory protein-like 1						innate immune response|negative regulation of calcium ion transport via voltage-gated calcium channel activity|negative regulation of exocytosis|regulation of neuron projection development	cytoplasm|integral to membrane|plasma membrane	protein binding|transmembrane receptor activity			ovary(3)|lung(1)|pancreas(1)	5																		---	---	---	---
IL1RAPL1	11141	broad.mit.edu	37	X	29914124	29914124	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:29914124delA	uc004dby.2	+							NM_014271	NP_055086			interleukin 1 receptor accessory protein-like 1						innate immune response|negative regulation of calcium ion transport via voltage-gated calcium channel activity|negative regulation of exocytosis|regulation of neuron projection development	cytoplasm|integral to membrane|plasma membrane	protein binding|transmembrane receptor activity			ovary(3)|lung(1)|pancreas(1)	5																		---	---	---	---
IL1RAPL1	11141	broad.mit.edu	37	X	29946079	29946085	+	Intron	DEL	AGACCAT	-	-	rs142520816		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:29946079_29946085delAGACCAT	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	30106214	30106214	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:30106214delT								IL1RAPL1 (132197 upstream) : MAGEB2 (127461 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	30516647	30516647	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:30516647delA								NR0B1 (189152 upstream) : CXorf21 (60294 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	35758592	35758592	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:35758592delT								FAM47B (795558 upstream) : MAGEB16 (57867 downstream)																																			---	---	---	---
PRRG1	5638	broad.mit.edu	37	X	37245014	37245015	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:37245014_37245015delTT	uc004ddn.2	+						PRRG1_uc004ddo.2_Intron|PRRG1_uc010ngx.1_5'Flank	NM_000950	NP_000941			proline rich Gla (G-carboxyglutamic acid) 1							extracellular region|integral to plasma membrane	calcium ion binding			ovary(1)|breast(1)	2																		---	---	---	---
SYTL5	94122	broad.mit.edu	37	X	37934159	37934160	+	Intron	DEL	AC	-	-	rs150823850		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:37934159_37934160delAC	uc004ddu.2	+						SYTL5_uc004ddv.2_Intron|SYTL5_uc004ddx.2_Intron	NM_001163335	NP_001156807			synaptotagmin-like 5 isoform 1						intracellular protein transport	membrane	metal ion binding|Rab GTPase binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	39787952	39787952	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:39787952delA								None (None upstream) : BCOR (122549 downstream)																																			---	---	---	---
MED14	9282	broad.mit.edu	37	X	40540221	40540221	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:40540221delA	uc004dex.3	-							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	40714222	40714222	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:40714222delA								LOC100132831 (21773 upstream) : USP9X (230666 downstream)																																			---	---	---	---
CASK	8573	broad.mit.edu	37	X	41673997	41673997	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:41673997delA	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	42093983	42093983	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:42093983delT								CASK (311696 upstream) : PPP1R2P9 (542636 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	43055805	43055805	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:43055805delA	uc004dfw.1	+											Homo sapiens cDNA FLJ31543 fis, clone NT2RI2000841.																														---	---	---	---
Unknown	0	broad.mit.edu	37	X	45942097	45942097	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:45942097delT								MIR222 (335567 upstream) : ZNF673 (364527 downstream)																																			---	---	---	---
UBA1	7317	broad.mit.edu	37	X	47073266	47073266	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47073266delA	uc004dhj.3	+						UBA1_uc004dhk.3_Intron|UBA1_uc004dhm.2_Intron	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	48033462	48033462	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48033462delA								SSX6 (53393 upstream) : SSX5 (12194 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	48131158	48131160	+	IGR	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48131158_48131160delTTT								SSX1 (4279 upstream) : SSX3 (74703 downstream)																																			---	---	---	---
GAGE10	643832	broad.mit.edu	37	X	49158062	49158064	+	5'Flank	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:49158062_49158064delTTT	uc010nir.1	+							NM_001098413	NP_001091883			G antigen 10												0	Ovarian(276;0.236)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	54700482	54700482	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54700482delT								GNL3L (108509 upstream) : ITIH5L (74850 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	61784569	61784569	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:61784569delA								None (None upstream) : SPIN4 (782539 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	61805340	61805340	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:61805340delA								None (None upstream) : SPIN4 (761768 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	61834232	61834233	+	IGR	INS	-	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:61834232_61834233insG								None (None upstream) : SPIN4 (732875 downstream)																																			---	---	---	---
HEPH	9843	broad.mit.edu	37	X	65420084	65420085	+	Intron	DEL	GT	-	-	rs66666374		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:65420084_65420085delGT	uc011moz.1	+						HEPH_uc004dwn.2_Intron|HEPH_uc004dwo.2_Intron|HEPH_uc010nkr.2_Intron|HEPH_uc011mpa.1_Intron	NM_138737	NP_620074			hephaestin isoform a						cellular iron ion homeostasis|copper ion transport|transmembrane transport	integral to membrane|plasma membrane	copper ion binding|oxidoreductase activity			lung(5)|ovary(4)	9																		---	---	---	---
AR	367	broad.mit.edu	37	X	66800010	66800011	+	Intron	DEL	AA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:66800010_66800011delAA	uc004dwu.1	+						AR_uc011mpd.1_Intron|AR_uc011mpe.1_Intron|AR_uc011mpf.1_Intron|AR_uc004dwv.1_Intron	NM_000044	NP_000035			androgen receptor isoform 1						cell death|cell growth|cell proliferation|cell-cell signaling|negative regulation of apoptosis|negative regulation of integrin biosynthetic process|positive regulation of cell proliferation|positive regulation of integrin biosynthetic process|positive regulation of NF-kappaB transcription factor activity|positive regulation of phosphorylation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase III promoter|regulation of establishment of protein localization in plasma membrane|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transport	cytoplasm|nuclear chromatin|nucleoplasm	androgen binding|androgen receptor activity|beta-catenin binding|enzyme binding|ligand-regulated transcription factor activity|protein dimerization activity|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding|zinc ion binding			ovary(3)|lung(2)|breast(2)|central_nervous_system(1)	8	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone(DB04839)|Dromostanolone(DB00858)|Finasteride(DB01216)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Nandrolone(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Testosterone(DB00624)									Androgen_Insensitivity_Syndrome				---	---	---	---
OPHN1	4983	broad.mit.edu	37	X	67533150	67533150	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:67533150delC	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																		---	---	---	---
OPHN1	4983	broad.mit.edu	37	X	67542247	67542248	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:67542247_67542248insA	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																		---	---	---	---
OPHN1	4983	broad.mit.edu	37	X	67630238	67630238	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:67630238delA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	68102236	68102236	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:68102236delG								EFNB1 (36207 upstream) : PJA1 (278346 downstream)																																			---	---	---	---
TAF1	6872	broad.mit.edu	37	X	70628174	70628174	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70628174delT	uc004dzu.3	+						BCYRN1_uc011mpt.1_Intron|TAF1_uc004dzt.3_Intron|TAF1_uc004dzv.3_Intron|TAF1_uc010nld.1_Intron|TAF1_uc010nle.1_Intron|TAF1_uc010nlf.1_Intron|TAF1_uc004dzx.2_Intron|TAF1_uc004dzy.2_Intron	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)																---	---	---	---
TAF1	6872	broad.mit.edu	37	X	70730191	70730191	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70730191delA	uc010nlf.1	+						BCYRN1_uc011mpt.1_Intron|TAF1_uc010nle.1_Intron|TAF1_uc004dzx.2_Intron|TAF1_uc004dzy.2_Intron|TAF1_uc004dzw.1_Intron|TAF1_uc010nlg.1_Intron					SubName: Full=Putative uncharacterized protein TAF1;						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)																---	---	---	---
Unknown	0	broad.mit.edu	37	X	72234618	72234621	+	IGR	DEL	AAAA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:72234618_72234621delAAAA								PABPC1L2B (9068 upstream) : PABPC1L2A (62556 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	72371835	72371836	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:72371835_72371836delTT								NAP1L6 (23916 upstream) : NAP1L2 (60319 downstream)																																			---	---	---	---
CHIC1	53344	broad.mit.edu	37	X	72846220	72846220	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:72846220delT	uc004ebk.3	+						CHIC1_uc010nlo.2_Intron|CHIC1_uc011mql.1_Intron|CHIC1_uc004ebl.3_Intron	NM_001039840	NP_001034929			cysteine-rich hydrophobic domain 1							cytoplasmic membrane-bounded vesicle|plasma membrane					0	Renal(35;0.156)																	---	---	---	---
NCRNA00183	554203	broad.mit.edu	37	X	73179783	73179784	+	Intron	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73179783_73179784delTG	uc004ebo.2	+						NCRNA00183_uc004ebp.2_Intron					Homo sapiens cDNA FLJ31610 fis, clone NT2RI2002865.												0																		---	---	---	---
NCRNA00182	100302692	broad.mit.edu	37	X	73266080	73266080	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73266080delT	uc010nlq.1	-						NCRNA00183_uc004ebp.2_Intron					Homo sapiens cDNA FLJ33139 fis, clone UTERU1000109.												0																		---	---	---	---
ABCB7	22	broad.mit.edu	37	X	74289304	74289304	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:74289304delA	uc004eca.2	-						ABCB7_uc004ebz.2_Intron|ABCB7_uc011mqn.1_Intron|ABCB7_uc010nls.2_Intron|ABCB7_uc010nlt.2_Intron	NM_004299	NP_004290			ATP-binding cassette, sub-family B, member 7						cellular iron ion homeostasis	integral to membrane|mitochondrial inner membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances|heme transporter activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	75674272	75674272	+	IGR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:75674272delG								MAGEE1 (22528 upstream) : MIR384 (465426 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	76251573	76251573	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:76251573delT								MIR325 (25647 upstream) : FGF16 (458074 downstream)																																			---	---	---	---
ATRX	546	broad.mit.edu	37	X	76892349	76892358	+	Intron	DEL	AGGAGGGAGG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:76892349_76892358delAGGAGGGAGG	uc004ecp.3	-						ATRX_uc004ecq.3_Intron|ATRX_uc004eco.3_Intron	NM_000489	NP_000480			transcriptional regulator ATRX isoform 1						DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent	nuclear heterochromatin	ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(14)|pancreas(12)|lung(1)|breast(1)|skin(1)|kidney(1)	30					Phosphatidylserine(DB00144)			Mis|F|N		Pancreatic neuroendocrine tumors		ATR-X (alpha thalassemia/mental retardation) syndrome						---	---	---	---
Unknown	0	broad.mit.edu	37	X	79812520	79812521	+	IGR	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:79812520_79812521delAC								FAM46D (111710 upstream) : BRWD3 (119162 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	80177590	80177590	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:80177590delA								BRWD3 (112357 upstream) : HMGN5 (191610 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	81230356	81230356	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:81230356delA								SH3BGRL (676314 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	81313515	81313515	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:81313515delT								SH3BGRL (759473 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	82099702	82099702	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:82099702delA								None (None upstream) : POU3F4 (663567 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	84000149	84000149	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:84000149delT								HDX (242691 upstream) : UBE2DNL (189008 downstream)																																			---	---	---	---
ZNF711	7552	broad.mit.edu	37	X	84502861	84502861	+	Intron	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:84502861delG	uc004eeo.2	+						ZNF711_uc004eep.2_Intron|ZNF711_uc004eeq.2_Intron	NM_021998	NP_068838			zinc finger protein 711						positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding|sequence-specific DNA binding|zinc ion binding			ovary(3)|skin(1)	4																		---	---	---	---
CHM	1121	broad.mit.edu	37	X	85259594	85259594	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:85259594delA	uc004eet.2	-						CHM_uc011mqz.1_Intron|CHM_uc004eeu.3_Intron|CHM_uc004eev.3_Intron	NM_000390	NP_000381			choroideremia isoform a						intracellular protein transport|protein geranylgeranylation|response to stimulus|visual perception	Rab-protein geranylgeranyltransferase complex	GTPase activator activity|Rab geranylgeranyltransferase activity			ovary(1)	1		all_lung(315;5.41e-06)																---	---	---	---
DACH2	117154	broad.mit.edu	37	X	85878494	85878494	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:85878494delA	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	87057097	87057098	+	IGR	DEL	TG	-	-	rs67134475		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:87057097_87057098delTG								KLHL4 (132047 upstream) : CPXCR1 (945128 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	87672238	87672239	+	IGR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:87672238_87672239insA								KLHL4 (747188 upstream) : CPXCR1 (329987 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	92037228	92037228	+	IGR	DEL	A	-	-	rs35105920		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:92037228delA								PCDH11X (159002 upstream) : NAP1L3 (888701 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	93507658	93507658	+	IGR	DEL	T	-	-	rs113940846		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:93507658delT								FAM133A (540397 upstream) : MIR548M (810482 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	95096298	95096298	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:95096298delC								MIR548M (778073 upstream) : LOC643486 (495788 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	95364650	95364650	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:95364650delA								None (None upstream) : LOC643486 (227436 downstream)																																			---	---	---	---
DIAPH2	1730	broad.mit.edu	37	X	96118619	96118619	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:96118619delA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	99521095	99521095	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:99521095delA								LOC442459 (326254 upstream) : PCDH19 (25555 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	100584069	100584069	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100584069delT								TAF7L (36024 upstream) : TIMM8A (16575 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	101386834	101386834	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:101386834delC								TCEAL2 (4151 upstream) : TCEAL6 (8101 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	102420613	102420616	+	IGR	DEL	TCTT	-	-	rs72165464		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:102420613_102420616delTCTT								NXF3 (72591 upstream) : BEX4 (49404 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	105220272	105220272	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:105220272delA								NRK (17676 upstream) : SERPINA7 (56925 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	105399482	105399483	+	IGR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:105399482_105399483insA								SERPINA7 (116766 upstream) : MUM1L1 (12815 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	105507786	105507787	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:105507786_105507787delTT								MUM1L1 (54838 upstream) : CXorf57 (347373 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	106270762	106270762	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:106270762delA								MORC4 (27320 upstream) : RBM41 (36888 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	106282848	106282850	+	IGR	DEL	AAG	-	-	rs72618349		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:106282848_106282850delAAG								MORC4 (39406 upstream) : RBM41 (24800 downstream)																																			---	---	---	---
TMEM164	84187	broad.mit.edu	37	X	109348300	109348301	+	Intron	INS	-	TT	TT			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:109348300_109348301insTT	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																		---	---	---	---
AMMECR1	9949	broad.mit.edu	37	X	109468163	109468163	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:109468163delT	uc004eoo.2	-						AMMECR1_uc004eop.2_Intron|AMMECR1_uc004eoq.2_Intron	NM_015365	NP_056180			AMMECR1 protein isoform 1												0																		---	---	---	---
PAK3	5063	broad.mit.edu	37	X	110390711	110390711	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:110390711delT	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	110813513	110813514	+	IGR	INS	-	TCTCTC	TCTCTC			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:110813513_110813514insTCTCTC								DCX (158107 upstream) : ALG13 (110899 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	110919724	110919724	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:110919724delT								DCX (264318 upstream) : ALG13 (4689 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	112600512	112600512	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:112600512delC								AMOT (516469 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	113500915	113500916	+	IGR	DEL	AG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:113500915_113500916delAG								None (None upstream) : HTR2C (317635 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	114145678	114145678	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:114145678delA								HTR2C (1054 upstream) : IL13RA2 (92861 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	115079036	115079036	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:115079036delA	uc004eqg.1	-											Homo sapiens hypothetical protein LOC642776, mRNA (cDNA clone IMAGE:3533146), partial cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	X	116683133	116683133	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:116683133delT								None (None upstream) : KLHL13 (348644 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	117386132	117386133	+	IGR	DEL	AC	-	-	rs67781833		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:117386132_117386133delAC								KLHL13 (135344 upstream) : WDR44 (93909 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	118598124	118598127	+	IGR	DEL	CGCA	-	-	rs10590034		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:118598124_118598127delCGCA								SLC25A43 (9693 upstream) : LOC100303728 (1870 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	118913001	118913008	+	IGR	DEL	GGAGGGAA	-	-	rs66547601		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:118913001_118913008delGGAGGGAA								ANKRD58 (18837 upstream) : RPL39 (7461 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	119486459	119486459	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:119486459delT								FAM70A (41068 upstream) : ATP1B4 (9481 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	120859391	120859394	+	IGR	DEL	TTTT	-	-	rs144549385		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:120859391_120859394delTTTT								GLUD2 (675597 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	122109983	122109983	+	IGR	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:122109983delC								None (None upstream) : GRIA3 (208113 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	123314732	123314732	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:123314732delT								STAG2 (78229 upstream) : SH2D1A (165416 downstream)																																			---	---	---	---
ODZ1	10178	broad.mit.edu	37	X	123587688	123587689	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:123587688_123587689delTT	uc004euj.2	-						ODZ1_uc011muj.1_Intron|ODZ1_uc010nqy.2_Intron	NM_014253	NP_055068			odz, odd Oz/ten-m homolog 1 isoform 3						immune response|negative regulation of cell proliferation|nervous system development|signal transduction	extracellular region	heparin binding			ovary(11)|breast(4)|large_intestine(2)|skin(2)|pancreas(2)|upper_aerodigestive_tract(1)|lung(1)	23																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	124699914	124699914	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:124699914delA								ODZ1 (602248 upstream) : DCAF12L2 (598600 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	126035443	126035443	+	IGR	DEL	A	-	-	rs112140403		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:126035443delA								CXorf64 (79677 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	126785457	126785457	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:126785457delA								CXorf64 (829691 upstream) : ACTRT1 (399486 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	126903600	126903600	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:126903600delT								CXorf64 (947834 upstream) : ACTRT1 (281343 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	127572669	127572670	+	IGR	DEL	AC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:127572669_127572670delAC								ACTRT1 (386287 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	128174839	128174839	+	IGR	DEL	A	-	-	rs75256475		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:128174839delA								ACTRT1 (988457 upstream) : SMARCA1 (405641 downstream)																																			---	---	---	---
APLN	8862	broad.mit.edu	37	X	128781742	128781742	+	3'UTR	DEL	G	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:128781742delG	uc004eus.2	-	3						NM_017413	NP_059109			apelin preproprotein						immune response|lactation|signal transduction		hormone activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	132637886	132637886	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:132637886delT								GPC4 (88681 upstream) : GPC3 (31890 downstream)																																			---	---	---	---
GPC3	2719	broad.mit.edu	37	X	132796078	132796078	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:132796078delT	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	133668425	133668425	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:133668425delT								HPRT1 (33729 upstream) : MIR450B (5790 downstream)																																			---	---	---	---
DDX26B	203522	broad.mit.edu	37	X	134704171	134704171	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:134704171delT	uc004eyw.3	+						DDX26B_uc004eyx.3_Intron	NM_182540	NP_872346			DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide												0	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
SLC9A6	10479	broad.mit.edu	37	X	135078915	135078915	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135078915delT	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)																	---	---	---	---
MAP7D3	79649	broad.mit.edu	37	X	135327915	135327916	+	Intron	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135327915_135327916insA	uc004ezt.2	-						MAP7D3_uc004ezs.2_Intron|MAP7D3_uc011mwc.1_Intron|MAP7D3_uc010nsa.1_Intron	NM_024597	NP_078873			MAP7 domain containing 3							cytoplasm|spindle				ovary(2)|central_nervous_system(1)|skin(1)	4	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	135531221	135531222	+	IGR	INS	-	AG	AG	rs35151752		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135531221_135531222insAG								GPR112 (32174 upstream) : BRS3 (38903 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	136059145	136059145	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:136059145delT	uc004fai.1	+											Homo sapiens cDNA FLJ31132 fis, clone IMR322000953.																														---	---	---	---
Unknown	0	broad.mit.edu	37	X	136337993	136337994	+	IGR	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:136337993_136337994delTT								GPR101 (224160 upstream) : ZIC3 (310352 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	136368664	136368665	+	IGR	INS	-	T	T	rs150333535		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:136368664_136368665insT								GPR101 (254831 upstream) : ZIC3 (279681 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	136678048	136678048	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:136678048delT								ZIC3 (23791 upstream) : None (None downstream)																																			---	---	---	---
FGF13	2258	broad.mit.edu	37	X	137870201	137870201	+	Intron	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:137870201delT	uc004faq.2	-						FGF13_uc011mwi.1_Intron|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	138481707	138481707	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:138481707delT								FGF13 (194522 upstream) : F9 (131188 downstream)																																			---	---	---	---
ATP11C	286410	broad.mit.edu	37	X	138850654	138850655	+	Intron	DEL	TT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:138850654_138850655delTT	uc004faz.2	-						ATP11C_uc004fax.2_5'Flank|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	138934013	138934013	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:138934013delT								ATP11C (19566 upstream) : MIR505 (72294 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	141025727	141025728	+	IGR	DEL	TC	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:141025727_141025728delTC								MAGEC1 (28545 upstream) : MAGEC2 (264402 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	142474080	142474080	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:142474080delA								SPANXN4 (352015 upstream) : SPANXN3 (122485 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	142760705	142760706	+	IGR	INS	-	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:142760705_142760706insA								SLITRK4 (37109 upstream) : SPANXN2 (34350 downstream)																																			---	---	---	---
SPANXN2	494119	broad.mit.edu	37	X	142795987	142795987	+	Intron	DEL	C	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:142795987delC	uc004fbz.2	-							NM_001009615	NP_001009615			SPANX-N2 protein											ovary(1)	1	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	142859140	142859140	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:142859140delT								SPANXN2 (54624 upstream) : UBE2NL (108033 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	145609216	145609217	+	IGR	INS	-	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:145609216_145609217insT								MIR891A (499826 upstream) : CXorf51 (282085 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	146324949	146324949	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:146324949delA								MIR508 (6404 upstream) : MIR509-2 (15329 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	147502547	147502547	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:147502547delT								FMR1NB (394367 upstream) : AFF2 (79592 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	148344782	148344782	+	IGR	DEL	C	-	-	rs56814175		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:148344782delC								AFF2 (262590 upstream) : IDS (215515 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	148882271	148882271	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:148882271delT								HSFX1 (23754 upstream) : MAGEA8 (127725 downstream)																																			---	---	---	---
MTM1	4534	broad.mit.edu	37	X	149826092	149826093	+	Intron	INS	-	A	A	rs112119260		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:149826092_149826093insA	uc004fef.3	+						MTM1_uc011mxx.1_Intron|MTM1_uc011mxy.1_Intron|MTM1_uc011mxz.1_Intron|MTM1_uc010nte.2_Intron	NM_000252	NP_000243			myotubularin						endosome to lysosome transport|intermediate filament organization|mitochondrion distribution|mitochondrion morphogenesis|phosphatidylinositol dephosphorylation|protein transport|regulation of vacuole organization	filopodium|late endosome|plasma membrane|ruffle	intermediate filament binding|phosphatidylinositol binding|phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein tyrosine phosphatase activity			upper_aerodigestive_tract(1)|ovary(1)|kidney(1)	3	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	150164852	150164852	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:150164852delA								HMGB3 (5606 upstream) : GPR50 (180207 downstream)																																			---	---	---	---
NSDHL	50814	broad.mit.edu	37	X	152026395	152026395	+	Intron	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:152026395delA	uc004fgt.1	+						NSDHL_uc004fgs.1_Intron	NM_001129765	NP_001123237			NAD(P) dependent steroid dehydrogenase-like						cholesterol biosynthetic process	endoplasmic reticulum membrane|integral to membrane	3-beta-hydroxy-delta5-steroid dehydrogenase activity|binding|C-3 sterol dehydrogenase (C-4 sterol decarboxylase) activity|sterol-4-alpha-carboxylate 3-dehydrogenase (decarboxylating) activity				0	Acute lymphoblastic leukemia(192;6.56e-05)				NADH(DB00157)													---	---	---	---
Unknown	0	broad.mit.edu	37	X	153264906	153264906	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153264906delT								TMEM187 (16260 upstream) : IRAK1 (11051 downstream)																																			---	---	---	---
F8	2157	broad.mit.edu	37	X	154148489	154148491	+	Intron	DEL	TTT	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:154148489_154148491delTTT	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	X	154505187	154505187	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:154505187delT								RAB39B (11335 upstream) : CLIC2 (315 downstream)																																			---	---	---	---
CLIC2	1193	broad.mit.edu	37	X	154518436	154518437	+	Intron	DEL	AA	-	-	rs79091604		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:154518436_154518437delAA	uc004fnf.2	-						CLIC2_uc010nvj.1_Intron	NM_001289	NP_001280			chloride intracellular channel 2						signal transduction	chloride channel complex|cytoplasm|nucleus	voltage-gated chloride channel activity			large_intestine(1)|ovary(1)|skin(1)	3	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)																	---	---	---	---
Unknown	0	broad.mit.edu	37	Y	9992532	9992532	+	IGR	DEL	A	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9992532delA								TTTY22 (341678 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	10070808	10070808	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:10070808delT								TTTY22 (419954 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	13262505	13262506	+	IGR	DEL	TG	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13262505_13262506delTG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	13415408	13415408	+	IGR	DEL	T	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13415408delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	13445284	13445285	+	IGR	INS	-	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13445284_13445285insG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	13447217	13447226	+	IGR	DEL	CACTCCGCTA	-	-			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13447217_13447226delCACTCCGCTA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	59019360	59019361	+	IGR	DEL	AT	-	-	rs138718736		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:59019360_59019361delAT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	59033281	59033287	+	IGR	DEL	TTGTTGT	-	-	rs146170488		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:59033281_59033287delTTGTTGT								None (None upstream) : None (None downstream)																																			---	---	---	---
LRRC47	57470	broad.mit.edu	37	1	3697831	3697831	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3697831C>T	uc001akx.1	-	7	1601	c.1573G>A	c.(1573-1575)GAT>AAT	p.D525N		NM_020710	NP_065761	Q8N1G4	LRC47_HUMAN	leucine rich repeat containing 47	525					translation		phenylalanine-tRNA ligase activity|RNA binding			large_intestine(1)|ovary(1)	2	all_cancers(77;0.0375)|Ovarian(185;0.0634)|all_lung(157;0.208)|Lung NSC(156;0.21)	all_epithelial(116;1.34e-16)|all_lung(118;2.53e-06)|Lung NSC(185;0.00028)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Lung SC(97;0.0743)|Ovarian(437;0.127)		Epithelial(90;5.49e-39)|OV - Ovarian serous cystadenocarcinoma(86;1.43e-22)|GBM - Glioblastoma multiforme(42;3.69e-16)|Colorectal(212;1.21e-05)|COAD - Colon adenocarcinoma(227;5.87e-05)|Kidney(185;0.000367)|BRCA - Breast invasive adenocarcinoma(365;0.000704)|KIRC - Kidney renal clear cell carcinoma(229;0.00567)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.124)														---	---	---	---
H6PD	9563	broad.mit.edu	37	1	9307041	9307041	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9307041T>C	uc001apt.2	+	3	917	c.644T>C	c.(643-645)CTG>CCG	p.L215P		NM_004285	NP_004276	O95479	G6PE_HUMAN	hexose-6-phosphate dehydrogenase precursor	215	Glucose 1-dehydrogenase.					endoplasmic reticulum lumen	6-phosphogluconolactonase activity|glucose 1-dehydrogenase|glucose-6-phosphate dehydrogenase activity|NADP binding				0	all_lung(157;0.23)	all_epithelial(116;1.28e-19)|all_lung(118;5.22e-06)|Lung NSC(185;1.98e-05)|Renal(390;0.000147)|Breast(348;0.00109)|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;1.88e-07)|COAD - Colon adenocarcinoma(227;7.47e-05)|Kidney(185;0.000244)|KIRC - Kidney renal clear cell carcinoma(229;0.000905)|STAD - Stomach adenocarcinoma(132;0.00176)|BRCA - Breast invasive adenocarcinoma(304;0.00183)|READ - Rectum adenocarcinoma(331;0.0419)	NADH(DB00157)													---	---	---	---
PIK3CD	5293	broad.mit.edu	37	1	9778917	9778917	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9778917G>A	uc001aqb.3	+	9	1394	c.1186G>A	c.(1186-1188)GCC>ACC	p.A396T	PIK3CD_uc010oaf.1_Missense_Mutation_p.A396T|PIK3CD_uc001aqe.3_Missense_Mutation_p.A361T	NM_005026	NP_005017	O00329	PK3CD_HUMAN	catalytic phosphatidylinositol 3-kinase delta	396					phosphatidylinositol-mediated signaling|protein phosphorylation	phosphatidylinositol 3-kinase complex|plasma membrane	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity|protein binding			lung(4)|skin(2)|central_nervous_system(1)	7	all_lung(157;0.222)	all_lung(118;2.44e-05)|Lung NSC(185;4.08e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0231)|Colorectal(212;7.52e-08)|COAD - Colon adenocarcinoma(227;1.78e-05)|Kidney(185;0.000322)|KIRC - Kidney renal clear cell carcinoma(229;0.00114)|BRCA - Breast invasive adenocarcinoma(304;0.0021)|STAD - Stomach adenocarcinoma(132;0.00395)|READ - Rectum adenocarcinoma(331;0.0419)														---	---	---	---
CASZ1	54897	broad.mit.edu	37	1	10715762	10715762	+	Missense_Mutation	SNP	C	T	T	rs150917673	byFrequency;by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10715762C>T	uc001aro.2	-	9	1929	c.1609G>A	c.(1609-1611)GTC>ATC	p.V537I	CASZ1_uc001arp.1_Missense_Mutation_p.V537I|CASZ1_uc009vmx.2_Missense_Mutation_p.V561I	NM_001079843	NP_001073312	Q86V15	CASZ1_HUMAN	castor homolog 1, zinc finger isoform a	537					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|zinc ion binding			skin(1)	1	Ovarian(185;0.203)|all_lung(157;0.204)	Lung NSC(185;4.96e-06)|all_lung(284;1.22e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00212)|Hepatocellular(190;0.00913)|Ovarian(437;0.0229)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;3.54e-08)|COAD - Colon adenocarcinoma(227;9.56e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000219)|Kidney(185;0.00142)|KIRC - Kidney renal clear cell carcinoma(229;0.00381)|READ - Rectum adenocarcinoma(331;0.0419)|STAD - Stomach adenocarcinoma(132;0.0623)														---	---	---	---
EXOSC10	5394	broad.mit.edu	37	1	11142746	11142746	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11142746G>A	uc001asa.2	-	10	1329	c.1279C>T	c.(1279-1281)CGC>TGC	p.R427C	EXOSC10_uc001asb.2_Missense_Mutation_p.R427C|EXOSC10_uc009vmy.1_Missense_Mutation_p.R427C	NM_001001998	NP_001001998	Q01780	EXOSX_HUMAN	exosome component 10 isoform 1	427					CUT catabolic process|histone mRNA catabolic process|maturation of 5.8S rRNA|nuclear polyadenylation-dependent rRNA catabolic process|nuclear retention of unspliced pre-mRNA at the site of transcription|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	cytoplasm|nuclear exosome (RNase complex)|nucleolus|transcriptionally active chromatin	3'-5' exonuclease activity|exoribonuclease activity|identical protein binding|nucleotide binding|protein serine/threonine kinase activity|RNA binding			upper_aerodigestive_tract(1)	1	Ovarian(185;0.249)	Lung NSC(185;1.74e-05)|all_lung(284;2.05e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00262)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;4.18e-07)|COAD - Colon adenocarcinoma(227;8.33e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000315)|Kidney(185;0.000832)|KIRC - Kidney renal clear cell carcinoma(229;0.00269)|READ - Rectum adenocarcinoma(331;0.0526)|STAD - Stomach adenocarcinoma(313;0.202)														---	---	---	---
PRDM2	7799	broad.mit.edu	37	1	14057532	14057532	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:14057532C>T	uc001avi.2	+	3	903	c.47C>T	c.(46-48)GCT>GTT	p.A16V	PRDM2_uc001avg.2_Missense_Mutation_p.A16V|PRDM2_uc001avh.2_Missense_Mutation_p.A16V|PRDM2_uc001avj.2_RNA	NM_012231	NP_036363	Q13029	PRDM2_HUMAN	retinoblastoma protein-binding zinc finger	16						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)														---	---	---	---
SPEN	23013	broad.mit.edu	37	1	16258453	16258453	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16258453C>T	uc001axk.1	+	11	5922	c.5718C>T	c.(5716-5718)AGC>AGT	p.S1906S	SPEN_uc010obp.1_Silent_p.S1865S	NM_015001	NP_055816	Q96T58	MINT_HUMAN	spen homolog, transcriptional regulator	1906					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	16464386	16464386	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16464386C>T	uc001aya.1	-	5	1411	c.1274G>A	c.(1273-1275)CGC>CAC	p.R425H	EPHA2_uc010oca.1_Missense_Mutation_p.R425H	NM_004431	NP_004422	P29317	EPHA2_HUMAN	ephrin receptor EphA2 precursor	425	Extracellular (Potential).|Fibronectin type-III 1.				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	16892157	16892157	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16892157T>C	uc009vos.1	-	28	4148	c.3260A>G	c.(3259-3261)AAA>AGA	p.K1087R	uc001ayw.2_5'Flank	NM_017940	NP_060410	Q3BBV0	NBPF1_HUMAN	hypothetical protein LOC55672	1087	NBPF 7.					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)														---	---	---	---
NBPF1	55672	broad.mit.edu	37	1	16913543	16913543	+	Splice_Site	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16913543A>G	uc009vos.1	-	11	1666	c.778_splice	c.e11+1	p.V260_splice	NBPF1_uc009vot.1_Intron|NBPF1_uc001ayz.1_Intron|NBPF1_uc010oce.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)														---	---	---	---
ATP13A2	23400	broad.mit.edu	37	1	17313587	17313587	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17313587T>C	uc001baa.2	-	26	3227	c.3037A>G	c.(3037-3039)ACC>GCC	p.T1013A	ATP13A2_uc001azz.1_Missense_Mutation_p.T160A|ATP13A2_uc001bab.2_Missense_Mutation_p.T1008A|ATP13A2_uc001bac.2_Missense_Mutation_p.T969A	NM_022089	NP_071372	Q9NQ11	AT132_HUMAN	ATPase type 13A2 isoform 1	1013	Helical; (Potential).				ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			skin(2)|ovary(1)|central_nervous_system(1)	4		Colorectal(325;0.000147)|Breast(348;0.00104)|Renal(390;0.00145)|Lung NSC(340;0.00566)|all_lung(284;0.00797)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|COAD - Colon adenocarcinoma(227;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;1.99e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.182)														---	---	---	---
PADI1	29943	broad.mit.edu	37	1	17566229	17566229	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17566229A>T	uc001bah.1	+	14	1675	c.1583A>T	c.(1582-1584)AAT>ATT	p.N528I	PADI1_uc010oco.1_Missense_Mutation_p.N85I|PADI1_uc010ocp.1_Missense_Mutation_p.N85I|PADI1_uc010ocq.1_5'UTR|PADI1_uc009vpb.1_5'UTR	NM_013358	NP_037490	Q9ULC6	PADI1_HUMAN	peptidylarginine deiminase type I	528					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)													---	---	---	---
CAPZB	832	broad.mit.edu	37	1	19671710	19671710	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19671710G>A	uc010ocz.1	-	7	1140	c.712C>T	c.(712-714)CAC>TAC	p.H238Y	CAPZB_uc001bce.2_Missense_Mutation_p.H209Y|CAPZB_uc009vpk.2_Missense_Mutation_p.H235Y|CAPZB_uc001bcd.2_Missense_Mutation_p.H197Y	NM_004930	NP_004921	P47756	CAPZB_HUMAN	F-actin capping protein beta subunit	209					actin cytoskeleton organization|actin filament capping|blood coagulation|cellular component movement	cytosol|F-actin capping protein complex|WASH complex	actin binding				0		Colorectal(325;3.93e-05)|Renal(390;0.000147)|all_lung(284;0.000169)|Lung NSC(340;0.000202)|Breast(348;0.000496)|Ovarian(437;0.00428)|Myeloproliferative disorder(586;0.0262)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Kidney(64;8.63e-06)|BRCA - Breast invasive adenocarcinoma(304;4.06e-05)|KIRC - Kidney renal clear cell carcinoma(64;0.000175)|GBM - Glioblastoma multiforme(114;0.000525)|STAD - Stomach adenocarcinoma(196;0.00779)|READ - Rectum adenocarcinoma(331;0.103)|Lung(427;0.173)														---	---	---	---
TMCO4	255104	broad.mit.edu	37	1	20009604	20009604	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20009604T>C	uc001bcn.2	-	16	2076	c.1834A>G	c.(1834-1836)ATG>GTG	p.M612V	TMCO4_uc001bcm.2_Missense_Mutation_p.M443V|TMCO4_uc001bco.1_Intron|TMCO4_uc001bcp.1_Intron	NM_181719	NP_859070	Q5TGY1	TMCO4_HUMAN	transmembrane and coiled-coil domains 4	612						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)														---	---	---	---
PLA2G2D	26279	broad.mit.edu	37	1	20442089	20442089	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20442089T>C	uc001bcz.2	-	3	220	c.203A>G	c.(202-204)GAC>GGC	p.D68G	PLA2G2D_uc009vpo.2_Intron	NM_012400	NP_036532	Q9UNK4	PA2GD_HUMAN	phospholipase A2, group IID precursor	68		Calcium (By similarity).			inflammatory response|lipid catabolic process|phospholipid metabolic process	extracellular region	calcium ion binding|phospholipase A2 activity				0		Colorectal(325;0.000147)|Renal(390;0.000469)|Lung NSC(340;0.00412)|all_lung(284;0.00419)|Breast(348;0.00526)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|COAD - Colon adenocarcinoma(152;1.15e-05)|BRCA - Breast invasive adenocarcinoma(304;8.01e-05)|Kidney(64;0.000175)|GBM - Glioblastoma multiforme(114;0.000798)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)											Multiple Myeloma(11;0.12)			---	---	---	---
DDOST	1650	broad.mit.edu	37	1	20979475	20979475	+	Intron	SNP	A	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20979475A>C	uc001bdo.1	-						DDOST_uc009vpw.1_Intron|DDOST_uc010odd.1_Intron|DDOST_uc010ode.1_Intron	NM_005216	NP_005207			dolichyl-diphosphooligosaccharide-protein						innate immune response|post-translational protein modification|response to cytokine stimulus|T cell activation	integral to membrane|microsome|oligosaccharyltransferase complex	dolichyl-diphosphooligosaccharide-protein glycotransferase activity|protein binding				0		all_lung(284;2.98e-05)|Lung NSC(340;3.25e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000147)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|COAD - Colon adenocarcinoma(152;1.17e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000141)|Kidney(64;0.000177)|GBM - Glioblastoma multiforme(114;0.00046)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)														---	---	---	---
NBPF3	84224	broad.mit.edu	37	1	21795231	21795231	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21795231G>A	uc001ber.2	+	3	534	c.184G>A	c.(184-186)GGC>AGC	p.G62S	NBPF3_uc001bes.2_Missense_Mutation_p.G6S|NBPF3_uc009vqb.2_Missense_Mutation_p.G62S|NBPF3_uc010odm.1_Intron	NM_032264	NP_115640	Q9H094	NBPF3_HUMAN	neuroblastoma breakpoint family, member 3	62						cytoplasm				upper_aerodigestive_tract(1)|ovary(1)	2		all_lung(284;2.16e-05)|Lung NSC(340;2.19e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00432)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|OV - Ovarian serous cystadenocarcinoma(117;7.53e-27)|COAD - Colon adenocarcinoma(152;1.18e-05)|GBM - Glioblastoma multiforme(114;3.47e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000143)|STAD - Stomach adenocarcinoma(196;0.00306)|KIRC - Kidney renal clear cell carcinoma(1967;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)												OREG0013205	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
ZBTB40	9923	broad.mit.edu	37	1	22839533	22839533	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22839533G>A	uc001bft.2	+	13	3089	c.2578G>A	c.(2578-2580)GGG>AGG	p.G860R	ZBTB40_uc001bfu.2_Missense_Mutation_p.G860R|ZBTB40_uc009vqi.1_Missense_Mutation_p.G748R	NM_001083621	NP_001077090	Q9NUA8	ZBT40_HUMAN	zinc finger and BTB domain containing 40	860					bone mineralization|regulation of transcription, DNA-dependent|response to DNA damage stimulus|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;2.86e-26)|Colorectal(126;8.55e-08)|COAD - Colon adenocarcinoma(152;4.1e-06)|GBM - Glioblastoma multiforme(114;1.39e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000712)|KIRC - Kidney renal clear cell carcinoma(1967;0.00374)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0693)|Lung(427;0.216)														---	---	---	---
KDM1A	23028	broad.mit.edu	37	1	23409681	23409681	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23409681C>T	uc001bgi.2	+	19	2532	c.2383C>T	c.(2383-2385)CGA>TGA	p.R795*	KDM1A_uc001bgj.2_Nonsense_Mutation_p.R819*	NM_015013	NP_055828	O60341	KDM1A_HUMAN	lysine-specific histone demethylase 1 isoform b	795	Demethylase activity.				blood coagulation|muscle cell development|negative regulation of apoptosis|negative regulation of DNA damage response, signal transduction by p53 class mediator|negative regulation of protein binding|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nuclear chromatin	androgen receptor binding|chromatin binding|enzyme binding|flavin adenine dinucleotide binding|histone demethylase activity (H3-dimethyl-K4 specific)|histone demethylase activity (H3-K9 specific)|ligand-dependent nuclear receptor transcription coactivator activity|MyoD binding|oxidoreductase activity|p53 binding|transcription regulatory region DNA binding			ovary(1)|lung(1)	2																		---	---	---	---
IL22RA1	58985	broad.mit.edu	37	1	24448013	24448013	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24448013T>C	uc001biq.1	-	7	1046	c.1007A>G	c.(1006-1008)CAG>CGG	p.Q336R	IL22RA1_uc010oeg.1_Missense_Mutation_p.Q268R|IL22RA1_uc009vrb.1_Missense_Mutation_p.Q200R|IL22RA1_uc010oeh.1_Missense_Mutation_p.Q336R	NM_021258	NP_067081	Q8N6P7	I22R1_HUMAN	interleukin 22 receptor, alpha 1 precursor	336	Cytoplasmic (Potential).					integral to membrane	interferon receptor activity			skin(1)	1		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000992)|all_lung(284;0.00138)|Ovarian(437;0.00348)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;3.84e-24)|Colorectal(126;6.43e-08)|COAD - Colon adenocarcinoma(152;3.51e-06)|GBM - Glioblastoma multiforme(114;5.06e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|KIRC - Kidney renal clear cell carcinoma(1967;0.00371)|STAD - Stomach adenocarcinoma(196;0.00911)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.148)														---	---	---	---
CD52	1043	broad.mit.edu	37	1	26646688	26646688	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26646688C>T	uc001bmc.2	+	2	179	c.81C>T	c.(79-81)AAC>AAT	p.N27N	UBXN11_uc001bma.2_5'Flank	NM_001803	NP_001794	P31358	CD52_HUMAN	CD52 antigen precursor	27					elevation of cytosolic calcium ion concentration|respiratory burst	anchored to membrane|integral to plasma membrane|membrane fraction					0		all_cancers(24;5.02e-24)|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;7.56e-28)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|BRCA - Breast invasive adenocarcinoma(304;0.000946)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.0137)|READ - Rectum adenocarcinoma(331;0.0649)	Alemtuzumab(DB00087)													---	---	---	---
AIM1L	55057	broad.mit.edu	37	1	26669262	26669262	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26669262G>T	uc001bmd.3	-	4	482	c.52C>A	c.(52-54)CTA>ATA	p.L18I		NM_001039775	NP_001034864	Q8N1P7	AIM1L_HUMAN	absent in melanoma 1-like	18							sugar binding			pancreas(1)	1		all_cancers(24;4.67e-25)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00637)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;1.51e-27)|Colorectal(126;1.61e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000792)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|STAD - Stomach adenocarcinoma(196;0.00154)|GBM - Glioblastoma multiforme(114;0.00858)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.165)|LUSC - Lung squamous cell carcinoma(448;0.239)														---	---	---	---
RPS6KA1	6195	broad.mit.edu	37	1	26883502	26883502	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26883502G>A	uc001bmr.1	+	13	1158	c.995G>A	c.(994-996)CGT>CAT	p.R332H	RPS6KA1_uc010ofe.1_Missense_Mutation_p.R240H|RPS6KA1_uc010off.1_Missense_Mutation_p.R316H|RPS6KA1_uc001bms.1_Missense_Mutation_p.R341H|RPS6KA1_uc009vsl.1_Missense_Mutation_p.R175H	NM_002953	NP_002944	Q15418	KS6A1_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide	332	AGC-kinase C-terminal.				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	27094434	27094434	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27094434C>T	uc001bmv.1	+	11	3515	c.3142C>T	c.(3142-3144)CCT>TCT	p.P1048S	ARID1A_uc001bmt.1_Missense_Mutation_p.P1048S|ARID1A_uc001bmu.1_Missense_Mutation_p.P1048S|ARID1A_uc001bmw.1_Missense_Mutation_p.P665S	NM_006015	NP_006006	O14497	ARI1A_HUMAN	AT rich interactive domain 1A isoform a	1048	ARID.				androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent	nBAF complex|npBAF complex|SWI/SNF complex	DNA binding|protein binding			ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	142		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)				Mis|N|F|S|D		clear cell ovarian carcinoma|RCC								---	---	---	---
SLC9A1	6548	broad.mit.edu	37	1	27436202	27436202	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27436202C>T	uc001bnm.2	-	3	1506	c.880G>A	c.(880-882)GGC>AGC	p.G294S	SLC9A1_uc010ofk.1_5'UTR|SLC9A1_uc001bnn.2_Missense_Mutation_p.G294S	NM_003047	NP_003038	P19634	SL9A1_HUMAN	solute carrier family 9, isoform A1	294	Extracellular (Potential).				regulation of pH	integral to membrane	sodium:hydrogen antiporter activity			ovary(1)|central_nervous_system(1)	2				UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;2.19e-50)|OV - Ovarian serous cystadenocarcinoma(117;1.8e-29)|Colorectal(126;7.61e-09)|COAD - Colon adenocarcinoma(152;9.32e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000521)|KIRC - Kidney renal clear cell carcinoma(1967;0.00079)|STAD - Stomach adenocarcinoma(196;0.00125)|READ - Rectum adenocarcinoma(331;0.046)	Amiloride(DB00594)													---	---	---	---
HCRTR1	3061	broad.mit.edu	37	1	32086433	32086433	+	Intron	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32086433C>A	uc009vtx.2	+						HCRTR1_uc001btb.2_Intron|HCRTR1_uc001btc.3_Intron|HCRTR1_uc001btd.2_Intron|HCRTR1_uc010ogl.1_Intron	NM_001525	NP_001516			orexin receptor 1						feeding behavior|neuropeptide signaling pathway|synaptic transmission	integral to plasma membrane				ovary(1)	1		Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.053)														---	---	---	---
HDAC1	3065	broad.mit.edu	37	1	32794717	32794717	+	Nonsense_Mutation	SNP	C	T	T	rs145372036		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32794717C>T	uc001bvb.1	+	7	748	c.685C>T	c.(685-687)CGA>TGA	p.R229*	HDAC1_uc010ohf.1_Nonsense_Mutation_p.R200*|HDAC1_uc001bvc.1_5'Flank	NM_004964	NP_004955	Q13547	HDAC1_HUMAN	histone deacetylase 1	229	Histone deacetylase.				anti-apoptosis|blood coagulation|embryonic digit morphogenesis|epidermal cell differentiation|eyelid development in camera-type eye|fungiform papilla formation|hair follicle placode formation|histone H3 deacetylation|histone H4 deacetylation|negative regulation by host of viral transcription|negative regulation of androgen receptor signaling pathway|negative regulation of cell cycle|nerve growth factor receptor signaling pathway|odontogenesis of dentine-containing tooth|positive regulation of cell proliferation|positive regulation of receptor biosynthetic process|positive regulation of transcription from RNA polymerase II promoter	cytosol|NuRD complex|Sin3 complex	activating transcription factor binding|histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|identical protein binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|RNA polymerase II transcription corepressor activity|sequence-specific DNA binding transcription factor activity			ovary(1)|lung(1)|breast(1)	3		Breast(348;0.000523)|Lung NSC(340;0.000992)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Lung SC(1967;0.113)		KIRC - Kidney renal clear cell carcinoma(1967;0.138)	Vorinostat(DB02546)													---	---	---	---
S100PBP	64766	broad.mit.edu	37	1	33318764	33318764	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33318764C>T	uc001bvz.2	+	6	1386	c.1109C>T	c.(1108-1110)ACG>ATG	p.T370M	S100PBP_uc001bwc.2_Missense_Mutation_p.T370M|S100PBP_uc001bwd.2_RNA	NM_022753	NP_073590	Q96BU1	S1PBP_HUMAN	S100P binding protein isoform a	370						nucleus	calcium-dependent protein binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244)																---	---	---	---
CSMD2	114784	broad.mit.edu	37	1	34046380	34046380	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34046380G>A	uc001bxn.1	-	49	7395	c.7366C>T	c.(7366-7368)CGG>TGG	p.R2456W	CSMD2_uc001bxm.1_Missense_Mutation_p.R2454W	NM_052896	NP_443128	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	2456	CUB 14.|Extracellular (Potential).					integral to membrane|plasma membrane	protein binding			ovary(6)|skin(5)|pancreas(1)	12		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)																---	---	---	---
CSMD2	114784	broad.mit.edu	37	1	34102053	34102053	+	Missense_Mutation	SNP	C	T	T	rs34594465		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34102053C>T	uc001bxn.1	-	30	4785	c.4756G>A	c.(4756-4758)GGG>AGG	p.G1586R	CSMD2_uc001bxm.1_Missense_Mutation_p.G1626R|CSMD2_uc001bxo.1_Missense_Mutation_p.G499R	NM_052896	NP_443128	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	1586	Extracellular (Potential).|Sushi 9.					integral to membrane|plasma membrane	protein binding			ovary(6)|skin(5)|pancreas(1)	12		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)																---	---	---	---
C1orf94	84970	broad.mit.edu	37	1	34666585	34666585	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34666585C>T	uc001bxs.3	+	3	1051	c.652C>T	c.(652-654)CAG>TAG	p.Q218*	C1orf94_uc001bxt.2_Nonsense_Mutation_p.Q408*	NM_032884	NP_116273	Q6P1W5	CA094_HUMAN	hypothetical protein LOC84970 isoform b	218							protein binding				0		Myeloproliferative disorder(586;0.0393)																---	---	---	---
DLGAP3	58512	broad.mit.edu	37	1	35334284	35334284	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35334284G>A	uc001byc.2	-	7	2407	c.2407C>T	c.(2407-2409)CGG>TGG	p.R803W		NM_001080418	NP_001073887	O95886	DLGP3_HUMAN	discs, large (Drosophila) homolog-associated	803					cell-cell signaling	cell junction|postsynaptic density|postsynaptic membrane				ovary(3)	3		Myeloproliferative disorder(586;0.0393)																---	---	---	---
NCDN	23154	broad.mit.edu	37	1	36029369	36029369	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36029369C>T	uc001bza.2	+	7	1739	c.1612C>T	c.(1612-1614)CGT>TGT	p.R538C	NCDN_uc001bzb.2_Missense_Mutation_p.R538C|NCDN_uc001bzc.2_Missense_Mutation_p.R521C	NM_001014839	NP_001014839	Q9UBB6	NCDN_HUMAN	neurochondrin isoform 1	538					neuron projection development	cytosol|dendrite|neuronal cell body				large_intestine(2)|pancreas(1)	3		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)																---	---	---	---
C1orf216	127703	broad.mit.edu	37	1	36181448	36181448	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36181448G>A	uc001bzh.1	-	2	963	c.475C>T	c.(475-477)CGC>TGC	p.R159C		NM_152374	NP_689587	Q8TAB5	CA216_HUMAN	hypothetical protein LOC127703	159										skin(1)	1		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.196)														OREG0013357	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
EIF2C1	26523	broad.mit.edu	37	1	36380998	36380998	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36380998G>A	uc001bzl.2	+	15	2096	c.1883G>A	c.(1882-1884)CGG>CAG	p.R628Q	EIF2C1_uc001bzk.2_Missense_Mutation_p.R553Q|EIF2C1_uc009vuy.2_RNA	NM_012199	NP_036331	Q9UL18	AGO1_HUMAN	eukaryotic translation initiation factor 2C, 1	628	Piwi.				negative regulation of translation involved in gene silencing by miRNA|nuclear-transcribed mRNA catabolic process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol|micro-ribonucleoprotein complex|polysome	protein binding|RNA binding			ovary(2)|skin(1)	3		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)																---	---	---	---
ADPRHL2	54936	broad.mit.edu	37	1	36558054	36558054	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36558054C>T	uc001bzt.2	+	5	786	c.733C>T	c.(733-735)CGC>TGC	p.R245C	ADPRHL2_uc001bzu.2_Missense_Mutation_p.R91C	NM_017825	NP_060295	Q9NX46	ARHL2_HUMAN	ADP-ribosylhydrolase like 2	245						cytoplasm|nucleus	metal ion binding|poly(ADP-ribose) glycohydrolase activity			pancreas(1)	1		Myeloproliferative disorder(586;0.0393)																---	---	---	---
MACF1	23499	broad.mit.edu	37	1	39823511	39823511	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39823511A>G	uc010oiu.1	+	9	7340	c.7209A>G	c.(7207-7209)TTA>TTG	p.L2403L	MACF1_uc010ois.1_Silent_p.L1901L|MACF1_uc001cda.1_Silent_p.L1809L|MACF1_uc001cdc.1_Silent_p.L988L|MACF1_uc001cdb.1_Silent_p.L988L	NM_033044	NP_149033	Q9UPN3	MACF1_HUMAN	microfilament and actin filament cross-linker	3968					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)															---	---	---	---
HPCAL4	51440	broad.mit.edu	37	1	40149806	40149806	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40149806C>T	uc001cdr.2	-	3	301	c.181G>A	c.(181-183)GCC>ACC	p.A61T	HPCAL4_uc010oix.1_Intron	NM_016257	NP_057341	Q9UM19	HPCL4_HUMAN	hippocalcin-like protein 4	61	EF-hand 2.				central nervous system development	intracellular	calcium ion binding			central_nervous_system(1)	1	all_cancers(7;4.65e-13)|Lung NSC(20;2.88e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;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)															---	---	---	---
NFYC	4802	broad.mit.edu	37	1	41220120	41220120	+	Intron	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41220120G>A	uc001cge.2	+						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|uc001cgg.2_5'Flank|MIR30C1_hsa-mir-30c-1|MI0000736_5'Flank	NM_001142588	NP_001136060			nuclear transcription factor Y, gamma isoform 1						protein folding|regulation of transcription from RNA polymerase II promoter	CCAAT-binding factor complex	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			breast(2)|kidney(1)	3	Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.72e-17)															---	---	---	---
SCMH1	22955	broad.mit.edu	37	1	41503057	41503057	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41503057G>A	uc001cgo.2	-	13	1936	c.1625C>T	c.(1624-1626)GCT>GTT	p.A542V	SCMH1_uc010ojr.1_Missense_Mutation_p.A384V|SCMH1_uc001cgp.2_Missense_Mutation_p.A481V|SCMH1_uc001cgr.2_Missense_Mutation_p.A481V|SCMH1_uc001cgs.2_Missense_Mutation_p.A552V|SCMH1_uc001cgt.2_Missense_Mutation_p.A481V|SCMH1_uc001cgq.2_Missense_Mutation_p.A495V|SCMH1_uc010ojs.1_RNA	NM_001031694	NP_001026864	Q96GD3	SCMH1_HUMAN	sex comb on midleg 1 isoform 1	542					anatomical structure morphogenesis|gene silencing|multicellular organismal development|negative regulation of transcription, DNA-dependent		DNA binding|sequence-specific DNA binding transcription factor activity				0	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)|Breast(333;0.162)	Myeloproliferative disorder(586;0.0393)																---	---	---	---
ZMYND12	84217	broad.mit.edu	37	1	42901019	42901019	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42901019T>C	uc001chj.2	-	6	1025	c.755A>G	c.(754-756)TAT>TGT	p.Y252C	ZMYND12_uc010ojt.1_Missense_Mutation_p.Y142C	NM_032257	NP_115633	Q9H0C1	ZMY12_HUMAN	zinc finger, MYND-type containing 12 isoform 1	252						intracellular	zinc ion binding			ovary(1)	1	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)																---	---	---	---
TMEM125	128218	broad.mit.edu	37	1	43738712	43738712	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43738712C>T	uc001cir.2	+	4	889	c.319C>T	c.(319-321)CGC>TGC	p.R107C	EBNA1BP2_uc001cio.2_5'Flank|TMEM125_uc001cis.2_Missense_Mutation_p.R107C	NM_144626	NP_653227	Q96AQ2	TM125_HUMAN	transmembrane protein 125	107			R -> L (in a breast cancer sample; somatic mutation).			integral to membrane		p.R107L(1)		breast(1)	1	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)																---	---	---	---
KDM4A	9682	broad.mit.edu	37	1	44137442	44137442	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44137442G>A	uc001cjx.2	+	11	1796	c.1630G>A	c.(1630-1632)GTG>ATG	p.V544M	KDM4A_uc010oki.1_Intron	NM_014663	NP_055478	O75164	KDM4A_HUMAN	jumonji domain containing 2A	544					interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	centrosome|nucleolus	histone demethylase activity (H3-K36 specific)|nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|zinc ion binding			skin(1)	1																		---	---	---	---
PLK3	1263	broad.mit.edu	37	1	45270162	45270162	+	Silent	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45270162G>T	uc001cmn.2	+	12	1594	c.1494G>T	c.(1492-1494)TCG>TCT	p.S498S	PLK3_uc001cmo.2_RNA	NM_004073	NP_004064	Q9H4B4	PLK3_HUMAN	polo-like kinase 3	498	POLO box 1.					membrane	ATP binding|protein binding|protein serine/threonine kinase activity				0	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
MUTYH	4595	broad.mit.edu	37	1	45799087	45799087	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45799087G>A	uc001cnm.2	-	3	553	c.337C>T	c.(337-339)CGG>TGG	p.R113W	MUTYH_uc009vxn.2_Intron|MUTYH_uc001cnf.2_Missense_Mutation_p.R88W|MUTYH_uc009vxo.2_Missense_Mutation_p.R88W|MUTYH_uc001cng.2_Missense_Mutation_p.R99W|MUTYH_uc001cnj.2_Translation_Start_Site|MUTYH_uc001cni.2_Missense_Mutation_p.R88W|MUTYH_uc001cnh.2_Missense_Mutation_p.R89W|MUTYH_uc001cno.2_Translation_Start_Site|MUTYH_uc001cnk.2_Translation_Start_Site|MUTYH_uc010oll.1_Intron|MUTYH_uc001cnl.2_Missense_Mutation_p.R102W|MUTYH_uc009vxp.2_Missense_Mutation_p.R116W|MUTYH_uc001cnn.2_Missense_Mutation_p.R103W	NM_012222	NP_036354	Q9UIF7	MUTYH_HUMAN	mutY homolog isoform 1	113					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				---	---	---	---
RAD54L	8438	broad.mit.edu	37	1	46736382	46736382	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46736382G>A	uc009vye.2	+	11	1208	c.1094G>A	c.(1093-1095)CGA>CAA	p.R365Q	RAD54L_uc001cpl.2_Missense_Mutation_p.R365Q|RAD54L_uc001cpm.1_Missense_Mutation_p.R185Q	NM_001142548	NP_001136020	Q92698	RAD54_HUMAN	RAD54-like protein	365					meiosis	nucleus	ATP binding|DNA binding|helicase activity			ovary(2)|skin(1)	3	Acute lymphoblastic leukemia(166;0.155)	Breast(1374;0.0634)		KIRC - Kidney renal clear cell carcinoma(1967;0.000896)									Direct_reversal_of_damage|Homologous_recombination					---	---	---	---
RNF11	26994	broad.mit.edu	37	1	51736936	51736936	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51736936G>A	uc001csi.3	+	3	891	c.407G>A	c.(406-408)TGC>TAC	p.C136Y		NM_014372	NP_055187	Q9Y3C5	RNF11_HUMAN	ring finger protein 11	136	RING-type.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus|ubiquitin ligase complex	DNA binding|protein binding|zinc ion binding				0																		---	---	---	---
NRD1	4898	broad.mit.edu	37	1	52266266	52266266	+	Silent	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52266266G>T	uc001ctc.3	-	23	2929	c.2607C>A	c.(2605-2607)ACC>ACA	p.T869T	NRD1_uc009vzb.2_Silent_p.T564T|NRD1_uc001ctd.3_Silent_p.T801T|NRD1_uc001cte.2_Silent_p.T737T|NRD1_uc001ctf.2_Silent_p.T801T|NRD1_uc010ong.1_RNA	NM_002525	NP_002516	O43847	NRDC_HUMAN	nardilysin isoform a	800					cell migration|cell proliferation|neuromuscular junction development|positive regulation of membrane protein ectodomain proteolysis|proteolysis|regulation of endopeptidase activity	cell surface|cytosol	epidermal growth factor binding|metalloendopeptidase activity|zinc ion binding				0																		---	---	---	---
CC2D1B	200014	broad.mit.edu	37	1	52823526	52823526	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52823526C>T	uc001ctq.1	-	14	1662	c.1524G>A	c.(1522-1524)CGG>CGA	p.R508R	CC2D1B_uc001ctr.2_Silent_p.R48R|CC2D1B_uc001cts.2_Silent_p.R193R	NM_032449	NP_115825	Q5T0F9	C2D1B_HUMAN	coiled-coil and C2 domain containing 1B	508										ovary(2)	2																		---	---	---	---
MRPL37	51253	broad.mit.edu	37	1	54666207	54666207	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54666207G>A	uc001cxa.3	+	1	368	c.291G>A	c.(289-291)CCG>CCA	p.P97P	CYB5RL_uc009vzo.2_5'Flank|CYB5RL_uc001cwx.3_5'Flank|CYB5RL_uc001cwy.3_5'Flank|MRPL37_uc009vzp.2_Missense_Mutation_p.R67H|MRPL37_uc001cxb.1_Silent_p.P97P|MRPL37_uc001cxc.3_Intron|MRPL37_uc010oob.1_RNA	NM_016491	NP_057575	Q9BZE1	RM37_HUMAN	mitochondrial ribosomal protein L37 precursor	97					translation	mitochondrial ribosome	structural constituent of ribosome				0																		---	---	---	---
DAB1	1600	broad.mit.edu	37	1	57538003	57538003	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57538003C>A	uc001cys.1	-	7	1065	c.391G>T	c.(391-393)GGG>TGG	p.G131W	DAB1_uc001cyt.1_Missense_Mutation_p.G131W|DAB1_uc001cyq.1_Missense_Mutation_p.G131W|DAB1_uc001cyr.1_Intron|DAB1_uc009vzw.1_Missense_Mutation_p.G131W|DAB1_uc009vzx.1_Missense_Mutation_p.G131W	NM_021080	NP_066566	O75553	DAB1_HUMAN	disabled homolog 1	131	PID.				cell differentiation|nervous system development					skin(2)|ovary(1)	3																		---	---	---	---
DAB1	1600	broad.mit.edu	37	1	57610998	57610998	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57610998C>T	uc001cys.1	-	5	846	c.172G>A	c.(172-174)GAC>AAC	p.D58N	DAB1_uc001cyt.1_Missense_Mutation_p.D58N|DAB1_uc001cyq.1_Missense_Mutation_p.D58N|DAB1_uc001cyr.1_Missense_Mutation_p.D58N|DAB1_uc009vzw.1_Missense_Mutation_p.D58N|DAB1_uc009vzx.1_Missense_Mutation_p.D58N	NM_021080	NP_066566	O75553	DAB1_HUMAN	disabled homolog 1	58	PID.				cell differentiation|nervous system development					skin(2)|ovary(1)	3																		---	---	---	---
C1orf87	127795	broad.mit.edu	37	1	60499273	60499273	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:60499273T>C	uc001czs.1	-	7	996	c.904A>G	c.(904-906)AGG>GGG	p.R302G		NM_152377	NP_689590	Q8N0U7	CA087_HUMAN	hypothetical protein LOC127795	302							calcium ion binding			ovary(1)|breast(1)	2																		---	---	---	---
NFIA	4774	broad.mit.edu	37	1	61869831	61869831	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:61869831G>A	uc001czw.2	+	8	1615	c.1131G>A	c.(1129-1131)CAG>CAA	p.Q377Q	NFIA_uc001czy.2_Silent_p.Q369Q|NFIA_uc010oos.1_Silent_p.Q422Q|NFIA_uc001czv.2_Silent_p.Q377Q|NFIA_uc001czx.2_Silent_p.Q25Q|NFIA_uc009wae.2_5'Flank	NM_001134673	NP_001128145	Q12857	NFIA_HUMAN	nuclear factor I/A isoform 1	377					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	62594566	62594566	+	Silent	SNP	C	T	T	rs113629200		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62594566C>T	uc001dab.2	+	41	5334	c.5220C>T	c.(5218-5220)CAC>CAT	p.H1740H	INADL_uc001dac.2_RNA|INADL_uc009wag.2_Silent_p.H524H	NM_176877	NP_795352	Q8NI35	INADL_HUMAN	InaD-like	1740	PDZ 10.				intracellular signal transduction|tight junction assembly	apical plasma membrane|perinuclear region of cytoplasm|tight junction	protein binding			ovary(3)|skin(1)	4																		---	---	---	---
JAK1	3716	broad.mit.edu	37	1	65323363	65323363	+	Silent	SNP	G	A	A	rs55788790		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65323363G>A	uc001dbu.1	-	10	1683	c.1434C>T	c.(1432-1434)ACC>ACT	p.T478T	JAK1_uc009wam.1_Silent_p.T466T	NM_002227	NP_002218	P23458	JAK1_HUMAN	janus kinase 1	478	SH2.				interferon-gamma-mediated signaling pathway|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|response to antibiotic|type I interferon-mediated signaling pathway	cytoskeleton|cytosol|endomembrane system|membrane|nucleus	ATP binding|growth hormone receptor binding|non-membrane spanning protein tyrosine kinase activity	p.T478S(1)|p.T478T(1)		haematopoietic_and_lymphoid_tissue(34)|prostate(7)|soft_tissue(6)|lung(4)|breast(3)|central_nervous_system(2)|liver(2)|large_intestine(1)|stomach(1)|ovary(1)	61				BRCA - Breast invasive adenocarcinoma(111;0.0485)				Mis		ALL								---	---	---	---
SYDE2	84144	broad.mit.edu	37	1	85656333	85656333	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85656333G>A	uc009wcm.2	-	2	897	c.848C>T	c.(847-849)ACT>ATT	p.T283I	SYDE2_uc001dku.3_Missense_Mutation_p.T283I	NM_032184	NP_115560	Q5VT97	SYDE2_HUMAN	synapse defective 1, Rho GTPase, homolog 2	283					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)														---	---	---	---
CLCA2	9635	broad.mit.edu	37	1	86905964	86905964	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86905964G>T	uc001dlr.3	+	8	1499	c.1337G>T	c.(1336-1338)GGT>GTT	p.G446V		NM_006536	NP_006527	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2 precursor	446	VWFA.|Extracellular (Potential).				cell adhesion	basal plasma membrane|cell junction|extracellular region|integral to plasma membrane	chloride channel activity			ovary(1)|breast(1)|skin(1)	3		Lung NSC(277;0.238)		all cancers(265;0.0233)|Epithelial(280;0.0452)														---	---	---	---
GBP1	2633	broad.mit.edu	37	1	89520420	89520420	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89520420T>C	uc001dmx.2	-	10	1830	c.1610A>G	c.(1609-1611)AAC>AGC	p.N537S		NM_002053	NP_002044	P32455	GBP1_HUMAN	guanylate binding protein 1,	537					interferon-gamma-mediated signaling pathway	plasma membrane	GTP binding|GTPase activity			ovary(1)|skin(1)	2		Lung NSC(277;0.123)		all cancers(265;0.0156)|Epithelial(280;0.0291)														---	---	---	---
GBP1	2633	broad.mit.edu	37	1	89521715	89521715	+	Missense_Mutation	SNP	G	A	A	rs142020556		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89521715G>A	uc001dmx.2	-	8	1572	c.1352C>T	c.(1351-1353)CCG>CTG	p.P451L		NM_002053	NP_002044	P32455	GBP1_HUMAN	guanylate binding protein 1,	451					interferon-gamma-mediated signaling pathway	plasma membrane	GTP binding|GTPase activity			ovary(1)|skin(1)	2		Lung NSC(277;0.123)		all cancers(265;0.0156)|Epithelial(280;0.0291)														---	---	---	---
ZNF644	84146	broad.mit.edu	37	1	91383718	91383718	+	Intron	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91383718A>G	uc001dnw.2	-						ZNF644_uc001dnv.2_Intron|ZNF644_uc001dnx.2_Intron	NM_201269	NP_958357			zinc finger protein 644 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|breast(1)|skin(1)	3		all_lung(203;0.00206)|Lung NSC(277;0.0519)|Lung SC(238;0.101)		all cancers(265;0.00102)|Epithelial(280;0.00766)|KIRC - Kidney renal clear cell carcinoma(1967;0.147)|OV - Ovarian serous cystadenocarcinoma(397;0.173)														---	---	---	---
HFM1	164045	broad.mit.edu	37	1	91851380	91851380	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91851380A>G	uc001doa.3	-	5	606	c.506T>C	c.(505-507)ATA>ACA	p.I169T	HFM1_uc010osu.1_Intron|HFM1_uc010osv.1_Intron|HFM1_uc001doc.1_Missense_Mutation_p.I169T	NM_001017975	NP_001017975	A2PYH4	HFM1_HUMAN	HFM1 protein	169							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)														---	---	---	---
FNBP1L	54874	broad.mit.edu	37	1	93987691	93987691	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93987691C>T	uc001dpw.2	+	3	193	c.193C>T	c.(193-195)CGG>TGG	p.R65W	FNBP1L_uc001dpv.2_Missense_Mutation_p.R65W	NM_001024948	NP_001020119	Q5T0N5	FBP1L_HUMAN	formin binding protein 1-like isoform 1	65	FCH.|Induction of membrane tubulation (By similarity).				endocytosis	cell cortex|cytoplasmic membrane-bounded vesicle|cytoskeleton|plasma membrane	lipid binding				0		all_lung(203;0.00206)|Lung NSC(277;0.00902)|Melanoma(281;0.155)		all cancers(265;0.00666)|GBM - Glioblastoma multiforme(16;0.0378)|Epithelial(280;0.111)														---	---	---	---
ARHGAP29	9411	broad.mit.edu	37	1	94639435	94639435	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94639435T>C	uc001dqj.3	-	23	4145	c.3776A>G	c.(3775-3777)CAA>CGA	p.Q1259R	ARHGAP29_uc009wdq.1_Intron	NM_004815	NP_004806	Q52LW3	RHG29_HUMAN	PTPL1-associated RhoGAP 1	1259	Interaction with PTPN13/PTPL1.				Rho protein signal transduction	cytosol	metal ion binding|Rho GTPase activator activity			breast(4)|skin(3)|lung(2)|upper_aerodigestive_tract(1)|ovary(1)	11		all_lung(203;0.000732)|Lung NSC(277;0.00328)		all cancers(265;0.0187)|Epithelial(280;0.159)														---	---	---	---
ABCD3	5825	broad.mit.edu	37	1	94955520	94955520	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94955520T>C	uc001dqn.3	+	15	1413	c.1311T>C	c.(1309-1311)GAT>GAC	p.D437D	ABCD3_uc010oto.1_Silent_p.D461D|ABCD3_uc010otp.1_Silent_p.D364D|ABCD3_uc009wdr.2_Silent_p.D327D|ABCD3_uc001dqo.3_Silent_p.D125D	NM_002858	NP_002849	P28288	ABCD3_HUMAN	ATP-binding cassette, sub-family D, member 3	437					peroxisomal long-chain fatty acid import|peroxisome organization	cytosol|integral to peroxisomal membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			skin(1)	1		all_lung(203;0.000434)|Lung NSC(277;0.0019)		all cancers(265;0.0261)|Epithelial(280;0.165)														---	---	---	---
EXTL2	2135	broad.mit.edu	37	1	101339853	101339853	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:101339853A>T	uc001dtk.1	-	5	975	c.638T>A	c.(637-639)ATT>AAT	p.I213N	EXTL2_uc001dtl.1_Missense_Mutation_p.I213N|EXTL2_uc010ouk.1_Missense_Mutation_p.I200N|EXTL2_uc001dtm.1_Missense_Mutation_p.I212N	NM_001439	NP_001430	Q9UBQ6	EXTL2_HUMAN	exostoses-like 2	213	Lumenal (Potential).				N-acetylglucosamine metabolic process|UDP-N-acetylgalactosamine metabolic process	extracellular region|integral to membrane|intrinsic to endoplasmic reticulum membrane	alpha-1,4-N-acetylgalactosaminyltransferase activity|glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|metal ion binding			skin(1)	1		all_epithelial(167;2.48e-06)|all_lung(203;0.000414)|Lung NSC(277;0.000946)		Epithelial(280;0.0425)|all cancers(265;0.0628)|COAD - Colon adenocarcinoma(174;0.148)|Colorectal(144;0.167)|Lung(183;0.195)														---	---	---	---
COL11A1	1301	broad.mit.edu	37	1	103345444	103345444	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:103345444G>T	uc001dul.2	-	66	5387	c.5069C>A	c.(5068-5070)TCC>TAC	p.S1690Y	COL11A1_uc001duk.2_Missense_Mutation_p.S886Y|COL11A1_uc001dum.2_Missense_Mutation_p.S1702Y|COL11A1_uc001dun.2_Missense_Mutation_p.S1651Y|COL11A1_uc009weh.2_Missense_Mutation_p.S1574Y	NM_001854	NP_001845	P12107	COBA1_HUMAN	alpha 1 type XI collagen isoform A	1690	Fibrillar collagen NC1.				collagen fibril organization|detection of mechanical stimulus involved in sensory perception of sound|visual perception	collagen type XI	extracellular matrix binding|extracellular matrix structural constituent|protein binding, bridging			ovary(6)|breast(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	12		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)														---	---	---	---
COL11A1	1301	broad.mit.edu	37	1	103427440	103427440	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:103427440C>A	uc001dul.2	-	41	3468	c.3150G>T	c.(3148-3150)CAG>CAT	p.Q1050H	COL11A1_uc001duk.2_Missense_Mutation_p.Q246H|COL11A1_uc001dum.2_Missense_Mutation_p.Q1062H|COL11A1_uc001dun.2_Missense_Mutation_p.Q1011H|COL11A1_uc009weh.2_Missense_Mutation_p.Q934H	NM_001854	NP_001845	P12107	COBA1_HUMAN	alpha 1 type XI collagen isoform A	1050	Triple-helical region.				collagen fibril organization|detection of mechanical stimulus involved in sensory perception of sound|visual perception	collagen type XI	extracellular matrix binding|extracellular matrix structural constituent|protein binding, bridging			ovary(6)|breast(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	12		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)														---	---	---	---
VAV3	10451	broad.mit.edu	37	1	108507464	108507464	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:108507464A>G	uc001dvk.1	-	1	82	c.28T>C	c.(28-30)TGG>CGG	p.W10R	VAV3_uc010ouw.1_Missense_Mutation_p.W10R|VAV3_uc001dvl.1_5'Flank|VAV3_uc010oux.1_Missense_Mutation_p.W10R	NM_006113	NP_006104	Q9UKW4	VAV3_HUMAN	vav 3 guanine nucleotide exchange factor isoform	10	CH.				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)														---	---	---	---
FNDC7	163479	broad.mit.edu	37	1	109276020	109276020	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109276020C>T	uc001dvx.2	+	10	2006	c.2006C>T	c.(2005-2007)ACG>ATG	p.T669M	FNDC7_uc010ova.1_Missense_Mutation_p.T436M	NM_001144937	NP_001138409	Q5VTL7	FNDC7_HUMAN	fibronectin type III domain containing 7	670	Fibronectin type-III 8.					extracellular region				ovary(1)|skin(1)	2		all_lung(203;0.00439)|Lung NSC(277;0.00683)|all_epithelial(167;0.00728)		Colorectal(144;0.0314)|Lung(183;0.0924)|COAD - Colon adenocarcinoma(174;0.119)|Epithelial(280;0.173)|all cancers(265;0.244)														---	---	---	---
RBM15	64783	broad.mit.edu	37	1	110884339	110884339	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110884339A>G	uc001dzl.1	+	1	2395	c.2312A>G	c.(2311-2313)GAT>GGT	p.D771G	RBM15_uc001dzm.1_Missense_Mutation_p.D771G|uc001dzj.2_5'Flank	NM_022768	NP_073605	Q96T37	RBM15_HUMAN	RNA binding motif protein 15	771					interspecies interaction between organisms	nucleus	nucleotide binding|protein binding|RNA binding			ovary(3)	3		all_cancers(81;2.89e-06)|all_epithelial(167;2.96e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)|Breast(1374;0.0634)		BRCA - Breast invasive adenocarcinoma(282;0.000224)|Epithelial(280;0.000476)|Kidney(133;0.000539)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|all cancers(265;0.00144)|Lung(183;0.0238)|Colorectal(144;0.103)|LUSC - Lung squamous cell carcinoma(189;0.135)				T	MKL1	acute megakaryocytic leukemia								---	---	---	---
DDX20	11218	broad.mit.edu	37	1	112299260	112299260	+	Intron	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112299260C>A	uc001ebs.2	+						C1orf183_uc001ebp.1_5'Flank|uc001ebr.2_5'Flank|DDX20_uc010owf.1_Intron	NM_007204	NP_009135			DEAD (Asp-Glu-Ala-Asp) box polypeptide 20						assembly of spliceosomal tri-snRNP|ncRNA metabolic process	Cajal body|cytoskeleton|cytosol|spliceosomal complex	ATP binding|ATP-dependent RNA helicase activity|DNA binding|protein binding			lung(1)|kidney(1)	2		all_cancers(81;1.06e-05)|all_epithelial(167;7.36e-06)|all_lung(203;2.44e-05)|Lung NSC(69;4.15e-05)		Lung(183;0.0234)|Colorectal(144;0.0282)|all cancers(265;0.0614)|Epithelial(280;0.0999)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
MAGI3	260425	broad.mit.edu	37	1	114092138	114092138	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114092138C>T	uc001edk.2	+	2	499	c.318C>T	c.(316-318)GGC>GGT	p.G106G	MAGI3_uc001edh.3_Silent_p.G106G|MAGI3_uc001edi.3_Silent_p.G106G|MAGI3_uc010owm.1_Silent_p.G106G	NM_001142782	NP_001136254	Q5TCQ9	MAGI3_HUMAN	membrane-associated guanylate kinase-related  3	106	PDZ 1.|Interaction with ADRB1 and TGFA (By similarity).				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)														---	---	---	---
DCLRE1B	64858	broad.mit.edu	37	1	114454678	114454678	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114454678G>T	uc001eeg.2	+	4	1635	c.1464G>T	c.(1462-1464)AAG>AAT	p.K488N	DCLRE1B_uc001eeh.2_Intron|DCLRE1B_uc001eei.2_Missense_Mutation_p.K362N	NM_022836	NP_073747	Q9H816	DCR1B_HUMAN	DNA cross-link repair 1B (PSO2 homolog, S.	488					cell cycle checkpoint|DNA repair|protection from non-homologous end joining at telomere|telomeric 3' overhang formation|telomeric loop formation	centrosome|chromosome, telomeric region|nucleus	5'-3' exonuclease activity|protein binding				0	Lung SC(450;0.184)	all_cancers(81;1.46e-05)|all_epithelial(167;2.42e-05)|all_lung(203;0.000353)|Lung NSC(69;0.000518)		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)									Direct_reversal_of_damage|Other_identified_genes_with_known_or_suspected_DNA_repair_function					---	---	---	---
AMPD1	270	broad.mit.edu	37	1	115231320	115231320	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115231320G>A	uc001efe.1	-	3	161	c.77C>T	c.(76-78)GCC>GTC	p.A26V	AMPD1_uc001eff.1_Missense_Mutation_p.A22V	NM_000036	NP_000027	P23109	AMPD1_HUMAN	adenosine monophosphate deaminase 1 (isoform M)	26					purine base metabolic process|purine ribonucleoside monophosphate biosynthetic process|purine-containing compound salvage	cytosol	AMP deaminase activity|metal ion binding			ovary(2)|large_intestine(1)|skin(1)	4	all_epithelial(7;7.83e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)	Adenosine monophosphate(DB00131)													---	---	---	---
IGSF3	3321	broad.mit.edu	37	1	117156651	117156651	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117156651C>T	uc001egr.1	-	4	1273	c.568G>A	c.(568-570)GAG>AAG	p.E190K	IGSF3_uc001egq.1_Missense_Mutation_p.E190K	NM_001007237	NP_001007238	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3 isoform 2	190	Ig-like C2-type 2.|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)														---	---	---	---
VTCN1	79679	broad.mit.edu	37	1	117699263	117699263	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117699263G>A	uc001ehb.2	-	3	450	c.378C>T	c.(376-378)GGC>GGT	p.G126G	VTCN1_uc001ehc.2_Silent_p.G31G|VTCN1_uc009whf.1_Intron	NM_024626	NP_078902	Q7Z7D3	VTCN1_HUMAN	V-set domain containing T cell activation	126	Ig-like V-type 1.|Extracellular (Potential).					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)														---	---	---	---
GDAP2	54834	broad.mit.edu	37	1	118455168	118455168	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118455168C>T	uc001ehf.2	-	4	753	c.454G>A	c.(454-456)GTA>ATA	p.V152I	GDAP2_uc001ehg.2_Missense_Mutation_p.V152I	NM_017686	NP_060156	Q9NXN4	GDAP2_HUMAN	ganglioside induced differentiation associated	152	Macro.									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)														---	---	---	---
GDAP2	54834	broad.mit.edu	37	1	118461278	118461278	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118461278G>A	uc001ehf.2	-	3	556	c.257C>T	c.(256-258)TCA>TTA	p.S86L	GDAP2_uc001ehg.2_Missense_Mutation_p.S86L	NM_017686	NP_060156	Q9NXN4	GDAP2_HUMAN	ganglioside induced differentiation associated	86	Macro.									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)														---	---	---	---
ADAM30	11085	broad.mit.edu	37	1	120438783	120438783	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120438783G>A	uc001eij.2	-	1	331	c.177C>T	c.(175-177)GTC>GTT	p.V59V		NM_021794	NP_068566	Q9UKF2	ADA30_HUMAN	ADAM metallopeptidase domain 30 preproprotein	59					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)														---	---	---	---
PDE4DIP	9659	broad.mit.edu	37	1	144865839	144865839	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144865839A>G	uc001elw.3	-	35	6032	c.5741T>C	c.(5740-5742)CTT>CCT	p.L1914P	NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Missense_Mutation_p.L1808P|PDE4DIP_uc001elv.3_Missense_Mutation_p.L921P|PDE4DIP_uc001ema.2_Missense_Mutation_p.L101P	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform	1914	Potential.				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								---	---	---	---
BCL9	607	broad.mit.edu	37	1	147096003	147096003	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:147096003G>A	uc001epq.2	+	10	4264	c.3524G>A	c.(3523-3525)GGC>GAC	p.G1175D	BCL9_uc010ozr.1_Missense_Mutation_p.G1089D	NM_004326	NP_004317	O00512	BCL9_HUMAN	B-cell CLL/lymphoma 9	1175	Pro-rich.				Wnt receptor signaling pathway	nucleus	protein binding			ovary(2)|large_intestine(2)|breast(1)|skin(1)	6	all_hematologic(923;0.115)							T	IGH@|IGL@	B-ALL								---	---	---	---
SV2A	9900	broad.mit.edu	37	1	149884988	149884988	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149884988G>A	uc001etg.2	-	2	896	c.405C>T	c.(403-405)GGC>GGT	p.G135G	SV2A_uc001eth.2_Silent_p.G135G	NM_014849	NP_055664	Q7L0J3	SV2A_HUMAN	synaptic vesicle glycoprotein 2	135	Cytoplasmic (Potential).				neurotransmitter transport	cell junction|endoplasmic reticulum|integral to membrane|synaptic vesicle membrane	transmembrane transporter activity			ovary(6)|pancreas(1)	7	Breast(34;0.00769)|all_hematologic(923;0.127)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.221)|STAD - Stomach adenocarcinoma(528;0.247)		Levetiracetam(DB01202)													---	---	---	---
SF3B4	10262	broad.mit.edu	37	1	149898338	149898338	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149898338T>C	uc001etj.1	-	3	687	c.636A>G	c.(634-636)GCA>GCG	p.A212A	SF3B4_uc001eti.1_5'Flank|SF3B4_uc001etk.1_Silent_p.A212A|SF3B4_uc009wll.1_Silent_p.A212A	NM_005850	NP_005841	Q15427	SF3B4_HUMAN	splicing factor 3b, subunit 4	212						nucleoplasm|U12-type spliceosomal complex	nucleotide binding|protein binding|RNA binding			ovary(1)	1	Breast(34;0.0009)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.221)|STAD - Stomach adenocarcinoma(528;0.247)															---	---	---	---
ADAMTSL4	54507	broad.mit.edu	37	1	150525383	150525383	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150525383G>A	uc001eux.2	+	5	324	c.88G>A	c.(88-90)GGA>AGA	p.G30R	ADAMTSL4_uc001euw.2_Missense_Mutation_p.G30R|ADAMTSL4_uc009wlw.2_Missense_Mutation_p.G30R|ADAMTSL4_uc010pcg.1_Missense_Mutation_p.G30R	NM_019032	NP_061905	Q6UY14	ATL4_HUMAN	thrombospondin repeat containing 1 isoform 1	30					apoptosis|positive regulation of apoptosis		metalloendopeptidase activity|protease binding			ovary(1)|skin(1)	2	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;3.18e-23)|all cancers(9;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(6;1.13e-14)|BRCA - Breast invasive adenocarcinoma(12;0.000503)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)															---	---	---	---
ANXA9	8416	broad.mit.edu	37	1	150958865	150958865	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150958865C>T	uc001ewa.2	+	8	996	c.526C>T	c.(526-528)CAG>TAG	p.Q176*		NM_003568	NP_003559	O76027	ANXA9_HUMAN	annexin A9	176	Annexin 2.				cell-cell adhesion	cell surface|cytosol	acetylcholine receptor activity|calcium ion binding|calcium-dependent phospholipid binding|phosphatidylserine binding|protein homodimerization activity				0	all_lung(15;1.09e-34)|Lung NSC(24;1.1e-30)|Lung SC(34;0.00202)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)															---	---	---	---
ZNF687	57592	broad.mit.edu	37	1	151263605	151263605	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151263605C>A	uc001exq.2	+	9	3732	c.3634C>A	c.(3634-3636)CCT>ACT	p.P1212T	ZNF687_uc009wmo.2_Missense_Mutation_p.P1212T|ZNF687_uc009wmp.2_3'UTR	NM_020832	NP_065883	Q8N1G0	ZN687_HUMAN	zinc finger protein 687	1212	C2H2-type 10.				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)															---	---	---	---
THEM4	117145	broad.mit.edu	37	1	151861728	151861728	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151861728G>A	uc001ezj.1	-	3	587	c.408C>T	c.(406-408)TGC>TGT	p.C136C	THEM4_uc001ezk.1_RNA	NM_053055	NP_444283	Q5T1C6	THEM4_HUMAN	thioesterase superfamily member 4	136					insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling	cytosol|ruffle membrane					0	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)															---	---	---	---
TCHH	7062	broad.mit.edu	37	1	152081809	152081809	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152081809T>C	uc001ezp.2	-	2	3884	c.3884A>G	c.(3883-3885)GAG>GGG	p.E1295G	TCHH_uc009wne.1_Missense_Mutation_p.E1295G	NM_007113	NP_009044	Q07283	TRHY_HUMAN	trichohyalin	1295	23 X 26 AA approximate tandem repeats.				keratinization	cytoskeleton	calcium ion binding			ovary(3)|kidney(1)|central_nervous_system(1)	5	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)															---	---	---	---
FLG	2312	broad.mit.edu	37	1	152281796	152281796	+	Missense_Mutation	SNP	G	T	T	rs144236267	byFrequency	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152281796G>T	uc001ezu.1	-	3	5602	c.5566C>A	c.(5566-5568)CGT>AGT	p.R1856S		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	1856	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	152283466	152283466	+	Missense_Mutation	SNP	C	T	T	rs150251062	byFrequency	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152283466C>T	uc001ezu.1	-	3	3932	c.3896G>A	c.(3895-3897)CGG>CAG	p.R1299Q	uc001ezv.2_5'Flank	NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	1299	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				---	---	---	---
S100A14	57402	broad.mit.edu	37	1	153588311	153588311	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153588311G>A	uc001fce.2	-	2	122	c.24C>T	c.(22-24)AAC>AAT	p.N8N	S100A16_uc001fcd.1_5'Flank	NM_020672	NP_065723	Q9HCY8	S10AE_HUMAN	S100 calcium binding protein A14	8					calcium ion homeostasis|defense response to bacterium|positive regulation of granulocyte chemotaxis|positive regulation of monocyte chemotaxis|response to lipopolysaccharide|toll-like receptor 4 signaling pathway	cell junction|microtubule cytoskeleton|perinuclear region of cytoplasm	calcium ion binding|chemokine receptor binding				0	all_lung(78;1.84e-32)|Lung NSC(65;6.67e-31)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)															---	---	---	---
CRTC2	200186	broad.mit.edu	37	1	153924897	153924897	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153924897C>T	uc010ped.1	-	9	798	c.728G>A	c.(727-729)CGG>CAG	p.R243Q	CRTC2_uc001fde.3_RNA|CRTC2_uc001fdf.3_5'UTR	NM_181715	NP_859066	Q53ET0	CRTC2_HUMAN	CREB regulated transcription coactivator 2	243					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)															---	---	---	---
AQP10	89872	broad.mit.edu	37	1	154296925	154296925	+	Missense_Mutation	SNP	C	T	T	rs141365858	byFrequency	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154296925C>T	uc001feu.2	+	6	915	c.875C>T	c.(874-876)GCC>GTC	p.A292V	AQP10_uc001fev.2_3'UTR|ATP8B2_uc001few.2_5'Flank	NM_080429	NP_536354	Q96PS8	AQP10_HUMAN	aquaporin 10	292	Extracellular (Potential).				response to toxin|transmembrane transport|water transport	integral to membrane|plasma membrane	transporter activity			central_nervous_system(1)	1	all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)													OREG0013832	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
CHRNB2	1141	broad.mit.edu	37	1	154544182	154544182	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154544182C>T	uc001ffg.2	+	5	1147	c.883C>T	c.(883-885)CCG>TCG	p.P295S		NM_000748	NP_000739	P17787	ACHB2_HUMAN	neuronal nicotinic acetylcholine receptor beta 2	295					B cell activation|behavioral response to nicotine|calcium ion transport|central nervous system projection neuron axonogenesis|lateral geniculate nucleus development|locomotory behavior|membrane depolarization|memory|negative regulation of action potential|optic nerve morphogenesis|positive regulation of B cell proliferation|positive regulation of dopamine secretion|regulation of circadian sleep/wake cycle, REM sleep|regulation of dendrite morphogenesis|regulation of dopamine metabolic process|regulation of synaptogenesis|response to cocaine|response to ethanol|response to hypoxia|sensory perception of pain|sensory perception of sound|smooth muscle contraction|social behavior|synaptic transmission involved in micturition|synaptic transmission, cholinergic|vestibulocochlear nerve development|visual learning|visual perception	cell junction|external side of plasma membrane|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity				0	all_lung(78;2.22e-29)|Lung NSC(65;3.66e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)		Nicotine(DB00184)													---	---	---	---
ZBTB7B	51043	broad.mit.edu	37	1	154988858	154988858	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154988858C>T	uc001fgk.3	+	4	1475	c.1317C>T	c.(1315-1317)TTC>TTT	p.F439F	ZBTB7B_uc009wpa.2_Silent_p.F439F|ZBTB7B_uc001fgj.3_Silent_p.F473F|ZBTB7B_uc010peq.1_Silent_p.F473F|ZBTB7B_uc001fgl.3_Silent_p.F439F	NM_015872	NP_056956	O15156	ZBT7B_HUMAN	zinc finger and BTB domain containing 7B	439	C2H2-type 4; atypical.				cell differentiation|ectoderm development|multicellular organismal development|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nucleus	DNA binding|zinc ion binding				0	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)															---	---	---	---
CLK2	1196	broad.mit.edu	37	1	155239459	155239459	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155239459G>A	uc001fjy.2	-	3	509	c.219C>T	c.(217-219)TAC>TAT	p.Y73Y	RAG1AP1_uc010pey.1_Intron|CLK2_uc001fjw.2_Silent_p.Y73Y|CLK2_uc001fjx.2_5'UTR|CLK2_uc009wqm.2_Silent_p.Y73Y	NM_003993	NP_003984	P49760	CLK2_HUMAN	CDC-like kinase 2	73						nucleus	ATP binding|protein serine/threonine kinase activity|protein tyrosine kinase activity				0	all_lung(78;2.32e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)										Other_conserved_DNA_damage_response_genes					---	---	---	---
RUSC1	23623	broad.mit.edu	37	1	155292496	155292496	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155292496G>A	uc001fkj.2	+	2	1161	c.932G>A	c.(931-933)CGG>CAG	p.R311Q	RAG1AP1_uc010pey.1_Intron|C1orf104_uc001fkh.1_5'Flank|C1orf104_uc001fki.2_Intron|RUSC1_uc001fkk.2_Missense_Mutation_p.R311Q|RUSC1_uc009wqn.1_RNA|RUSC1_uc009wqo.1_5'Flank|RUSC1_uc001fkl.2_5'Flank|RUSC1_uc001fkp.2_5'Flank|RUSC1_uc001fkq.2_5'Flank|RUSC1_uc010pgb.1_5'Flank|RUSC1_uc009wqp.1_5'Flank|RUSC1_uc001fkn.2_5'Flank|RUSC1_uc001fko.2_5'Flank|RUSC1_uc001fkr.2_5'Flank|RUSC1_uc001fks.2_5'Flank	NM_001105203	NP_001098673	Q9BVN2	RUSC1_HUMAN	RUN and SH3 domain containing 1 isoform a	311						cytoplasm|nucleolus	SH3/SH2 adaptor activity			ovary(2)	2	Hepatocellular(266;0.0877)|all_hematologic(923;0.145)		Epithelial(20;1.55e-10)|all cancers(21;4.15e-10)|BRCA - Breast invasive adenocarcinoma(34;0.000549)|LUSC - Lung squamous cell carcinoma(543;0.127)															---	---	---	---
GON4L	54856	broad.mit.edu	37	1	155722380	155722380	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155722380T>C	uc001flz.2	-	30	5941	c.5844A>G	c.(5842-5844)GCA>GCG	p.A1948A	GON4L_uc001flx.1_5'Flank|GON4L_uc009wrg.1_Splice_Site|GON4L_uc001fly.1_Splice_Site_p.G1948_splice|GON4L_uc009wrh.1_Splice_Site_p.G1948_splice|GON4L_uc001fma.1_Silent_p.A1948A	NM_001037533	NP_001032622	Q3T8J9	GON4L_HUMAN	gon-4-like isoform a	1948					regulation of transcription, DNA-dependent	cytoplasm|nucleus	DNA binding			ovary(3)	3	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)																	---	---	---	---
PAQR6	79957	broad.mit.edu	37	1	156213644	156213644	+	3'UTR	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156213644G>T	uc001fnu.1	-	8					PAQR6_uc010phf.1_3'UTR|PAQR6_uc001fny.1_3'UTR|PAQR6_uc001fnv.1_3'UTR|PAQR6_uc010phg.1_3'UTR|PAQR6_uc001fnx.1_3'UTR|PAQR6_uc001fnw.1_3'UTR|PAQR6_uc001fnz.1_3'UTR|PAQR6_uc010phh.1_3'UTR|PAQR6_uc001foa.1_3'UTR|PAQR6_uc001fob.1_RNA	NM_198406	NP_940798			progestin and adipoQ receptor family member VI							integral to membrane	receptor activity				0	Hepatocellular(266;0.158)																	---	---	---	---
VHLL	391104	broad.mit.edu	37	1	156268818	156268818	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156268818G>A	uc001fok.2	-	1	611	c.163C>T	c.(163-165)CGG>TGG	p.R55W		NM_001004319	NP_001004319	Q6RSH7	VHLL_HUMAN	von Hippel-Lindau tumor suppressor-like	55	Beta-domain.				protein ubiquitination	nucleus				ovary(1)	1	Hepatocellular(266;0.158)																	---	---	---	---
NTRK1	4914	broad.mit.edu	37	1	156844776	156844776	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156844776C>T	uc001fqh.1	+	11	1386	c.1330C>T	c.(1330-1332)CGG>TGG	p.R444W	NTRK1_uc001fqf.1_Missense_Mutation_p.R408W|NTRK1_uc009wsi.1_Missense_Mutation_p.R143W|NTRK1_uc001fqi.1_Missense_Mutation_p.R438W|NTRK1_uc009wsk.1_Missense_Mutation_p.R438W	NM_002529	NP_002520	P04629	NTRK1_HUMAN	neurotrophic tyrosine kinase, receptor, type 1	444	Cytoplasmic (Potential).				activation of adenylate cyclase activity|activation of MAPKK activity|activation of phospholipase C activity|cell differentiation|nerve growth factor receptor signaling pathway|nervous system development|phosphatidylinositol-mediated signaling|Ras protein signal transduction	endosome|integral to plasma membrane	ATP binding|neurotrophin receptor activity|transmembrane receptor protein serine/threonine kinase activity|transmembrane receptor protein tyrosine kinase activity			lung(9)|ovary(6)|stomach(1)|central_nervous_system(1)	17	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)				Imatinib(DB00619)			T	TPM3|TPR|TFG	papillary thyroid					TSP Lung(10;0.080)			---	---	---	---
ARHGEF11	9826	broad.mit.edu	37	1	156925516	156925516	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156925516G>A	uc001fqo.2	-	19	2667	c.1627C>T	c.(1627-1629)CCC>TCC	p.P543S	ARHGEF11_uc001fqn.2_Missense_Mutation_p.P583S|ARHGEF11_uc001fqp.1_Missense_Mutation_p.P72S	NM_014784	NP_055599	O15085	ARHGB_HUMAN	Rho guanine nucleotide exchange factor (GEF) 11	543					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)																	---	---	---	---
ETV3	2117	broad.mit.edu	37	1	157106152	157106152	+	5'UTR	SNP	C	T	T	rs2231852	byFrequency;by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157106152C>T	uc001fqr.2	-	2					ETV3_uc001fqt.2_5'UTR	NM_001145312	NP_001138784			ets variant gene 3 isoform 1								sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0	Hepatocellular(266;0.158)	Prostate(1639;0.174)																---	---	---	---
FCRL5	83416	broad.mit.edu	37	1	157494244	157494244	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157494244T>C	uc001fqu.2	-	10	2222	c.2064A>G	c.(2062-2064)CCA>CCG	p.P688P	FCRL5_uc009wsm.2_Silent_p.P688P|FCRL5_uc010phv.1_Silent_p.P688P|FCRL5_uc010phw.1_Silent_p.P603P	NM_031281	NP_112571	Q96RD9	FCRL5_HUMAN	Fc receptor-like 5	688	Extracellular (Potential).|Ig-like C2-type 7.					integral to membrane|plasma membrane	receptor activity			ovary(3)|breast(2)|central_nervous_system(1)	6	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.231)																---	---	---	---
FCRL3	115352	broad.mit.edu	37	1	157665164	157665164	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157665164C>A	uc001frb.2	-	8	1658	c.1366G>T	c.(1366-1368)GGC>TGC	p.G456C	FCRL3_uc001fqx.3_RNA|FCRL3_uc001fqy.3_RNA|FCRL3_uc001fqz.3_Missense_Mutation_p.G456C|FCRL3_uc009wsn.2_RNA|FCRL3_uc009wso.2_RNA|FCRL3_uc001fra.2_Missense_Mutation_p.G182C|FCRL3_uc001frc.1_Missense_Mutation_p.G456C	NM_052939	NP_443171	Q96P31	FCRL3_HUMAN	Fc receptor-like 3 precursor	456	Ig-like C2-type 5.|Extracellular (Potential).					integral to membrane|plasma membrane	receptor activity			ovary(3)|breast(1)	4	all_hematologic(112;0.0378)																	---	---	---	---
FCRL3	115352	broad.mit.edu	37	1	157666067	157666067	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157666067G>A	uc001frb.2	-	7	1187	c.895C>T	c.(895-897)CTG>TTG	p.L299L	FCRL3_uc001fqx.3_RNA|FCRL3_uc001fqy.3_RNA|FCRL3_uc001fqz.3_Silent_p.L299L|FCRL3_uc009wsn.2_RNA|FCRL3_uc009wso.2_RNA|FCRL3_uc001fra.2_Silent_p.L25L|FCRL3_uc001frc.1_Silent_p.L299L	NM_052939	NP_443171	Q96P31	FCRL3_HUMAN	Fc receptor-like 3 precursor	299	Ig-like C2-type 4.|Extracellular (Potential).					integral to membrane|plasma membrane	receptor activity			ovary(3)|breast(1)	4	all_hematologic(112;0.0378)																	---	---	---	---
ATP1A2	477	broad.mit.edu	37	1	160094924	160094924	+	Splice_Site	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160094924A>G	uc001fvc.2	+	7	763	c.631_splice	c.e7-2	p.V211_splice	ATP1A2_uc001fvb.2_Splice_Site_p.V211_splice|ATP1A2_uc010piz.1_Splice_Site_p.V56_splice|ATP1A2_uc001fvd.2_5'Flank	NM_000702	NP_000693			Na+/K+ -ATPase alpha 2 subunit proprotein						ATP biosynthetic process		ATP binding|metal ion binding|sodium:potassium-exchanging ATPase activity			central_nervous_system(3)|ovary(2)|skin(2)	7	all_cancers(52;1.11e-16)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)|LUSC - Lung squamous cell carcinoma(543;0.246)															---	---	---	---
ATP1A4	480	broad.mit.edu	37	1	160156152	160156152	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160156152C>T	uc001fve.3	+	21	3535	c.3056C>T	c.(3055-3057)CCG>CTG	p.P1019L	ATP1A4_uc001fvf.3_RNA|ATP1A4_uc001fvg.2_Missense_Mutation_p.P522L|ATP1A4_uc001fvh.2_Missense_Mutation_p.P155L	NM_144699	NP_653300	Q13733	AT1A4_HUMAN	Na+/K+ -ATPase alpha 4 subunit isoform 1	1019	Cytoplasmic (Potential).				ATP biosynthetic process|ATP hydrolysis coupled proton transport|regulation of cellular pH|sperm motility	sodium:potassium-exchanging ATPase complex	ATP binding|metal ion binding|sodium:potassium-exchanging ATPase activity			ovary(2)|skin(2)	4	all_cancers(52;2.56e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)															---	---	---	---
SLAMF6	114836	broad.mit.edu	37	1	160465878	160465878	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160465878G>T	uc001fwe.1	-	2	415	c.355C>A	c.(355-357)CTG>ATG	p.L119M	SLAMF6_uc001fwd.1_Missense_Mutation_p.L119M|SLAMF6_uc010pjh.1_Missense_Mutation_p.L70M|SLAMF6_uc010pji.1_Intron|SLAMF6_uc010pjj.1_Intron|SLAMF6_uc009wtm.1_Missense_Mutation_p.L70M	NM_052931	NP_443163	Q96DU3	SLAF6_HUMAN	activating NK receptor precursor	119	Extracellular (Potential).					integral to membrane|plasma membrane	receptor activity			ovary(1)|skin(1)	2	all_cancers(52;1.05e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0923)															---	---	---	---
NDUFS2	4720	broad.mit.edu	37	1	161183198	161183198	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161183198T>G	uc001fyv.2	+	12	1593	c.1145T>G	c.(1144-1146)TTT>TGT	p.F382C	NDUFS2_uc001fyw.2_Missense_Mutation_p.F382C|NDUFS2_uc010pkj.1_Missense_Mutation_p.F331C|NDUFS2_uc001fyx.2_Missense_Mutation_p.F356C|FCER1G_uc001fyz.1_5'Flank|FCER1G_uc001fza.1_5'Flank	NM_004550	NP_004541	O75306	NDUS2_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 2	382					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)													---	---	---	---
NR1I3	9970	broad.mit.edu	37	1	161202949	161202949	+	Intron	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161202949C>T	uc001fzx.2	-						TOMM40L_uc009wuf.1_Intron|NR1I3_uc001fzf.2_Intron|NR1I3_uc001fzg.2_Intron|NR1I3_uc001fzh.2_Intron|NR1I3_uc001fzi.2_Intron|NR1I3_uc001fzj.2_Intron|NR1I3_uc001fzk.2_Intron|NR1I3_uc001fzl.2_Intron|NR1I3_uc001fzm.2_Intron|NR1I3_uc001fzn.2_Intron|NR1I3_uc009wug.2_Intron|NR1I3_uc001fzp.2_Intron|NR1I3_uc001fzo.2_Intron|NR1I3_uc001fzq.2_Intron|NR1I3_uc001fzr.2_Intron|NR1I3_uc001fzs.2_Intron|NR1I3_uc001fzt.2_Intron|NR1I3_uc001fzu.2_Intron|NR1I3_uc001fzv.2_Intron|NR1I3_uc001fzw.2_Intron|NR1I3_uc001fzy.2_Intron|NR1I3_uc001fzz.2_Intron|NR1I3_uc001gaa.2_Intron|NR1I3_uc001gab.2_Intron|NR1I3_uc001gac.2_Intron|NR1I3_uc010pkm.1_Intron|NR1I3_uc010pkn.1_Intron	NM_001077480	NP_001070948			constitutive androstane receptor isoform 2						regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	androgen receptor activity|protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|thyroid hormone receptor activity|transcription coactivator activity|zinc ion binding			ovary(1)|skin(1)	2	all_cancers(52;1.86e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00376)															---	---	---	---
FCGR2B	2213	broad.mit.edu	37	1	161641177	161641177	+	Intron	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161641177C>A	uc001gaz.1	+						FCGR2B_uc009wum.1_Intron|FCGR2B_uc001gay.1_Intron|FCGR2B_uc001gba.1_Intron|FCGR2B_uc001gbb.1_Intron|FCGR2B_uc009wun.1_Intron	NM_004001	NP_003992			Fc fragment of IgG, low affinity IIb, receptor						immune response|interspecies interaction between organisms|regulation of immune response	integral to membrane|plasma membrane	IgG binding|receptor activity				0	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Immune globulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)			T	?	ALL								---	---	---	---
FMO3	2328	broad.mit.edu	37	1	171076863	171076863	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171076863C>T	uc001ghi.2	+	4	480	c.369C>T	c.(367-369)GGC>GGT	p.G123G	FMO3_uc001ghh.2_Silent_p.G123G|FMO3_uc010pmb.1_Silent_p.G103G|FMO3_uc010pmc.1_Silent_p.G60G	NM_001002294	NP_001002294	P31513	FMO3_HUMAN	flavin containing monooxygenase 3	123					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)																	---	---	---	---
RC3H1	149041	broad.mit.edu	37	1	173930312	173930312	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173930312C>T	uc001gju.3	-	12	2360	c.2273G>A	c.(2272-2274)CGA>CAA	p.R758Q	RC3H1_uc010pms.1_Missense_Mutation_p.R758Q|RC3H1_uc001gjv.2_Missense_Mutation_p.R758Q|RC3H1_uc010pmt.1_Missense_Mutation_p.R758Q	NM_172071	NP_742068	Q5TC82	RC3H1_HUMAN	roquin	758	Pro-rich.				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																		---	---	---	---
GPR52	9293	broad.mit.edu	37	1	174417414	174417414	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:174417414T>C	uc001gka.1	+	1	203	c.165T>C	c.(163-165)ATT>ATC	p.I55I	RABGAP1L_uc001gjw.2_Intron|RABGAP1L_uc001gjx.2_Intron|RABGAP1L_uc001gjy.2_Intron|RABGAP1L_uc001gjz.2_Intron	NM_005684	NP_005675	Q9Y2T5	GPR52_HUMAN	G protein-coupled receptor 52	55	Helical; Name=1; (Potential).					integral to plasma membrane	G-protein coupled receptor activity			skin(1)	1																		---	---	---	---
PAPPA2	60676	broad.mit.edu	37	1	176671867	176671867	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176671867T>C	uc001gkz.2	+	9	4525	c.3361T>C	c.(3361-3363)TCA>CCA	p.S1121P	PAPPA2_uc009www.2_RNA	NM_020318	NP_064714	Q9BXP8	PAPP2_HUMAN	pappalysin 2 isoform 1	1121					cell differentiation|proteolysis|regulation of cell growth	extracellular region|intracellular|membrane	metalloendopeptidase activity|zinc ion binding			ovary(7)|central_nervous_system(5)|skin(2)|lung(1)|breast(1)	16																		---	---	---	---
LHX4	89884	broad.mit.edu	37	1	180235536	180235536	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180235536C>T	uc001goe.1	+	3	481	c.258C>T	c.(256-258)GGC>GGT	p.G86G		NM_033343	NP_203129	Q969G2	LHX4_HUMAN	LIM homeobox protein 4	86	LIM zinc-binding 1.					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1																		---	---	---	---
CACNA1E	777	broad.mit.edu	37	1	181706764	181706764	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181706764G>A	uc001gow.2	+	23	3691	c.3526G>A	c.(3526-3528)GTC>ATC	p.V1176I	CACNA1E_uc009wxs.2_Missense_Mutation_p.V1064I|CACNA1E_uc001gox.1_Missense_Mutation_p.V402I|CACNA1E_uc009wxt.2_Missense_Mutation_p.V402I	NM_000721	NP_000712	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type,	1176	Extracellular (Potential).|III.				energy reserve metabolic process|membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6																		---	---	---	---
CACNA1E	777	broad.mit.edu	37	1	181731743	181731743	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181731743T>C	uc001gow.2	+	33	4804	c.4639T>C	c.(4639-4641)TTC>CTC	p.F1547L	CACNA1E_uc009wxs.2_Missense_Mutation_p.F1435L|CACNA1E_uc001gox.1_Missense_Mutation_p.F773L|CACNA1E_uc009wxt.2_Missense_Mutation_p.F773L	NM_000721	NP_000712	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type,	1547	Helical; Name=S3 of repeat IV.|IV.				energy reserve metabolic process|membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6																		---	---	---	---
ZNF648	127665	broad.mit.edu	37	1	182025786	182025786	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182025786C>T	uc001goz.2	-	2	1568	c.1360G>A	c.(1360-1362)GGC>AGC	p.G454S		NM_001009992	NP_001009992	Q5T619	ZN648_HUMAN	zinc finger protein 648	454	C2H2-type 7.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
APOBEC4	403314	broad.mit.edu	37	1	183617241	183617241	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183617241C>T	uc001gqn.2	-	2	948	c.676G>A	c.(676-678)GCA>ACA	p.A226T	RGL1_uc010pof.1_Intron|RGL1_uc001gqm.2_Intron|RGL1_uc010pog.1_Intron|RGL1_uc010poh.1_Intron	NM_203454	NP_982279	Q8WW27	ABEC4_HUMAN	apolipoprotein B	226					mRNA processing		hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines|zinc ion binding				0																		---	---	---	---
C1orf25	81627	broad.mit.edu	37	1	185125603	185125603	+	Intron	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185125603C>T	uc001grf.3	-						C1orf26_uc001grg.3_5'Flank|C1orf26_uc001grh.3_5'Flank|C1orf25_uc010pon.1_Intron	NM_030934	NP_112196			N2,N2-dimethylguanosine tRNA							intracellular	RNA binding|tRNA (guanine-N2-)-methyltransferase activity|zinc ion binding				0																		---	---	---	---
IVNS1ABP	10625	broad.mit.edu	37	1	185270128	185270128	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185270128T>C	uc001grl.2	-	10	1719	c.1096A>G	c.(1096-1098)ATG>GTG	p.M366V	IVNS1ABP_uc001gri.2_Missense_Mutation_p.M26V|IVNS1ABP_uc001grj.2_Missense_Mutation_p.M26V|IVNS1ABP_uc009wyj.2_Missense_Mutation_p.M148V|IVNS1ABP_uc009wyk.2_RNA|IVNS1ABP_uc001grm.2_Missense_Mutation_p.M26V	NM_006469	NP_006460	Q9Y6Y0	NS1BP_HUMAN	influenza virus NS1A binding protein	366	Sufficient for AHR interaction and signaling.				interspecies interaction between organisms|response to virus|RNA splicing|transcription from RNA polymerase III promoter	cytoplasm|cytoskeleton|spliceosomal complex|transcription factor complex				ovary(4)|central_nervous_system(1)	5																		---	---	---	---
HMCN1	83872	broad.mit.edu	37	1	185931751	185931751	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185931751G>A	uc001grq.1	+	12	2159	c.1930G>A	c.(1930-1932)GCC>ACC	p.A644T	HMCN1_uc001grr.1_5'UTR	NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1 precursor	644	Ig-like C2-type 3.				response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23																		---	---	---	---
HMCN1	83872	broad.mit.edu	37	1	186092202	186092202	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186092202C>T	uc001grq.1	+	81	12578	c.12349C>T	c.(12349-12351)CGT>TGT	p.R4117C		NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1 precursor	4117	Ig-like C2-type 40.				response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23																		---	---	---	---
HMCN1	83872	broad.mit.edu	37	1	186113746	186113746	+	Missense_Mutation	SNP	G	A	A	rs149329415		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186113746G>A	uc001grq.1	+	91	14406	c.14177G>A	c.(14176-14178)GGC>GAC	p.G4726D	HMCN1_uc001grs.1_Missense_Mutation_p.G295D	NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1 precursor	4726	TSP type-1 4.				response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23																		---	---	---	---
PRG4	10216	broad.mit.edu	37	1	186276755	186276755	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186276755C>T	uc001gru.3	+	7	1955	c.1904C>T	c.(1903-1905)ACC>ATC	p.T635I	PRG4_uc001grt.3_Missense_Mutation_p.T594I|PRG4_uc009wyl.2_Missense_Mutation_p.T542I|PRG4_uc009wym.2_Missense_Mutation_p.T501I|PRG4_uc010poo.1_Intron	NM_005807	NP_005798	Q92954	PRG4_HUMAN	proteoglycan 4 isoform A	635	59 X 8 AA repeats of K-X-P-X-P-T-T-X.				cell proliferation|immune response	extracellular region	polysaccharide binding|protein binding|scavenger receptor activity			skin(1)	1																		---	---	---	---
TPR	7175	broad.mit.edu	37	1	186328983	186328983	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186328983C>T	uc001grv.2	-	12	1634	c.1337G>A	c.(1336-1338)CGT>CAT	p.R446H	TPR_uc010pop.1_Missense_Mutation_p.R522H	NM_003292	NP_003283	P12270	TPR_HUMAN	nuclear pore complex-associated protein TPR	446	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								---	---	---	---
FAM5C	339479	broad.mit.edu	37	1	190129847	190129847	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:190129847G>A	uc001gse.1	-	7	1367	c.1135C>T	c.(1135-1137)CTT>TTT	p.L379F	FAM5C_uc010pot.1_Missense_Mutation_p.L277F	NM_199051	NP_950252	Q76B58	FAM5C_HUMAN	family with sequence similarity 5, member C	379						extracellular region				lung(2)|ovary(1)|kidney(1)|skin(1)	5	Prostate(682;0.198)																	---	---	---	---
FAM5C	339479	broad.mit.edu	37	1	190129967	190129967	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:190129967A>G	uc001gse.1	-	7	1247	c.1015T>C	c.(1015-1017)TCT>CCT	p.S339P	FAM5C_uc010pot.1_Missense_Mutation_p.S237P	NM_199051	NP_950252	Q76B58	FAM5C_HUMAN	family with sequence similarity 5, member C	339						extracellular region				lung(2)|ovary(1)|kidney(1)|skin(1)	5	Prostate(682;0.198)																	---	---	---	---
ASPM	259266	broad.mit.edu	37	1	197098315	197098315	+	Splice_Site	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197098315A>G	uc001gtu.2	-	9	3017	c.2760_splice	c.e9+1	p.K920_splice	ASPM_uc001gtv.2_Splice_Site_p.K920_splice|ASPM_uc001gtw.3_Intron	NM_018136	NP_060606			asp (abnormal spindle)-like, microcephaly						mitosis	cytoplasm|nucleus	calmodulin binding			ovary(4)|central_nervous_system(2)	6																		---	---	---	---
DENND1B	163486	broad.mit.edu	37	1	197564380	197564380	+	Silent	SNP	A	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197564380A>C	uc001guf.3	-	14	1343	c.1005T>G	c.(1003-1005)GCT>GCG	p.A335A	DENND1B_uc010ppe.1_Silent_p.A315A|DENND1B_uc010ppf.1_RNA|DENND1B_uc001gue.3_Silent_p.A305A	NM_144977	NP_659414	Q6P3S1	DEN1B_HUMAN	DENN/MADD domain containing 1B isoform 2	335	dDENN.					clathrin-coated vesicle|cytosol	guanyl-nucleotide exchange factor activity				0																		---	---	---	---
PTPRC	5788	broad.mit.edu	37	1	198666000	198666000	+	Missense_Mutation	SNP	C	A	A	rs149798940	byFrequency	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:198666000C>A	uc001gur.1	+	4	434	c.254C>A	c.(253-255)CCG>CAG	p.P85Q	PTPRC_uc001gus.1_Missense_Mutation_p.P85Q|PTPRC_uc001gut.1_Intron|PTPRC_uc009wze.1_Intron|PTPRC_uc009wzf.1_Intron|PTPRC_uc010ppg.1_Intron|PTPRC_uc001guu.1_Missense_Mutation_p.P128Q|PTPRC_uc001guv.1_Intron|PTPRC_uc001guw.1_Intron	NM_002838	NP_002829	P08575	PTPRC_HUMAN	protein tyrosine phosphatase, receptor type, C	85	Extracellular (Potential).				axon guidance|B cell proliferation|B cell receptor signaling pathway|defense response to virus|immunoglobulin biosynthetic process|negative regulation of cytokine-mediated signaling pathway|negative regulation of protein kinase activity|negative regulation of T cell mediated cytotoxicity|positive regulation of antigen receptor-mediated signaling pathway|positive regulation of B cell proliferation|positive regulation of protein kinase activity|positive regulation of T cell proliferation|regulation of S phase|release of sequestered calcium ion into cytosol|T cell differentiation|T cell receptor signaling pathway	focal adhesion|integral to plasma membrane|membrane raft	protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			breast(4)|skin(3)|ovary(2)|lung(1)|kidney(1)|pancreas(1)	12																		---	---	---	---
CACNA1S	779	broad.mit.edu	37	1	201023674	201023674	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201023674T>G	uc001gvv.2	-	29	3852	c.3625A>C	c.(3625-3627)AGC>CGC	p.S1209R		NM_000069	NP_000060	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type,	1209	IV.|Extracellular (Potential).				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)													---	---	---	---
IGFN1	91156	broad.mit.edu	37	1	201182754	201182754	+	Intron	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201182754G>A	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																		---	---	---	---
SHISA4	149345	broad.mit.edu	37	1	201860965	201860965	+	Silent	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201860965G>T	uc001gxa.2	+	5	676	c.585G>T	c.(583-585)CCG>CCT	p.P195P		NM_198149	NP_937792	Q96DD7	SHSA4_HUMAN	shisa homolog 4 precursor	195	Cytoplasmic (Potential).|Pro-rich.					integral to membrane					0																		---	---	---	---
PPP1R12B	4660	broad.mit.edu	37	1	202465946	202465946	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202465946C>T	uc001gya.1	+	18	2630	c.2486C>T	c.(2485-2487)ACG>ATG	p.T829M	PPP1R12B_uc001gxz.1_Missense_Mutation_p.T829M|PPP1R12B_uc001gyb.1_Missense_Mutation_p.T55M|PPP1R12B_uc001gyc.1_Missense_Mutation_p.T55M	NM_002481	NP_002472	O60237	MYPT2_HUMAN	protein phosphatase 1, regulatory (inhibitor)	829					regulation of muscle contraction|signal transduction	cytoplasm	enzyme activator activity			ovary(3)	3			BRCA - Breast invasive adenocarcinoma(75;0.166)															---	---	---	---
TMEM183A	92703	broad.mit.edu	37	1	202985125	202985125	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202985125C>T	uc001gyu.1	+	5	623	c.565C>T	c.(565-567)CGA>TGA	p.R189*	TMEM183A_uc009xai.1_Nonsense_Mutation_p.R189*|TMEM183A_uc001gyv.1_RNA|TMEM183A_uc001gyw.1_Nonsense_Mutation_p.R188*|TMEM183A_uc001gyx.1_Nonsense_Mutation_p.R188*	NM_001079809	NP_001073277	Q8IXX5	T183A_HUMAN	transmembrane protein 183B	189						integral to membrane					0			BRCA - Breast invasive adenocarcinoma(75;0.18)															---	---	---	---
FMOD	2331	broad.mit.edu	37	1	203316449	203316449	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203316449T>C	uc001gzr.2	-	2	1086	c.950A>G	c.(949-951)AAC>AGC	p.N317S	FMOD_uc010pqi.1_RNA	NM_002023	NP_002014	Q06828	FMOD_HUMAN	fibromodulin precursor	317	LRR 10.				transforming growth factor beta receptor complex assembly	extracellular space|proteinaceous extracellular matrix				ovary(2)|breast(1)	3			BRCA - Breast invasive adenocarcinoma(75;0.171)															---	---	---	---
PIK3C2B	5287	broad.mit.edu	37	1	204400821	204400821	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204400821A>C	uc001haw.2	-	29	4735	c.4256T>G	c.(4255-4257)CTC>CGC	p.L1419R	PIK3C2B_uc010pqv.1_Missense_Mutation_p.L1391R	NM_002646	NP_002637	O00750	P3C2B_HUMAN	phosphoinositide-3-kinase, class 2 beta	1419	PX.				cell communication|phosphatidylinositol-mediated signaling	endoplasmic reticulum|microsome|nucleus|phosphatidylinositol 3-kinase complex|plasma membrane	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity|protein binding			lung(2)|breast(2)|stomach(1)|prostate(1)|central_nervous_system(1)	7	all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193)													OREG0014134	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
PIK3C2B	5287	broad.mit.edu	37	1	204418318	204418318	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204418318G>T	uc001haw.2	-	15	2820	c.2341C>A	c.(2341-2343)CTG>ATG	p.L781M	PIK3C2B_uc010pqv.1_Missense_Mutation_p.L781M	NM_002646	NP_002637	O00750	P3C2B_HUMAN	phosphoinositide-3-kinase, class 2 beta	781					cell communication|phosphatidylinositol-mediated signaling	endoplasmic reticulum|microsome|nucleus|phosphatidylinositol 3-kinase complex|plasma membrane	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity|protein binding			lung(2)|breast(2)|stomach(1)|prostate(1)|central_nervous_system(1)	7	all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193)															---	---	---	---
MDM4	4194	broad.mit.edu	37	1	204501904	204501904	+	Intron	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204501904T>C	uc001hba.2	+						MDM4_uc001hbd.1_Intron|MDM4_uc010pqw.1_Intron|MDM4_uc010pqx.1_Intron|MDM4_uc001hay.1_Intron|MDM4_uc001hbb.2_Intron|MDM4_uc010pqy.1_Intron|MDM4_uc001hbc.2_Intron|MDM4_uc009xbe.1_Intron	NM_002393	NP_002384			mouse double minute 4 homolog						apoptosis|cell proliferation|cellular response to hypoxia|G0 to G1 transition|negative regulation of apoptosis|negative regulation of cell cycle arrest|negative regulation of cell proliferation|negative regulation of protein catabolic process|negative regulation of transcription from RNA polymerase II promoter|protein complex assembly|protein stabilization	nucleus	enzyme binding|zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3	all_cancers(21;0.00146)|all_neural(3;0.0218)|Glioma(3;0.0382)|Breast(84;0.112)|all_epithelial(62;0.118)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;3.15e-47)|all cancers(3;3.56e-32)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|Epithelial(59;0.143)|BRCA - Breast invasive adenocarcinoma(75;0.143)					A		GBM|bladder|retinoblastoma								---	---	---	---
ELK4	2005	broad.mit.edu	37	1	205589189	205589189	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205589189G>A	uc001hcy.1	-	3	2235	c.985C>T	c.(985-987)CCC>TCC	p.P329S	ELK4_uc001hcz.2_Missense_Mutation_p.P329S	NM_001973	NP_001964	P28324	ELK4_HUMAN	ELK4 protein isoform a	329						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								---	---	---	---
SLC41A1	254428	broad.mit.edu	37	1	205766095	205766095	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205766095G>A	uc001hdh.1	-	8	1901	c.1029C>T	c.(1027-1029)GAC>GAT	p.D343D	SLC41A1_uc001hdg.1_5'Flank|uc001hdi.1_5'Flank	NM_173854	NP_776253	Q8IVJ1	S41A1_HUMAN	solute carrier family 41 member 1	343						integral to membrane|plasma membrane	magnesium ion transmembrane transporter activity			skin(2)	2	Breast(84;0.0799)		BRCA - Breast invasive adenocarcinoma(75;0.0252)															---	---	---	---
SRGAP2	23380	broad.mit.edu	37	1	206611390	206611390	+	Silent	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206611390G>T	uc001hdy.2	+	13	1782	c.1449G>T	c.(1447-1449)CGG>CGT	p.R483R	SRGAP2_uc010prt.1_Silent_p.R406R|SRGAP2_uc001hdx.2_Silent_p.R483R|SRGAP2_uc010pru.1_Silent_p.R406R|SRGAP2_uc010prv.1_Silent_p.R407R	NM_015326	NP_056141	O75044	FNBP2_HUMAN	SLIT-ROBO Rho GTPase activating protein 2	570	Rho-GAP.				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)																	---	---	---	---
CD34	947	broad.mit.edu	37	1	208061172	208061172	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208061172G>A	uc001hgw.1	-	8	1327	c.1069C>T	c.(1069-1071)CGA>TGA	p.R357*	CD34_uc001hgv.1_Nonsense_Mutation_p.R199*|CD34_uc001hgx.1_3'UTR|CD34_uc010psj.1_Nonsense_Mutation_p.R222*	NM_001025109	NP_001020280	P28906	CD34_HUMAN	CD34 antigen isoform a	357	Cytoplasmic (Potential).				cell-cell adhesion|leukocyte migration|regulation of immune response	integral to membrane	carbohydrate binding			ovary(1)	1																		---	---	---	---
SERTAD4	56256	broad.mit.edu	37	1	210411408	210411408	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:210411408G>A	uc001hhy.2	+	2	282	c.103G>A	c.(103-105)GGA>AGA	p.G35R	SERTAD4_uc009xcw.2_Missense_Mutation_p.G35R	NM_019605	NP_062551	Q9NUC0	SRTD4_HUMAN	SERTA domain containing 4	35							protein binding			ovary(1)|pancreas(1)	2				OV - Ovarian serous cystadenocarcinoma(81;0.0237)|all cancers(67;0.127)														---	---	---	---
TRAF5	7188	broad.mit.edu	37	1	211546014	211546014	+	Silent	SNP	C	T	T	rs147270768	byFrequency	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:211546014C>T	uc001hih.2	+	11	1704	c.1644C>T	c.(1642-1644)GCC>GCT	p.A548A	TRAF5_uc001hii.2_Silent_p.A548A|TRAF5_uc010psx.1_Silent_p.A559A|TRAF5_uc010psy.1_Silent_p.A442A|TRAF5_uc001hij.2_Silent_p.A548A	NM_004619	NP_004610	O00463	TRAF5_HUMAN	TNF receptor-associated factor 5	548	MATH.				apoptosis|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|regulation of apoptosis	CD40 receptor complex|centrosome|internal side of plasma membrane	protein binding|ubiquitin-protein ligase activity|zinc ion binding			lung(2)|breast(2)|ovary(1)	5				OV - Ovarian serous cystadenocarcinoma(81;0.00946)|all cancers(67;0.0808)|Epithelial(68;0.144)														---	---	---	---
NEK2	4751	broad.mit.edu	37	1	211843642	211843642	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:211843642G>A	uc001hir.1	-	5	892	c.746C>T	c.(745-747)ACG>ATG	p.T249M	NEK2_uc001hiq.1_Missense_Mutation_p.T249M|NEK2_uc001his.3_Missense_Mutation_p.T249M|NEK2_uc001hit.1_RNA	NM_002497	NP_002488	P51955	NEK2_HUMAN	NIMA-related kinase 2	249	Protein kinase.				cell division|centrosome separation|G2/M transition of mitotic cell cycle|meiosis|protein autophosphorylation|regulation of mitosis	centrosome|condensed chromosome kinetochore|cytosol|nucleolus	ATP binding|metal ion binding|protein binding|protein phosphatase binding|protein serine/threonine kinase activity			breast(2)|stomach(1)	3				OV - Ovarian serous cystadenocarcinoma(81;0.00203)|all cancers(67;0.0339)|Epithelial(68;0.0546)														---	---	---	---
TMEM206	55248	broad.mit.edu	37	1	212560431	212560431	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212560431C>T	uc001hjc.3	-	3	313	c.145G>A	c.(145-147)GAG>AAG	p.E49K	TMEM206_uc010pte.1_Missense_Mutation_p.E110K	NM_018252	NP_060722	Q9H813	TM206_HUMAN	transmembrane protein 206	49	Cytoplasmic (Potential).					integral to membrane				breast(1)	1				all cancers(67;0.012)|OV - Ovarian serous cystadenocarcinoma(81;0.0121)|GBM - Glioblastoma multiforme(131;0.0377)|Epithelial(68;0.148)														---	---	---	---
CENPF	1063	broad.mit.edu	37	1	214792011	214792011	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214792011C>T	uc001hkm.2	+	4	629	c.455C>T	c.(454-456)CCA>CTA	p.P152L		NM_016343	NP_057427	P49454	CENPF_HUMAN	centromere protein F	152	Interaction with SNAP25 and required for localization to the cytoplasm (By similarity).|Potential.				cell differentiation|cell division|cell proliferation|DNA replication|G2 phase of mitotic cell cycle|kinetochore assembly|metaphase plate congression|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|muscle organ development|negative regulation of transcription, DNA-dependent|protein transport|regulation of G2/M transition of mitotic cell cycle|regulation of striated muscle tissue development|response to drug	condensed chromosome outer kinetochore|cytosol|midbody|nuclear envelope|nuclear matrix|perinuclear region of cytoplasm|spindle pole	chromatin binding|dynein binding|protein C-terminus binding|protein homodimerization activity|transcription factor binding			ovary(6)|central_nervous_system(4)|large_intestine(2)|skin(1)	13				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)														---	---	---	---
CENPF	1063	broad.mit.edu	37	1	214819293	214819293	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214819293G>A	uc001hkm.2	+	13	6554	c.6380G>A	c.(6379-6381)CGC>CAC	p.R2127H		NM_016343	NP_057427	P49454	CENPF_HUMAN	centromere protein F	2223	Potential.|2-1.|2 X 177 AA tandem repeats.|Interaction with NDE1 and NDEL1.				cell differentiation|cell division|cell proliferation|DNA replication|G2 phase of mitotic cell cycle|kinetochore assembly|metaphase plate congression|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|muscle organ development|negative regulation of transcription, DNA-dependent|protein transport|regulation of G2/M transition of mitotic cell cycle|regulation of striated muscle tissue development|response to drug	condensed chromosome outer kinetochore|cytosol|midbody|nuclear envelope|nuclear matrix|perinuclear region of cytoplasm|spindle pole	chromatin binding|dynein binding|protein C-terminus binding|protein homodimerization activity|transcription factor binding	p.R2127H(1)		ovary(6)|central_nervous_system(4)|large_intestine(2)|skin(1)	13				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)														---	---	---	---
SPATA17	128153	broad.mit.edu	37	1	217955552	217955552	+	Missense_Mutation	SNP	C	T	T	rs145142638	byFrequency	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:217955552C>T	uc001hlh.1	+	8	786	c.760C>T	c.(760-762)CGC>TGC	p.R254C	SPATA17_uc009xdr.1_RNA|SPATA17_uc001hli.2_Missense_Mutation_p.R254C	NM_138796	NP_620151	Q96L03	SPT17_HUMAN	spermatogenesis associated 17	254						cytoplasm	calmodulin binding			pancreas(1)	1				OV - Ovarian serous cystadenocarcinoma(81;0.0516)|all cancers(67;0.0891)|GBM - Glioblastoma multiforme(131;0.117)														---	---	---	---
RAB3GAP2	25782	broad.mit.edu	37	1	220324711	220324711	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220324711G>A	uc010puk.1	-	35	4228	c.4064C>T	c.(4063-4065)GCA>GTA	p.A1355V	RAB3GAP2_uc001hmf.2_RNA|RAB3GAP2_uc001hmg.2_Missense_Mutation_p.A935V|RAB3GAP2_uc001hmh.2_3'UTR	NM_012414	NP_036546	Q9H2M9	RBGPR_HUMAN	rab3 GTPase-activating protein, non-catalytic	1355					intracellular protein transport	cytoplasm|soluble fraction	GTPase activator activity|protein heterodimerization activity			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(131;0.0443)														---	---	---	---
DISP1	84976	broad.mit.edu	37	1	223177546	223177546	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223177546C>T	uc001hnu.1	+	8	2954	c.2807C>T	c.(2806-2808)GCT>GTT	p.A936V		NM_032890	NP_116279	Q96F81	DISP1_HUMAN	dispatched A	936					diaphragm development|protein homotrimerization|regulation of protein secretion|smoothened signaling pathway	basolateral plasma membrane|integral to membrane	hedgehog receptor activity|peptide transporter activity				0				GBM - Glioblastoma multiforme(131;0.102)														---	---	---	---
CAPN2	824	broad.mit.edu	37	1	223943271	223943271	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223943271G>A	uc001hob.3	+	10	1449	c.1225G>A	c.(1225-1227)GTG>ATG	p.V409M	CAPN2_uc010puy.1_Missense_Mutation_p.V331M|CAPN2_uc001hoc.2_5'Flank	NM_001748	NP_001739	P17655	CAN2_HUMAN	calpain 2 isoform 1	409	Domain III.				proteolysis	cytoplasm|plasma membrane				lung(3)|breast(1)|skin(1)	5				GBM - Glioblastoma multiforme(131;0.109)														---	---	---	---
ITPKB	3707	broad.mit.edu	37	1	226924388	226924388	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226924388C>A	uc010pvo.1	-	2	1112	c.772G>T	c.(772-774)GAG>TAG	p.E258*	ITPKB_uc001hqh.2_Nonsense_Mutation_p.E258*	NM_002221	NP_002212	P27987	IP3KB_HUMAN	1D-myo-inositol-trisphosphate 3-kinase B	258							ATP binding|calmodulin binding|inositol trisphosphate 3-kinase activity			ovary(4)|central_nervous_system(1)	5		Prostate(94;0.0773)																---	---	---	---
OBSCN	84033	broad.mit.edu	37	1	228509533	228509533	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228509533C>T	uc009xez.1	+	55	15035	c.14991C>T	c.(14989-14991)AGC>AGT	p.S4997S	OBSCN_uc001hsn.2_Silent_p.S4997S	NM_001098623	NP_001092093	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and	4997					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)																---	---	---	---
COG2	22796	broad.mit.edu	37	1	230798937	230798937	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230798937G>A	uc001htw.2	+	4	502	c.351G>A	c.(349-351)ATG>ATA	p.M117I	COG2_uc001htx.2_Missense_Mutation_p.M117I|COG2_uc010pwc.1_5'UTR	NM_007357	NP_031383	Q14746	COG2_HUMAN	component of oligomeric golgi complex 2 isoform	117					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)																---	---	---	---
SIPA1L2	57568	broad.mit.edu	37	1	232626723	232626723	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232626723T>C	uc001hvg.2	-	3	1861	c.1703A>G	c.(1702-1704)GAA>GGA	p.E568G		NM_020808	NP_065859	Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like	568					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	233134062	233134062	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233134062G>A	uc001hvl.2	-	32	5961	c.5726C>T	c.(5725-5727)GCA>GTA	p.A1909V	PCNXL2_uc001hvk.1_Missense_Mutation_p.A561V|PCNXL2_uc001hvm.1_RNA	NM_014801	NP_055616	A6NKB5	PCX2_HUMAN	pecanex-like 2	1909						integral to membrane				central_nervous_system(1)|pancreas(1)	2		all_cancers(173;0.0347)|Prostate(94;0.137)																---	---	---	---
ACTN2	88	broad.mit.edu	37	1	236902754	236902754	+	Silent	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236902754C>A	uc001hyf.2	+	10	1233	c.1029C>A	c.(1027-1029)ATC>ATA	p.I343I	ACTN2_uc001hyg.2_Silent_p.I135I|ACTN2_uc009xgi.1_Silent_p.I343I|ACTN2_uc010pxu.1_Intron|ACTN2_uc001hyh.2_Silent_p.I31I	NM_001103	NP_001094	P35609	ACTN2_HUMAN	actinin, alpha 2	343	Spectrin 1.				focal adhesion assembly|microspike assembly|muscle filament sliding|platelet activation|platelet degranulation|protein homotetramerization|regulation of apoptosis|synaptic transmission	actin filament|cytosol|dendritic spine|extracellular region|filopodium|focal adhesion|nucleolus|platelet alpha granule lumen|pseudopodium|Z disc	actin binding|calcium ion binding|FATZ 1 binding|identical protein binding|integrin binding|protein dimerization activity|structural constituent of muscle|titin binding|titin Z domain binding|ZASP binding			ovary(4)|skin(1)	5	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.00661)|Acute lymphoblastic leukemia(190;0.109)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00168)															---	---	---	---
ACTN2	88	broad.mit.edu	37	1	236920825	236920825	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236920825G>A	uc001hyf.2	+	18	2398	c.2194G>A	c.(2194-2196)GCC>ACC	p.A732T	ACTN2_uc001hyg.2_Missense_Mutation_p.A524T|ACTN2_uc009xgi.1_Missense_Mutation_p.A732T|ACTN2_uc010pxu.1_Missense_Mutation_p.A421T|ACTN2_uc001hyh.2_Missense_Mutation_p.A420T	NM_001103	NP_001094	P35609	ACTN2_HUMAN	actinin, alpha 2	732	Spectrin 4.				focal adhesion assembly|microspike assembly|muscle filament sliding|platelet activation|platelet degranulation|protein homotetramerization|regulation of apoptosis|synaptic transmission	actin filament|cytosol|dendritic spine|extracellular region|filopodium|focal adhesion|nucleolus|platelet alpha granule lumen|pseudopodium|Z disc	actin binding|calcium ion binding|FATZ 1 binding|identical protein binding|integrin binding|protein dimerization activity|structural constituent of muscle|titin binding|titin Z domain binding|ZASP binding			ovary(4)|skin(1)	5	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.00661)|Acute lymphoblastic leukemia(190;0.109)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00168)															---	---	---	---
CHRM3	1131	broad.mit.edu	37	1	240072247	240072247	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240072247C>T	uc001hyp.2	+	5	2275	c.1496C>T	c.(1495-1497)GCC>GTC	p.A499V		NM_000740	NP_000731	P20309	ACM3_HUMAN	cholinergic receptor, muscarinic 3	499	Helical; Name=6; (By similarity).				cell proliferation|energy reserve metabolic process|nervous system development|protein modification process|regulation of insulin secretion	basolateral plasma membrane|cell junction|integral to plasma membrane|postsynaptic membrane	muscarinic acetylcholine receptor activity|phosphatidylinositol phospholipase C activity			ovary(4)|skin(1)	5	Ovarian(103;0.127)	all_cancers(173;0.00567)|all_neural(198;0.203)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)		Anisotropine Methylbromide(DB00517)|Atropine(DB00572)|Benzquinamide(DB00767)|Cevimeline(DB00185)|Cryptenamine(DB00785)|Cyclizine(DB01176)|Darifenacin(DB00496)|Diphemanil Methylsulfate(DB00729)|Diphenidol(DB01231)|Homatropine Methylbromide(DB00725)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Solifenacin(DB01591)|Thiethylperazine(DB00372)|Tiotropium(DB01409)|Tolterodine(DB01036)|Tridihexethyl(DB00505)													---	---	---	---
SCCPDH	51097	broad.mit.edu	37	1	246890298	246890298	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246890298G>A	uc001ibr.2	+	2	642	c.295G>A	c.(295-297)GTA>ATA	p.V99I		NM_016002	NP_057086	Q8NBX0	SCPDH_HUMAN	saccharopine dehydrogenase (putative)	99						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	247063740	247063740	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247063740A>T	uc001ibu.1	-	8	1156	c.1149T>A	c.(1147-1149)TTT>TTA	p.F383L	AHCTF1_uc001ibv.1_Missense_Mutation_p.F392L|AHCTF1_uc009xgs.1_5'Flank	NM_015446	NP_056261	Q8WYP5	ELYS_HUMAN	transcription factor ELYS	383	Necessary for cytoplasmic localization (By similarity).				cytokinesis|mitotic prometaphase|mRNA transport|nuclear pore complex assembly|protein transport|transmembrane transport	condensed chromosome kinetochore|cytosol|nuclear matrix|nuclear membrane|nuclear pore|nucleoplasm	DNA binding			ovary(5)|skin(2)	7	all_cancers(71;3.05e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)															---	---	---	---
OR6F1	343169	broad.mit.edu	37	1	247875374	247875374	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247875374G>A	uc001idj.1	-	1	684	c.684C>T	c.(682-684)ATC>ATT	p.I228I		NM_001005286	NP_001005286	Q8NGZ6	OR6F1_HUMAN	olfactory receptor, family 6, subfamily F,	228	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.0168)															---	---	---	---
OR1C1	26188	broad.mit.edu	37	1	247920953	247920953	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247920953G>A	uc010pza.1	-	1	756	c.756C>T	c.(754-756)TAC>TAT	p.Y252Y		NM_012353	NP_036485	Q15619	OR1C1_HUMAN	olfactory receptor, family 1, subfamily C,	252	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1	all_cancers(71;4.34e-05)|all_epithelial(71;1.13e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0786)|Lung NSC(105;0.0858)	all_cancers(173;0.0247)	OV - Ovarian serous cystadenocarcinoma(106;0.0168)															---	---	---	---
OR2W3	343171	broad.mit.edu	37	1	248059482	248059482	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248059482C>T	uc001idp.1	+	3	863	c.594C>T	c.(592-594)ACC>ACT	p.T198T	OR2W3_uc010pzb.1_Silent_p.T198T	NM_001001957	NP_001001957	Q7Z3T1	OR2W3_HUMAN	olfactory receptor, family 2, subfamily W,	198	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|breast(1)|pancreas(1)	3	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0319)															---	---	---	---
CPSF3	51692	broad.mit.edu	37	2	9611523	9611523	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9611523C>T	uc002qzo.1	+	17	1943	c.1908C>T	c.(1906-1908)AGC>AGT	p.S636S	CPSF3_uc002qzp.1_Silent_p.S599S|CPSF3_uc002qzq.1_Silent_p.S213S	NM_016207	NP_057291	Q9UKF6	CPSF3_HUMAN	cleavage and polyadenylation specific factor 3,	636					histone mRNA 3'-end processing|mRNA cleavage|mRNA export from nucleus|mRNA polyadenylation|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	mRNA cleavage and polyadenylation specificity factor complex|ribonucleoprotein complex	5'-3' exonuclease activity|endoribonuclease activity|metal ion binding|protein binding|RNA binding			breast(2)	2	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)	all_cancers(51;2.39e-25)|all_epithelial(98;8.75e-19)|Lung NSC(108;2.38e-06)|Ovarian(717;0.0308)		all cancers(51;2.2e-40)|Epithelial(75;6.71e-35)|OV - Ovarian serous cystadenocarcinoma(76;4.35e-21)|STAD - Stomach adenocarcinoma(1183;0.00644)														---	---	---	---
NOL10	79954	broad.mit.edu	37	2	10729712	10729712	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10729712G>A	uc002raq.2	-	18	1713	c.1588C>T	c.(1588-1590)CGT>TGT	p.R530C	NOL10_uc010yje.1_Missense_Mutation_p.R504C|NOL10_uc010yjf.1_Missense_Mutation_p.R480C|NOL10_uc002rap.2_Missense_Mutation_p.R480C	NM_024894	NP_079170	Q9BSC4	NOL10_HUMAN	nucleolar protein 10	530	Potential.					nucleolus					0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.172)|OV - Ovarian serous cystadenocarcinoma(76;0.207)														---	---	---	---
GREB1	9687	broad.mit.edu	37	2	11758537	11758537	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11758537C>T	uc002rbk.1	+	22	3836	c.3536C>T	c.(3535-3537)CCC>CTC	p.P1179L	GREB1_uc002rbp.1_Missense_Mutation_p.P177L	NM_014668	NP_055483	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	1179	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)														---	---	---	---
GREB1	9687	broad.mit.edu	37	2	11773069	11773069	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11773069G>A	uc002rbk.1	+	28	5171	c.4871G>A	c.(4870-4872)CGG>CAG	p.R1624Q	GREB1_uc002rbp.1_Missense_Mutation_p.R622Q	NM_014668	NP_055483	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	1624						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)														---	---	---	---
NBAS	51594	broad.mit.edu	37	2	15614225	15614225	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15614225C>T	uc002rcc.1	-	15	1591	c.1565G>A	c.(1564-1566)CGC>CAC	p.R522H	NBAS_uc002rcd.1_RNA	NM_015909	NP_056993	A2RRP1	NBAS_HUMAN	neuroblastoma-amplified protein	522										ovary(2)|liver(1)|skin(1)	4																		---	---	---	---
NBAS	51594	broad.mit.edu	37	2	15614424	15614424	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15614424G>A	uc002rcc.1	-	15	1392	c.1366C>T	c.(1366-1368)CGA>TGA	p.R456*	NBAS_uc002rcd.1_RNA	NM_015909	NP_056993	A2RRP1	NBAS_HUMAN	neuroblastoma-amplified protein	456										ovary(2)|liver(1)|skin(1)	4																		---	---	---	---
NT5C1B	93034	broad.mit.edu	37	2	18765854	18765854	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:18765854C>T	uc002rcz.2	-	5	933	c.829G>A	c.(829-831)GAC>AAC	p.D277N	NT5C1B_uc002rcy.2_Missense_Mutation_p.D277N|NT5C1B_uc010exr.2_Missense_Mutation_p.D219N|NT5C1B_uc010yju.1_Missense_Mutation_p.D217N|NT5C1B_uc002rda.2_Missense_Mutation_p.D217N|NT5C1B_uc010yjv.1_Missense_Mutation_p.D294N|NT5C1B_uc010yjw.1_Missense_Mutation_p.D260N|NT5C1B_uc010exs.2_Missense_Mutation_p.D279N|NT5C1B_uc002rdb.1_Missense_Mutation_p.D69N	NM_001002006	NP_001002006	Q96P26	5NT1B_HUMAN	5' nucleotidase, cytosolic IB isoform 1	277					purine base metabolic process|purine nucleotide catabolic process	cytosol	5'-nucleotidase activity|magnesium ion binding|nucleotide binding			skin(2)|ovary(1)	3	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.177)	Ovarian(717;0.208)																---	---	---	---
NCOA1	8648	broad.mit.edu	37	2	24927973	24927973	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24927973C>T	uc002rfk.2	+	10	1226	c.968C>T	c.(967-969)GCC>GTC	p.A323V	NCOA1_uc010eye.2_Missense_Mutation_p.A323V|NCOA1_uc002rfi.2_Missense_Mutation_p.A172V|NCOA1_uc002rfj.2_Missense_Mutation_p.A323V|NCOA1_uc002rfl.2_Missense_Mutation_p.A323V	NM_003743	NP_003734	Q15788	NCOA1_HUMAN	nuclear receptor coactivator 1 isoform 1	323									PAX3/NCOA1(8)	soft_tissue(8)|ovary(1)|lung(1)|skin(1)	11	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)							T	PAX3	alveolar rhadomyosarcoma								---	---	---	---
DNMT3A	1788	broad.mit.edu	37	2	25457192	25457192	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25457192G>T	uc002rgc.2	-	23	2952	c.2695C>A	c.(2695-2697)CGC>AGC	p.R899S	DNMT3A_uc002rgd.2_Missense_Mutation_p.R899S|DNMT3A_uc010eyi.2_RNA|DNMT3A_uc002rgb.2_Missense_Mutation_p.R710S	NM_022552	NP_072046	Q9Y6K1	DNM3A_HUMAN	DNA cytosine methyltransferase 3 alpha isoform	899					regulation of gene expression by genetic imprinting	cytoplasm|euchromatin|nuclear matrix	DNA (cytosine-5-)-methyltransferase activity|DNA binding|metal ion binding|protein binding			haematopoietic_and_lymphoid_tissue(133)|lung(4)|ovary(3)	140	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)							Mis|F|N|S		AML								---	---	---	---
ASXL2	55252	broad.mit.edu	37	2	25966041	25966041	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25966041G>A	uc002rgs.2	-	12	3386	c.3165C>T	c.(3163-3165)CAC>CAT	p.H1055H	ASXL2_uc002rgt.1_Intron	NM_018263	NP_060733	Q76L83	ASXL2_HUMAN	additional sex combs like 2	1055					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|protein binding			pancreas(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
KIF3C	3797	broad.mit.edu	37	2	26203385	26203385	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26203385G>A	uc002rgu.2	-	1	2059	c.1402C>T	c.(1402-1404)CTG>TTG	p.L468L	KIF3C_uc010eyj.1_RNA|KIF3C_uc010ykr.1_Silent_p.L468L	NM_002254	NP_002245	O14782	KIF3C_HUMAN	kinesin family member 3C	468	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)																	---	---	---	---
GTF3C2	2976	broad.mit.edu	37	2	27566374	27566374	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27566374G>A	uc002rjv.1	-	3	411	c.48C>T	c.(46-48)CCC>CCT	p.P16P	GTF3C2_uc002rju.1_Silent_p.P27P|GTF3C2_uc002rjw.1_Silent_p.P16P|GTF3C2_uc010eyz.1_Silent_p.P16P	NM_001521	NP_001512	Q8WUA4	TF3C2_HUMAN	general transcription factor IIIC, polypeptide	16						transcription factor TFIIIC complex				ovary(1)|skin(1)	2	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
PPM1G	5496	broad.mit.edu	37	2	27607889	27607889	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27607889C>T	uc002rkl.2	-	6	583	c.476G>A	c.(475-477)CGC>CAC	p.R159H	PPM1G_uc002rkm.2_Missense_Mutation_p.R9H	NM_002707	NP_002698	O15355	PPM1G_HUMAN	protein phosphatase 1G	159					cell cycle arrest|protein dephosphorylation	cytoplasm|nucleus|protein serine/threonine phosphatase complex	metal ion binding|protein serine/threonine phosphatase activity			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
XDH	7498	broad.mit.edu	37	2	31587012	31587012	+	Intron	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31587012G>A	uc002rnv.1	-							NM_000379	NP_000370			xanthine dehydrogenase						purine nucleotide catabolic process|xanthine catabolic process	cytosol|extracellular region|peroxisome	2 iron, 2 sulfur cluster binding|electron carrier activity|flavin adenine dinucleotide binding|iron ion binding|molybdopterin cofactor binding|protein homodimerization activity|xanthine dehydrogenase activity|xanthine oxidase activity			skin(4)|breast(2)|ovary(1)|central_nervous_system(1)	8	Acute lymphoblastic leukemia(172;0.155)				Allopurinol(DB00437)|Carvedilol(DB01136)|Daunorubicin(DB00694)|Deferoxamine(DB00746)|Desflurane(DB01189)|Menadione(DB00170)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|NADH(DB00157)|Nitrofurazone(DB00336)|Papaverine(DB01113)|Procarbazine(DB01168)|Pyrazinamide(DB00339)|Rasburicase(DB00049)|Spermine(DB00127)|Trifluoperazine(DB00831)|Vitamin E(DB00163)													---	---	---	---
FAM98A	25940	broad.mit.edu	37	2	33810305	33810305	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33810305G>A	uc002rpa.1	-	8	1169	c.1095C>T	c.(1093-1095)GGC>GGT	p.G365G	FAM98A_uc010yne.1_Silent_p.G170G|FAM98A_uc010ynd.1_Silent_p.G196G|FAM98A_uc002roz.1_Silent_p.G203G	NM_015475	NP_056290	Q8NCA5	FA98A_HUMAN	hypothetical protein LOC25940	366	Gly-rich.									ovary(1)	1	all_hematologic(175;0.115)																	---	---	---	---
CRIM1	51232	broad.mit.edu	37	2	36749338	36749338	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:36749338C>T	uc002rpd.2	+	13	2349	c.2310C>T	c.(2308-2310)GAC>GAT	p.D770D		NM_016441	NP_057525	Q9NZV1	CRIM1_HUMAN	cysteine-rich motor neuron 1 precursor	770	Extracellular (Potential).|VWFC 5.				nervous system development|regulation of cell growth	extracellular region|integral to membrane|plasma membrane	insulin-like growth factor binding|insulin-like growth factor receptor activity|serine-type endopeptidase inhibitor activity			ovary(2)|skin(1)	3		all_hematologic(82;0.131)|Acute lymphoblastic leukemia(82;0.154)																---	---	---	---
ABCG8	64241	broad.mit.edu	37	2	44100918	44100918	+	Intron	SNP	T	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44100918T>G	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)																---	---	---	---
STON1-GTF2A1L	286749	broad.mit.edu	37	2	48873957	48873957	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48873957C>T	uc010yol.1	+	5	2772	c.2725C>T	c.(2725-2727)CAG>TAG	p.Q909*	STON1-GTF2A1L_uc002rwp.1_Nonsense_Mutation_p.Q956*|GTF2A1L_uc002rws.1_Nonsense_Mutation_p.Q252*|GTF2A1L_uc010yom.1_Nonsense_Mutation_p.Q218*|GTF2A1L_uc002rwt.2_Nonsense_Mutation_p.Q252*	NM_006873	NP_006864	B7ZL16	B7ZL16_HUMAN	stonin 1	909					endocytosis|intracellular protein transport|transcription initiation from RNA polymerase II promoter	clathrin adaptor complex|transcription factor TFIIA complex				ovary(3)|pancreas(1)|skin(1)	5		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.176)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)															---	---	---	---
FSHR	2492	broad.mit.edu	37	2	49190038	49190038	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:49190038A>G	uc002rww.2	-	10	1996	c.1922T>C	c.(1921-1923)CTG>CCG	p.L641P	FSHR_uc002rwx.2_Missense_Mutation_p.L579P|FSHR_uc010fbn.2_Missense_Mutation_p.L615P	NM_000145	NP_000136	P23945	FSHR_HUMAN	follicle stimulating hormone receptor isoform 1	641	Cytoplasmic (Potential).				female gamete generation|male gonad development|spermatogenesis	integral to membrane|plasma membrane	follicle-stimulating hormone receptor activity|protein binding			ovary(4)|lung(2)|central_nervous_system(1)|skin(1)	8		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.181)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Choriogonadotropin alfa(DB00097)|Follitropin beta(DB00066)|Menotropins(DB00032)|Urofollitropin(DB00094)									Gonadal_Dysgenesis_46_XX				---	---	---	---
USP34	9736	broad.mit.edu	37	2	61415812	61415812	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61415812G>A	uc002sbe.2	-	80	10088	c.10066C>T	c.(10066-10068)CGT>TGT	p.R3356C	USP34_uc002sbd.2_Missense_Mutation_p.R158C	NM_014709	NP_055524	Q70CQ2	UBP34_HUMAN	ubiquitin specific protease 34	3356					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	p.R3356P(1)		ovary(8)|breast(5)|skin(3)|lung(2)|prostate(1)	19			Epithelial(17;0.229)															---	---	---	---
USP34	9736	broad.mit.edu	37	2	61508298	61508298	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61508298C>T	uc002sbe.2	-	38	5100	c.5078G>A	c.(5077-5079)CGT>CAT	p.R1693H	USP34_uc002sbf.2_5'Flank	NM_014709	NP_055524	Q70CQ2	UBP34_HUMAN	ubiquitin specific protease 34	1693					positive regulation of canonical Wnt receptor signaling pathway|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(8)|breast(5)|skin(3)|lung(2)|prostate(1)	19			Epithelial(17;0.229)															---	---	---	---
XPO1	7514	broad.mit.edu	37	2	61722581	61722581	+	Intron	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61722581A>G	uc002sbj.2	-						XPO1_uc010fcl.2_Intron|XPO1_uc010ypn.1_Intron|XPO1_uc002sbk.2_Intron|XPO1_uc002sbh.2_5'Flank	NM_003400	NP_003391			exportin 1						intracellular protein transport|mitotic prometaphase|mRNA metabolic process|mRNA transport|viral genome transport in host cell|viral infectious cycle	annulate lamellae|Cajal body|cytosol|kinetochore|nuclear envelope|nucleolus|ribonucleoprotein complex	protein binding|protein transporter activity|RNA binding			ovary(1)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1)	4			LUSC - Lung squamous cell carcinoma(7;5.71e-05)|Epithelial(17;0.0662)|all cancers(80;0.226)															---	---	---	---
FAM161A	84140	broad.mit.edu	37	2	62066719	62066719	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62066719C>T	uc010ypo.1	-	3	1522	c.1420G>A	c.(1420-1422)GCA>ACA	p.A474T	FAM161A_uc002sbm.3_Missense_Mutation_p.A474T|FAM161A_uc002sbn.3_Missense_Mutation_p.A284T|FAM161A_uc010fcm.1_RNA|FAM161A_uc010fcn.1_Missense_Mutation_p.A365T	NM_032180	NP_115556	Q3B820	F161A_HUMAN	hypothetical protein LOC84140	474					response to stimulus|visual perception	centrosome				large_intestine(2)|ovary(1)	3																		---	---	---	---
CCT4	10575	broad.mit.edu	37	2	62099411	62099411	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62099411C>T	uc002sbo.2	-	12	1446	c.1297G>A	c.(1297-1299)GCC>ACC	p.A433T	CCT4_uc010ypp.1_Missense_Mutation_p.A377T|CCT4_uc010ypq.1_Missense_Mutation_p.A283T|CCT4_uc010ypr.1_Missense_Mutation_p.A377T|CCT4_uc010yps.1_Missense_Mutation_p.A403T	NM_006430	NP_006421	P50991	TCPD_HUMAN	chaperonin containing TCP1, subunit 4 (delta)	433					'de novo' posttranslational protein folding	melanosome|microtubule organizing center|nucleus	ATP binding|unfolded protein binding			ovary(2)	2	Lung NSC(7;0.035)|all_lung(7;0.0691)		LUSC - Lung squamous cell carcinoma(7;6.5e-06)|Epithelial(17;0.0647)|all cancers(80;0.221)															---	---	---	---
SPRED2	200734	broad.mit.edu	37	2	65571870	65571870	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65571870G>A	uc002sdr.3	-	2	722	c.187C>T	c.(187-189)CGA>TGA	p.R63*	SPRED2_uc010fcw.2_Nonsense_Mutation_p.R60*|SPRED2_uc010fcx.1_RNA	NM_181784	NP_861449	Q7Z698	SPRE2_HUMAN	sprouty-related protein with EVH-1 domain 2	63	WH1.				inactivation of MAPK activity|multicellular organismal development	transport vesicle membrane	stem cell factor receptor binding			ovary(1)|lung(1)|central_nervous_system(1)	3																		---	---	---	---
ARHGAP25	9938	broad.mit.edu	37	2	69015041	69015041	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69015041A>G	uc002seu.2	+	4	783	c.419A>G	c.(418-420)GAG>GGG	p.E140G	ARHGAP25_uc010yqk.1_Missense_Mutation_p.E114G|ARHGAP25_uc010fdg.2_Missense_Mutation_p.E140G|ARHGAP25_uc010yql.1_Intron|ARHGAP25_uc002sev.2_Missense_Mutation_p.E133G|ARHGAP25_uc002sew.2_Missense_Mutation_p.E133G|ARHGAP25_uc002sex.2_Missense_Mutation_p.E133G|ARHGAP25_uc010fdh.1_RNA	NM_001007231	NP_001007232	P42331	RHG25_HUMAN	Rho GTPase activating protein 25 isoform a	140	PH.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(2)|breast(2)	4																		---	---	---	---
DYSF	8291	broad.mit.edu	37	2	71755438	71755438	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71755438C>T	uc002sie.2	+	13	1567	c.1191C>T	c.(1189-1191)GCC>GCT	p.A397A	DYSF_uc010feg.2_Silent_p.A428A|DYSF_uc010feh.2_Silent_p.A397A|DYSF_uc002sig.3_Silent_p.A397A|DYSF_uc010yqx.1_RNA|DYSF_uc010fee.2_Silent_p.A397A|DYSF_uc010fef.2_Silent_p.A428A|DYSF_uc010fei.2_Silent_p.A428A|DYSF_uc010fek.2_Silent_p.A429A|DYSF_uc010fej.2_Silent_p.A398A|DYSF_uc010fel.2_Silent_p.A398A|DYSF_uc010feo.2_Silent_p.A429A|DYSF_uc010fem.2_Silent_p.A398A|DYSF_uc010fen.2_Silent_p.A429A|DYSF_uc002sif.2_Silent_p.A398A	NM_003494	NP_003485	O75923	DYSF_HUMAN	dysferlin isoform 8	397	Cytoplasmic (Potential).|C2 3.					cytoplasmic vesicle membrane|integral to membrane|sarcolemma	calcium-dependent phospholipid binding			ovary(3)|breast(2)|pancreas(1)|skin(1)	7																		---	---	---	---
ALMS1	7840	broad.mit.edu	37	2	73717248	73717248	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73717248G>A	uc002sje.1	+	12	8276	c.8165G>A	c.(8164-8166)CGA>CAA	p.R2722Q	ALMS1_uc002sjf.1_Missense_Mutation_p.R2678Q|ALMS1_uc002sjg.2_Missense_Mutation_p.R2108Q|ALMS1_uc002sjh.1_Missense_Mutation_p.R2108Q	NM_015120	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	2720					G2/M transition of mitotic cell cycle	centrosome|cilium|cytosol|microtubule basal body|spindle pole				skin(3)|ovary(2)|breast(2)|pancreas(1)|lung(1)	9																		---	---	---	---
C2orf89	129293	broad.mit.edu	37	2	85097639	85097639	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85097639G>T	uc010ysl.1	-	2	468	c.379C>A	c.(379-381)CTG>ATG	p.L127M	C2orf89_uc002sou.3_Missense_Mutation_p.L127M|C2orf89_uc010fgc.1_Missense_Mutation_p.L127M	NM_001080824	NP_001074293	Q86V40	CB089_HUMAN	hypothetical protein LOC129293 precursor	127	Extracellular (Potential).					integral to membrane				ovary(1)	1																		---	---	---	---
C2orf68	388969	broad.mit.edu	37	2	85836566	85836566	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85836566C>T	uc002sqc.2	-	3	442	c.370G>A	c.(370-372)GTC>ATC	p.V124I	USP39_uc002sqb.2_Intron|USP39_uc010ysu.1_5'Flank|USP39_uc010ysv.1_5'Flank	NM_001013649	NP_001013671	Q2NKX9	CB068_HUMAN	hypothetical protein LOC388969	124										central_nervous_system(1)	1																		---	---	---	---
KDM3A	55818	broad.mit.edu	37	2	86705121	86705121	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86705121C>T	uc002sri.3	+	13	2388	c.2061C>T	c.(2059-2061)TGC>TGT	p.C687C	KDM3A_uc010ytj.1_Silent_p.C687C|KDM3A_uc010ytk.1_Silent_p.C635C	NM_018433	NP_060903	Q9Y4C1	KDM3A_HUMAN	jumonji domain containing 1A	687	C6-type (Potential).				androgen receptor signaling pathway|cell differentiation|formaldehyde biosynthetic process|histone H3-K9 demethylation|hormone-mediated signaling pathway|positive regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	cytoplasm|nucleus	androgen receptor binding|iron ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			breast(2)|ovary(1)|central_nervous_system(1)|skin(1)	5																		---	---	---	---
TEKT4	150483	broad.mit.edu	37	2	95542378	95542378	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:95542378G>A	uc002stw.1	+	6	1265	c.1172G>A	c.(1171-1173)CGC>CAC	p.R391H	uc002stv.1_Intron|TEKT4_uc010fhr.1_RNA	NM_144705	NP_653306	Q8WW24	TEKT4_HUMAN	tektin 4	391	Potential.				cell projection organization|microtubule cytoskeleton organization	cilium axoneme|flagellar axoneme|microtubule				ovary(1)|breast(1)|skin(1)	3																		---	---	---	---
ITPRIPL1	150771	broad.mit.edu	37	2	96993296	96993296	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96993296C>T	uc002svx.2	+	3	1262	c.927C>T	c.(925-927)ACC>ACT	p.T309T	ITPRIPL1_uc010yuk.1_Silent_p.T301T|ITPRIPL1_uc002svy.2_Silent_p.T317T|ITPRIPL1_uc010yul.1_Silent_p.T301T	NM_001008949	NP_001008949	Q6GPH6	IPIL1_HUMAN	inositol 1,4,5-triphosphate receptor interacting	309	Cytoplasmic (Potential).					integral to membrane		p.T317T(1)		central_nervous_system(2)|ovary(1)	3																		---	---	---	---
NEURL3	93082	broad.mit.edu	37	2	97165105	97165105	+	Intron	SNP	A	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97165105A>T	uc010fhx.2	-						NEURL3_uc002swc.2_Intron					Homo sapiens cDNA FLJ54814 complete cds.												0																		---	---	---	---
CNNM4	26504	broad.mit.edu	37	2	97475139	97475139	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97475139C>T	uc002swx.2	+	7	2311	c.2213C>T	c.(2212-2214)ACC>ATC	p.T738I	CNNM4_uc010yuy.1_Silent_p.H254H	NM_020184	NP_064569	Q6P4Q7	CNNM4_HUMAN	cyclin M4	738					biomineral tissue development|ion transport|response to stimulus|visual perception	integral to membrane|plasma membrane				breast(2)|ovary(1)	3																		---	---	---	---
TMEM131	23505	broad.mit.edu	37	2	98426220	98426220	+	Silent	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98426220C>A	uc002syh.3	-	19	2215	c.1986G>T	c.(1984-1986)GTG>GTT	p.V662V		NM_015348	NP_056163	Q92545	TM131_HUMAN	RW1 protein	662						integral to membrane				ovary(4)|central_nervous_system(2)	6																		---	---	---	---
VWA3B	200403	broad.mit.edu	37	2	98928714	98928714	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98928714G>A	uc002syo.2	+	28	4051	c.3787G>A	c.(3787-3789)GCC>ACC	p.A1263T	VWA3B_uc002syr.1_3'UTR|VWA3B_uc002sys.2_RNA	NM_144992	NP_659429	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B	1263										ovary(3)|large_intestine(2)|skin(1)	6																		---	---	---	---
CNGA3	1261	broad.mit.edu	37	2	98994199	98994199	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98994199G>A	uc002syt.2	+	3	568	c.151G>A	c.(151-153)GCC>ACC	p.A51T	CNGA3_uc002syu.2_Missense_Mutation_p.A51T|CNGA3_uc010fij.2_5'UTR	NM_001298	NP_001289	Q16281	CNGA3_HUMAN	cyclic nucleotide gated channel alpha 3 isoform	51					signal transduction|visual perception	integral to membrane	cGMP binding			ovary(5)|upper_aerodigestive_tract(1)	6																		---	---	---	---
FHL2	2274	broad.mit.edu	37	2	106002900	106002900	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106002900C>A	uc002tcu.2	-	2	411	c.74G>T	c.(73-75)AGC>ATC	p.S25I	FHL2_uc002tdc.2_5'UTR|FHL2_uc002tdd.2_Missense_Mutation_p.S25I|FHL2_uc002tcv.2_Missense_Mutation_p.S25I|FHL2_uc002tcw.2_Missense_Mutation_p.S25I|FHL2_uc002tcx.2_Missense_Mutation_p.S25I|FHL2_uc010fje.2_5'UTR|FHL2_uc002tcy.2_Missense_Mutation_p.S25I|FHL2_uc002tcz.2_Missense_Mutation_p.S135I|FHL2_uc002tda.2_RNA|FHL2_uc002tdb.2_Missense_Mutation_p.S141I|FHL2_uc002tde.1_Missense_Mutation_p.S118I	NM_201557	NP_963851	Q14192	FHL2_HUMAN	four and a half LIM domains 2	25	C4-type (Potential).				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																		---	---	---	---
GCC2	9648	broad.mit.edu	37	2	109088540	109088540	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109088540C>T	uc002tec.2	+	6	2909	c.2755C>T	c.(2755-2757)CGA>TGA	p.R919*	GCC2_uc002ted.2_Nonsense_Mutation_p.R818*	NM_181453	NP_852118	Q8IWJ2	GCC2_HUMAN	GRIP and coiled-coil domain-containing 2	919	Potential.				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																		---	---	---	---
RANBP2	5903	broad.mit.edu	37	2	109371498	109371498	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109371498G>A	uc002tem.3	+	16	2466	c.2340G>A	c.(2338-2340)CCG>CCA	p.P780P		NM_006267	NP_006258	P49792	RBP2_HUMAN	RAN binding protein 2	780					carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA transport|protein folding|protein import into nucleus|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear pore	peptidyl-prolyl cis-trans isomerase activity|Ran GTPase binding|zinc ion binding		RANBP2/ALK(16)	soft_tissue(16)|lung(1)|pancreas(1)	18																		---	---	---	---
BUB1	699	broad.mit.edu	37	2	111430296	111430296	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:111430296G>T	uc002tgc.2	-	4	476	c.364C>A	c.(364-366)CTT>ATT	p.L122I	BUB1_uc010yxh.1_Missense_Mutation_p.L102I|BUB1_uc010fkb.2_Missense_Mutation_p.L122I|BUB1_uc002tgd.2_Missense_Mutation_p.L122I	NM_004336	NP_004327	O43683	BUB1_HUMAN	budding uninhibited by benzimidazoles 1	122	BUB1 N-terminal.|Necessary for interaction with CASC5.|Necessary for kinetochore localization.			L->G: Loss of interaction with CASC5.	apoptosis|cell division|chromosome segregation|interspecies interaction between organisms|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|regulation of sister chromatid cohesion	condensed chromosome kinetochore|cytosol	ATP binding|protein binding|protein serine/threonine kinase activity			lung(2)|breast(2)|stomach(1)|ovary(1)|kidney(1)	7		Ovarian(717;0.0822)		BRCA - Breast invasive adenocarcinoma(221;0.0556)														---	---	---	---
ANAPC1	64682	broad.mit.edu	37	2	112614259	112614259	+	Intron	SNP	A	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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																		---	---	---	---
TMEM87B	84910	broad.mit.edu	37	2	112843693	112843693	+	Intron	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112843693C>T	uc002thm.2	+							NM_032824	NP_116213			transmembrane protein 87B precursor							integral to membrane					0																		---	---	---	---
ZC3H6	376940	broad.mit.edu	37	2	113080379	113080379	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113080379G>A	uc002thq.1	+	9	1634	c.1240G>A	c.(1240-1242)GAT>AAT	p.D414N		NM_198581	NP_940983	P61129	ZC3H6_HUMAN	zinc finger CCCH-type domain containing 6	414	Pro-rich.						nucleic acid binding|zinc ion binding			ovary(3)|central_nervous_system(1)	4																		---	---	---	---
SLC20A1	6574	broad.mit.edu	37	2	113414767	113414767	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113414767G>A	uc002tib.2	+	6	1173	c.727G>A	c.(727-729)GCC>ACC	p.A243T	SLC20A1_uc002tic.1_Missense_Mutation_p.A55T	NM_005415	NP_005406	Q8WUM9	S20A1_HUMAN	solute carrier family 20 (phosphate	243	Helical; (Potential).				phosphate metabolic process|positive regulation of I-kappaB kinase/NF-kappaB cascade	integral to plasma membrane	inorganic phosphate transmembrane transporter activity|receptor activity|sodium-dependent phosphate transmembrane transporter activity			ovary(2)	2																		---	---	---	---
DPP10	57628	broad.mit.edu	37	2	116525877	116525877	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:116525877A>G	uc002tla.1	+	13	1575	c.1118A>G	c.(1117-1119)GAG>GGG	p.E373G	DPP10_uc002tlb.1_Missense_Mutation_p.E323G|DPP10_uc002tlc.1_Missense_Mutation_p.E369G|DPP10_uc002tle.2_Missense_Mutation_p.E377G|DPP10_uc002tlf.1_Missense_Mutation_p.E366G	NM_020868	NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl peptidase 10 isoform long	373	Extracellular (Potential).				proteolysis	integral to membrane|membrane fraction	serine-type peptidase activity			ovary(5)|large_intestine(2)|skin(2)|breast(1)	10																		---	---	---	---
GLI2	2736	broad.mit.edu	37	2	121747438	121747438	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121747438C>T	uc010flp.2	+	13	3978	c.3948C>T	c.(3946-3948)CAC>CAT	p.H1316H	GLI2_uc002tmq.1_Intron|GLI2_uc002tmr.1_Intron|GLI2_uc002tmt.3_Silent_p.H988H|GLI2_uc002tmu.3_Silent_p.H971H	NM_005270	NP_005261	P10070	GLI2_HUMAN	GLI-Kruppel family member GLI2	1316					axon guidance|branching morphogenesis of a tube|cell proliferation|cerebellar cortex morphogenesis|developmental growth|embryonic digestive tract development|epidermal cell differentiation|floor plate formation|heart development|hindgut morphogenesis|kidney development|lung development|negative regulation of transcription from RNA polymerase II promoter|odontogenesis of dentine-containing tooth|osteoblast development|osteoblast differentiation|pituitary gland development|positive regulation of DNA replication|positive regulation of T cell differentiation in thymus|positive regulation of transcription from RNA polymerase II promoter|proximal/distal pattern formation|skeletal system development|smoothened signaling pathway involved in ventral spinal cord interneuron specification|spinal cord ventral commissure morphogenesis	nucleus|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|lung(2)|breast(1)|central_nervous_system(1)|pancreas(1)	13	Renal(3;0.0496)	Prostate(154;0.0623)																---	---	---	---
CNTNAP5	129684	broad.mit.edu	37	2	125405387	125405387	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:125405387G>A	uc002tno.2	+	13	2290	c.1926G>A	c.(1924-1926)GTG>GTA	p.V642V	CNTNAP5_uc010flu.2_Silent_p.V643V	NM_130773	NP_570129	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5 precursor	642	Extracellular (Potential).|Fibrinogen C-terminal.				cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(10)	10				BRCA - Breast invasive adenocarcinoma(221;0.248)														---	---	---	---
ERCC3	2071	broad.mit.edu	37	2	128046272	128046272	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128046272C>A	uc002toh.1	-	7	1086	c.991G>T	c.(991-993)GGG>TGG	p.G331W	ERCC3_uc002toe.1_Missense_Mutation_p.G86W|ERCC3_uc002tof.1_Missense_Mutation_p.G267W|ERCC3_uc002tog.1_Missense_Mutation_p.G267W|ERCC3_uc010flx.1_Missense_Mutation_p.G86W	NM_000122	NP_000113	P19447	ERCC3_HUMAN	excision repair cross-complementing rodent	331	Helicase ATP-binding.				cell cycle checkpoint|DNA topological change|hair cell differentiation|induction of apoptosis|interspecies interaction between organisms|mRNA capping|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA duplex unwinding|nucleotide-excision repair, DNA incision|positive regulation of transcription from RNA polymerase II promoter|positive regulation of viral transcription|protein localization|response to oxidative stress|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase I promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	holo TFIIH complex	3'-5' DNA helicase activity|ATP binding|damaged DNA binding|protein C-terminus binding|protein N-terminus binding|transcription factor binding			ovary(2)|lung(2)|breast(2)|kidney(1)	7	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.073)				Mis|S			skin basal cell|skin squamous cell|melanoma		Direct_reversal_of_damage|NER	Xeroderma_Pigmentosum				---	---	---	---
WDR33	55339	broad.mit.edu	37	2	128466300	128466300	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128466300G>A	uc002tpg.1	-	21	3915	c.3732C>T	c.(3730-3732)CAC>CAT	p.H1244H		NM_018383	NP_060853	Q9C0J8	WDR33_HUMAN	WD repeat domain 33 isoform 1	1244					postreplication repair|spermatogenesis	collagen|nucleus	protein binding				0	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0695)														---	---	---	---
LRP1B	53353	broad.mit.edu	37	2	141200145	141200145	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141200145G>A	uc002tvj.1	-	66	11314	c.10342C>T	c.(10342-10344)CAT>TAT	p.H3448Y		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	3448	Extracellular (Potential).|LDL-receptor class A 24.				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)			---	---	---	---
LYPD6B	130576	broad.mit.edu	37	2	150069635	150069635	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:150069635C>T	uc002twv.1	+	6	859	c.458C>T	c.(457-459)ACG>ATG	p.T153M	LYPD6B_uc002tww.1_Missense_Mutation_p.T115M|LYPD6B_uc002twx.1_Missense_Mutation_p.T115M	NM_177964	NP_808879	Q8NI32	LPD6B_HUMAN	LY6/PLAUR domain containing 6B	129	UPAR/Ly6.					anchored to membrane|plasma membrane					0																		---	---	---	---
RIF1	55183	broad.mit.edu	37	2	152273312	152273312	+	Intron	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152273312G>A	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	152501056	152501056	+	Silent	SNP	T	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152501056T>G	uc010fnx.2	-	56	7761	c.7570A>C	c.(7570-7572)AGA>CGA	p.R2524R		NM_004543	NP_004534	P20929	NEBU_HUMAN	nebulin isoform 3	2524					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)														---	---	---	---
KCNJ3	3760	broad.mit.edu	37	2	155555583	155555583	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:155555583C>T	uc002tyv.1	+	1	491	c.296C>T	c.(295-297)GCG>GTG	p.A99V	KCNJ3_uc010zce.1_Missense_Mutation_p.A99V	NM_002239	NP_002230	P48549	IRK3_HUMAN	potassium inwardly-rectifying channel J3	99	Helical; Name=M1; (By similarity).				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)													---	---	---	---
GPD2	2820	broad.mit.edu	37	2	157407127	157407127	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:157407127C>T	uc002tzf.3	+	8	1200	c.840C>T	c.(838-840)GAC>GAT	p.D280D	GPD2_uc010zch.1_Silent_p.D53D|GPD2_uc002tzd.3_Silent_p.D280D|GPD2_uc002tze.1_RNA	NM_001083112	NP_001076581	P43304	GPDM_HUMAN	glycerol-3-phosphate dehydrogenase 2,	280					cellular lipid metabolic process	glycerol-3-phosphate dehydrogenase complex|mitochondrial inner membrane	calcium ion binding|sn-glycerol-3-phosphate:ubiquinone-8 oxidoreductase activity			ovary(1)	1																		---	---	---	---
CCDC148	130940	broad.mit.edu	37	2	159201729	159201729	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:159201729G>A	uc002tzq.2	-	3	512	c.249C>T	c.(247-249)GTC>GTT	p.V83V	CCDC148_uc002tzr.2_Intron|CCDC148_uc010foh.2_Intron|CCDC148_uc010foi.1_Silent_p.V30V|CCDC148_uc010foj.1_Intron|CCDC148_uc010fok.1_Intron|CCDC148_uc002tzs.1_Silent_p.V83V	NM_138803	NP_620158	Q8NFR7	CC148_HUMAN	coiled-coil domain containing 148	83										ovary(2)	2																		---	---	---	---
ITGB6	3694	broad.mit.edu	37	2	160993949	160993949	+	Silent	SNP	G	A	A	rs139038668		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160993949G>A	uc002ubh.2	-	10	1672	c.1656C>T	c.(1654-1656)TGC>TGT	p.C552C	ITGB6_uc010fou.2_Silent_p.C552C|ITGB6_uc010zcq.1_Silent_p.C510C|ITGB6_uc010fov.1_Silent_p.C552C	NM_000888	NP_000879	P18564	ITB6_HUMAN	integrin, beta 6 precursor	552	Extracellular (Potential).|III.|Cysteine-rich tandem repeats.				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																		---	---	---	---
FIGN	55137	broad.mit.edu	37	2	164466900	164466900	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:164466900G>T	uc002uck.1	-	3	1753	c.1442C>A	c.(1441-1443)CCT>CAT	p.P481H		NM_018086	NP_060556	Q5HY92	FIGN_HUMAN	fidgetin	481						nuclear matrix	ATP binding|nucleoside-triphosphatase activity			large_intestine(2)|ovary(1)|skin(1)	4																		---	---	---	---
COBLL1	22837	broad.mit.edu	37	2	165557205	165557205	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165557205C>T	uc010zcw.1	-	13	1726	c.1602G>A	c.(1600-1602)GTG>GTA	p.V534V	COBLL1_uc002ucp.2_Silent_p.V468V|COBLL1_uc002ucq.2_Silent_p.V429V|COBLL1_uc010zcx.1_Silent_p.V475V|COBLL1_uc002ucs.1_RNA|COBLL1_uc002ucn.2_5'Flank|COBLL1_uc002uco.2_Silent_p.V198V	NM_014900	NP_055715	Q53SF7	COBL1_HUMAN	COBL-like 1	506										ovary(2)|pancreas(1)	3																		---	---	---	---
SCN2A	6326	broad.mit.edu	37	2	166223735	166223735	+	Missense_Mutation	SNP	C	T	T	rs115231482	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166223735C>T	uc002udc.2	+	19	3819	c.3529C>T	c.(3529-3531)CGG>TGG	p.R1177W	SCN2A_uc002udd.2_Missense_Mutation_p.R1177W|SCN2A_uc002ude.2_Missense_Mutation_p.R1177W	NM_001040142	NP_001035232	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha	1177					myelination	node of Ranvier|voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|breast(1)|pancreas(1)	8					Lamotrigine(DB00555)													---	---	---	---
XIRP2	129446	broad.mit.edu	37	2	168114392	168114392	+	3'UTR	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168114392G>A	uc002udx.2	+	10					XIRP2_uc010fpn.2_Missense_Mutation_p.G479R|XIRP2_uc010fpo.2_Missense_Mutation_p.G446R|XIRP2_uc010fpp.2_Missense_Mutation_p.G446R|XIRP2_uc010fpq.2_3'UTR|XIRP2_uc010fpr.2_Missense_Mutation_p.G224R	NM_152381	NP_689594			xin actin-binding repeat containing 2 isoform 1						actin cytoskeleton organization	cell junction	actin binding			skin(7)|ovary(6)|pancreas(1)	14																		---	---	---	---
UBR3	130507	broad.mit.edu	37	2	170806482	170806482	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170806482G>A	uc010zdi.1	+	23	3452	c.3452G>A	c.(3451-3453)CGC>CAC	p.R1151H	UBR3_uc002ufr.3_RNA|UBR3_uc010fqa.2_5'UTR|UBR3_uc002uft.3_Missense_Mutation_p.R4H	NM_172070	NP_742067	Q6ZT12	UBR3_HUMAN	E3 ubiquitin-protein ligase UBR3	1151					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	171243767	171243767	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171243767C>T	uc002ufy.2	+	14	1669	c.1526C>T	c.(1525-1527)GCA>GTA	p.A509V	MYO3B_uc002ufv.2_Missense_Mutation_p.A496V|MYO3B_uc010fqb.1_Missense_Mutation_p.A496V|MYO3B_uc002ufz.2_Missense_Mutation_p.A509V|MYO3B_uc002ufw.2_RNA|MYO3B_uc002ufx.2_RNA|MYO3B_uc002ugb.2_RNA	NM_138995	NP_620482	Q8WXR4	MYO3B_HUMAN	myosin IIIB isoform 2	509	Myosin head-like.				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																		---	---	---	---
TTN	7273	broad.mit.edu	37	2	179398768	179398768	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179398768C>T	uc010zfg.1	-	307	95094	c.94870G>A	c.(94870-94872)GCC>ACC	p.A31624T	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.A25319T|TTN_uc010zfi.1_Missense_Mutation_p.A25252T|TTN_uc010zfj.1_Missense_Mutation_p.A25127T	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	32551							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	179424439	179424439	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179424439C>T	uc010zfg.1	-	275	78940	c.78716G>A	c.(78715-78717)CGT>CAT	p.R26239H	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.R19934H|TTN_uc010zfi.1_Missense_Mutation_p.R19867H|TTN_uc010zfj.1_Missense_Mutation_p.R19742H	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	27166							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	179453540	179453540	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179453540T>C	uc010zfg.1	-	253	55432	c.55208A>G	c.(55207-55209)GAA>GGA	p.E18403G	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.E12098G|TTN_uc010zfi.1_Missense_Mutation_p.E12031G|TTN_uc010zfj.1_Missense_Mutation_p.E11906G	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	19330							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	179454027	179454027	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179454027C>T	uc010zfg.1	-	253	54945	c.54721G>A	c.(54721-54723)GCT>ACT	p.A18241T	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.A11936T|TTN_uc010zfi.1_Missense_Mutation_p.A11869T|TTN_uc010zfj.1_Missense_Mutation_p.A11744T	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	19168							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	179587174	179587174	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179587174G>A	uc010zfg.1	-	74	18832	c.18608C>T	c.(18607-18609)CCC>CTC	p.P6203L	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Missense_Mutation_p.P2864L	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	7130							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)															---	---	---	---
ZNF385B	151126	broad.mit.edu	37	2	180383246	180383246	+	Intron	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:180383246G>A	uc002unn.3	-						ZNF385B_uc002unj.2_Intron|ZNF385B_uc002unk.2_Intron|ZNF385B_uc002unl.2_Intron|ZNF385B_uc002unm.2_Intron	NM_152520	NP_689733			zinc finger protein 385B isoform 1							nucleus	nucleic acid binding|zinc ion binding			ovary(1)	1			Epithelial(96;0.174)|OV - Ovarian serous cystadenocarcinoma(117;0.201)															---	---	---	---
ITGA4	3676	broad.mit.edu	37	2	182339944	182339944	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:182339944C>T	uc002unu.2	+	4	1248	c.485C>T	c.(484-486)ACT>ATT	p.T162I	ITGA4_uc010zfl.1_Missense_Mutation_p.T162I	NM_000885	NP_000876	P13612	ITA4_HUMAN	integrin alpha 4 precursor	162	FG-GAP 2.|Extracellular (Potential).				blood coagulation|integrin-mediated signaling pathway|leukocyte cell-cell adhesion|leukocyte migration|regulation of immune response	integrin complex	identical protein binding|receptor activity			ovary(3)|lung(1)|central_nervous_system(1)|pancreas(1)	6			OV - Ovarian serous cystadenocarcinoma(117;0.0593)		Natalizumab(DB00108)													---	---	---	---
ITGA4	3676	broad.mit.edu	37	2	182399098	182399098	+	Splice_Site	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:182399098G>A	uc002unu.2	+	26	3646	c.2883_splice	c.e26+1	p.H961_splice	ITGA4_uc002unv.2_Splice_Site_p.H206_splice	NM_000885	NP_000876			integrin alpha 4 precursor						blood coagulation|integrin-mediated signaling pathway|leukocyte cell-cell adhesion|leukocyte migration|regulation of immune response	integrin complex	identical protein binding|receptor activity			ovary(3)|lung(1)|central_nervous_system(1)|pancreas(1)	6			OV - Ovarian serous cystadenocarcinoma(117;0.0593)		Natalizumab(DB00108)													---	---	---	---
PDE1A	5136	broad.mit.edu	37	2	183129093	183129093	+	Silent	SNP	G	A	A	rs148985621		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:183129093G>A	uc002uos.2	-	3	234	c.150C>T	c.(148-150)GTC>GTT	p.V50V	PDE1A_uc010zfp.1_5'UTR|PDE1A_uc002uoq.1_Silent_p.V50V|PDE1A_uc010zfq.1_Silent_p.V50V|PDE1A_uc002uor.2_Silent_p.V34V|PDE1A_uc002uov.1_RNA	NM_001003683	NP_001003683	P54750	PDE1A_HUMAN	phosphodiesterase 1A isoform 2	50					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)															---	---	---	---
TMEFF2	23671	broad.mit.edu	37	2	193044423	193044423	+	Intron	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:193044423G>A	uc002utc.2	-						TMEFF2_uc002utd.1_Intron	NM_016192	NP_057276			transmembrane protein with EGF-like and two							extracellular region|integral to membrane				lung(2)|pancreas(1)|breast(1)|skin(1)	5			OV - Ovarian serous cystadenocarcinoma(117;0.0835)															---	---	---	---
DNAH7	56171	broad.mit.edu	37	2	196636411	196636411	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196636411C>T	uc002utj.3	-	61	11507	c.11406G>A	c.(11404-11406)TCG>TCA	p.S3802S	DNAH7_uc002uti.3_Silent_p.S285S	NM_018897	NP_061720	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	3802					ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			skin(10)|ovary(2)	12																		---	---	---	---
GTF3C3	9330	broad.mit.edu	37	2	197654592	197654592	+	Intron	SNP	A	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197654592A>T	uc002uts.2	-						GTF3C3_uc010zgu.1_Intron|GTF3C3_uc002utu.2_Intron	NM_012086	NP_036218			general transcription factor IIIC, polypeptide							transcription factor TFIIIC complex	DNA binding|protein binding			ovary(3)|breast(3)|pancreas(1)	7																		---	---	---	---
SATB2	23314	broad.mit.edu	37	2	200213902	200213902	+	Intron	SNP	A	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:200213902A>C	uc002uuy.1	-						SATB2_uc010fsq.1_Intron|SATB2_uc002uuz.1_Intron|SATB2_uc002uva.1_Intron|SATB2_uc002uvb.1_5'Flank	NM_015265	NP_056080			SATB homeobox 2							cytoplasm|nuclear matrix	sequence-specific DNA binding transcription factor activity			ovary(1)	1																		---	---	---	---
FZD7	8324	broad.mit.edu	37	2	202899989	202899989	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202899989C>A	uc002uyw.1	+	1	680	c.619C>A	c.(619-621)CCC>ACC	p.P207T		NM_003507	NP_003498	O75084	FZD7_HUMAN	frizzled 7 precursor	207	Extracellular (Potential).				axonogenesis|brain development|canonical Wnt receptor signaling pathway|cellular response to retinoic acid|G-protein signaling, coupled to cGMP nucleotide second messenger|gonad development|mesenchymal to epithelial transition|negative regulation of cell-substrate adhesion|negative regulation of ectodermal cell fate specification|positive regulation of epithelial cell proliferation involved in wound healing|positive regulation of phosphorylation|positive regulation of transcription, DNA-dependent|regulation of catenin import into nucleus|vasculature development|Wnt receptor signaling pathway, calcium modulating pathway	apical part of cell|cytoplasm|integral to membrane|neuron projection membrane	G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding			skin(2)|ovary(1)|breast(1)	4																OREG0015146	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
FZD7	8324	broad.mit.edu	37	2	202900525	202900525	+	Silent	SNP	G	A	A	rs140334850		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202900525G>A	uc002uyw.1	+	1	1216	c.1155G>A	c.(1153-1155)GCG>GCA	p.A385A		NM_003507	NP_003498	O75084	FZD7_HUMAN	frizzled 7 precursor	385	Helical; Name=4; (Potential).				axonogenesis|brain development|canonical Wnt receptor signaling pathway|cellular response to retinoic acid|G-protein signaling, coupled to cGMP nucleotide second messenger|gonad development|mesenchymal to epithelial transition|negative regulation of cell-substrate adhesion|negative regulation of ectodermal cell fate specification|positive regulation of epithelial cell proliferation involved in wound healing|positive regulation of phosphorylation|positive regulation of transcription, DNA-dependent|regulation of catenin import into nucleus|vasculature development|Wnt receptor signaling pathway, calcium modulating pathway	apical part of cell|cytoplasm|integral to membrane|neuron projection membrane	G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding			skin(2)|ovary(1)|breast(1)	4																OREG0015146	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
WDR12	55759	broad.mit.edu	37	2	203772679	203772679	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203772679A>G	uc002uzl.2	-	2	795	c.45T>C	c.(43-45)TAT>TAC	p.Y15Y	WDR12_uc010ftt.2_Silent_p.Y15Y	NM_018256	NP_060726	Q9GZL7	WDR12_HUMAN	WD repeat domain 12 protein	15					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)	nucleoplasm|PeBoW complex|preribosome, large subunit precursor	protein binding				0																		---	---	---	---
RAPH1	65059	broad.mit.edu	37	2	204354422	204354422	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204354422T>A	uc002vad.2	-	4	842	c.617A>T	c.(616-618)AAT>ATT	p.N206I	RAPH1_uc002vae.2_Missense_Mutation_p.N206I|RAPH1_uc002vaf.2_Missense_Mutation_p.N206I	NM_213589	NP_998754	Q70E73	RAPH1_HUMAN	Ras association and pleckstrin homology domains	206					cell-matrix adhesion|signal transduction	cytoplasm|cytoskeleton|filopodium|lamellipodium|nucleus|plasma membrane				ovary(3)|breast(3)|central_nervous_system(2)|lung(1)|skin(1)	10																		---	---	---	---
PARD3B	117583	broad.mit.edu	37	2	205978267	205978267	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:205978267C>G	uc002var.1	+	6	853	c.646C>G	c.(646-648)CAT>GAT	p.H216D	PARD3B_uc010fub.1_Missense_Mutation_p.H216D|PARD3B_uc002vao.1_Missense_Mutation_p.H216D|PARD3B_uc002vap.1_Missense_Mutation_p.H216D|PARD3B_uc002vaq.1_Missense_Mutation_p.H216D	NM_152526	NP_689739	Q8TEW8	PAR3L_HUMAN	par-3 partitioning defective 3 homolog B isoform	216	PDZ 1.				cell cycle|cell division	endomembrane system|tight junction				skin(2)|ovary(1)|breast(1)	4		all_cancers(1;2.88e-06)|all_epithelial(1;3.23e-06)		Epithelial(149;0.0739)														---	---	---	---
PARD3B	117583	broad.mit.edu	37	2	205983711	205983711	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:205983711C>T	uc002var.1	+	7	954	c.747C>T	c.(745-747)CAC>CAT	p.H249H	PARD3B_uc010fub.1_Silent_p.H249H|PARD3B_uc002vao.1_Silent_p.H249H|PARD3B_uc002vap.1_Silent_p.H249H|PARD3B_uc002vaq.1_Silent_p.H249H	NM_152526	NP_689739	Q8TEW8	PAR3L_HUMAN	par-3 partitioning defective 3 homolog B isoform	249	PDZ 1.				cell cycle|cell division	endomembrane system|tight junction				skin(2)|ovary(1)|breast(1)	4		all_cancers(1;2.88e-06)|all_epithelial(1;3.23e-06)		Epithelial(149;0.0739)														---	---	---	---
NRP2	8828	broad.mit.edu	37	2	206587398	206587398	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206587398C>T	uc002vaw.2	+	4	1421	c.630C>T	c.(628-630)TAC>TAT	p.Y210Y	NRP2_uc002vat.2_Silent_p.Y210Y|NRP2_uc002vau.2_Silent_p.Y210Y|NRP2_uc002vav.2_Silent_p.Y210Y|NRP2_uc002vax.2_Silent_p.Y210Y|NRP2_uc002vay.2_Silent_p.Y210Y|NRP2_uc010fud.2_Silent_p.Y210Y	NM_201266	NP_957718	O60462	NRP2_HUMAN	neuropilin 2 isoform 1 precursor	210	Extracellular (Potential).|CUB 2.				angiogenesis|axon guidance|cell adhesion	integral to membrane|membrane fraction|plasma membrane	heparin binding|metal ion binding|semaphorin receptor activity|vascular endothelial growth factor receptor activity			skin(2)|ovary(1)|central_nervous_system(1)	4																		---	---	---	---
INO80D	54891	broad.mit.edu	37	2	206870106	206870106	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206870106T>C	uc002vaz.3	-	11	2475	c.2070A>G	c.(2068-2070)ATA>ATG	p.I690M		NM_017759	NP_060229	Q53TQ3	IN80D_HUMAN	INO80 complex subunit D	690					DNA recombination|DNA repair|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(1)	1																		---	---	---	---
CRYGC	1420	broad.mit.edu	37	2	208993108	208993108	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208993108C>T	uc002vco.3	-	3	382	c.344G>A	c.(343-345)CGC>CAC	p.R115H		NM_020989	NP_066269	P07315	CRGC_HUMAN	crystallin, gamma C	115	Beta/gamma crystallin 'Greek key' 3.				visual perception	cytoplasm|nucleus	protein binding|structural constituent of eye lens				0				LUSC - Lung squamous cell carcinoma(261;0.0703)|Epithelial(149;0.0858)|Lung(261;0.133)														---	---	---	---
PTH2R	5746	broad.mit.edu	37	2	209308074	209308074	+	Nonsense_Mutation	SNP	C	T	T	rs149710383		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:209308074C>T	uc002vdb.2	+	6	724	c.511C>T	c.(511-513)CGA>TGA	p.R171*	PTH2R_uc010zjb.1_Nonsense_Mutation_p.R182*	NM_005048	NP_005039	P49190	PTH2R_HUMAN	parathyroid hormone 2 receptor precursor	171	Cytoplasmic (Potential).					integral to plasma membrane	parathyroid hormone receptor activity			ovary(1)|breast(1)|skin(1)	3				Epithelial(149;0.0684)|Lung(261;0.0785)|LUSC - Lung squamous cell carcinoma(261;0.0836)														---	---	---	---
MAP2	4133	broad.mit.edu	37	2	210559705	210559705	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210559705G>A	uc002vde.1	+	7	3059	c.2811G>A	c.(2809-2811)GCG>GCA	p.A937A	MAP2_uc002vdc.1_Silent_p.A937A|MAP2_uc002vdd.1_Intron|MAP2_uc002vdf.1_Intron|MAP2_uc002vdg.1_Intron|MAP2_uc002vdh.1_Intron|MAP2_uc002vdi.1_Silent_p.A933A	NM_002374	NP_002365	P11137	MAP2_HUMAN	microtubule-associated protein 2 isoform 1	937					central nervous system neuron development|dendrite morphogenesis|negative regulation of microtubule depolymerization	cytoplasm|microtubule|microtubule associated complex	beta-dystroglycan binding|calmodulin binding|structural molecule activity			ovary(9)|upper_aerodigestive_tract(2)|large_intestine(2)|pancreas(2)|central_nervous_system(1)|skin(1)	17		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Estramustine(DB01196)													---	---	---	---
CPS1	1373	broad.mit.edu	37	2	211457621	211457621	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:211457621A>G	uc002vee.3	+	11	1237	c.1105A>G	c.(1105-1107)AAA>GAA	p.K369E	CPS1_uc010fur.2_Missense_Mutation_p.K375E|CPS1_uc010fus.2_5'Flank	NM_001875	NP_001866	P31327	CPSM_HUMAN	carbamoyl-phosphate synthetase 1 isoform b	369	Glutamine amidotransferase type-1.				carbamoyl phosphate biosynthetic process|citrulline biosynthetic process|glutamine metabolic process|glycogen catabolic process|nitric oxide metabolic process|positive regulation of vasodilation|response to lipopolysaccharide|triglyceride catabolic process|urea cycle	mitochondrial nucleoid	ATP binding|carbamoyl-phosphate synthase (ammonia) activity			ovary(8)|central_nervous_system(3)|breast(1)|skin(1)	13				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)														---	---	---	---
CPS1	1373	broad.mit.edu	37	2	211540487	211540487	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:211540487C>T	uc002vee.3	+	36	4329	c.4197C>T	c.(4195-4197)AAC>AAT	p.N1399N	CPS1_uc010fur.2_Silent_p.N1405N|CPS1_uc010fus.2_Silent_p.N948N	NM_001875	NP_001866	P31327	CPSM_HUMAN	carbamoyl-phosphate synthetase 1 isoform b	1399					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)														---	---	---	---
IKZF2	22807	broad.mit.edu	37	2	213921663	213921663	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:213921663T>G	uc002vem.2	-	4	469	c.300A>C	c.(298-300)CAA>CAC	p.Q100H	IKZF2_uc010fuu.2_Intron|IKZF2_uc002vej.2_Missense_Mutation_p.Q47H|IKZF2_uc002vek.2_RNA|IKZF2_uc010fuv.2_Missense_Mutation_p.Q100H|IKZF2_uc002vel.2_Missense_Mutation_p.Q47H|IKZF2_uc010fuw.2_5'UTR|IKZF2_uc010fux.2_Intron|IKZF2_uc010fuy.2_Missense_Mutation_p.Q100H|IKZF2_uc002ven.2_Missense_Mutation_p.Q100H	NM_016260	NP_057344	Q9UKS7	IKZF2_HUMAN	helios isoform 1	100					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)														---	---	---	---
SPAG16	79582	broad.mit.edu	37	2	215274888	215274888	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215274888G>A	uc002veq.2	+	16	1837	c.1745G>A	c.(1744-1746)GGC>GAC	p.G582D	SPAG16_uc002ver.2_Missense_Mutation_p.G528D|SPAG16_uc010zjk.1_Missense_Mutation_p.G488D|VWC2L_uc002vet.2_5'Flank|VWC2L_uc010zjl.1_5'Flank	NM_024532	NP_078808	Q8N0X2	SPG16_HUMAN	sperm associated antigen 16 isoform 1	582	WD 6.				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)														---	---	---	---
ABCA12	26154	broad.mit.edu	37	2	215876354	215876354	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215876354C>T	uc002vew.2	-	17	2361	c.2141G>A	c.(2140-2142)CGA>CAA	p.R714Q	ABCA12_uc002vev.2_Missense_Mutation_p.R396Q|ABCA12_uc010zjn.1_5'UTR	NM_173076	NP_775099	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A, member 12	714					cellular homeostasis|lipid transport	integral to membrane	ATP binding|ATPase activity			ovary(6)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	11		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)														---	---	---	---
ATIC	471	broad.mit.edu	37	2	216213898	216213898	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216213898G>T	uc002vex.3	+	15	1759	c.1585G>T	c.(1585-1587)GAG>TAG	p.E529*	ATIC_uc010zjo.1_Nonsense_Mutation_p.E470*|ATIC_uc002vey.3_Nonsense_Mutation_p.E528*	NM_004044	NP_004035	P31939	PUR9_HUMAN	5-aminoimidazole-4-carboxamide ribonucleotide	529					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	216273121	216273121	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216273121G>A	uc002vfa.2	-	16	2594	c.2328C>T	c.(2326-2328)AAC>AAT	p.N776N	FN1_uc002vfb.2_Silent_p.N776N|FN1_uc002vfc.2_Silent_p.N776N|FN1_uc002vfd.2_Silent_p.N776N|FN1_uc002vfe.2_Silent_p.N776N|FN1_uc002vff.2_Silent_p.N776N|FN1_uc002vfg.2_Silent_p.N776N|FN1_uc002vfh.2_Silent_p.N776N|FN1_uc002vfi.2_Silent_p.N776N|FN1_uc002vfj.2_Silent_p.N776N	NM_212482	NP_997647	P02751	FINC_HUMAN	fibronectin 1 isoform 1 preproprotein	776	Fibronectin type-III 2.				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)													---	---	---	---
TNS1	7145	broad.mit.edu	37	2	218683462	218683462	+	Missense_Mutation	SNP	G	A	A	rs149785174	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:218683462G>A	uc002vgt.2	-	24	3679	c.3281C>T	c.(3280-3282)CCG>CTG	p.P1094L	TNS1_uc002vgr.2_Missense_Mutation_p.P1081L|TNS1_uc002vgs.2_Missense_Mutation_p.P1073L|TNS1_uc010zjv.1_Missense_Mutation_p.P1073L	NM_022648	NP_072174	Q9HBL0	TENS1_HUMAN	tensin	1094	Ser-rich.					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)														---	---	---	---
CYP27A1	1593	broad.mit.edu	37	2	219676971	219676971	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219676971G>A	uc002viz.3	+	3	907	c.473G>A	c.(472-474)CGC>CAC	p.R158H		NM_000784	NP_000775	Q02318	CP27A_HUMAN	cytochrome P450, family 27, subfamily A,	158					bile acid biosynthetic process|xenobiotic metabolic process	mitochondrial matrix	cholestanetriol 26-monooxygenase activity|electron carrier activity|heme binding			ovary(1)	1		Renal(207;0.0474)		Epithelial(149;9.48e-07)|all cancers(144;0.000171)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.00981)	Cholecalciferol(DB00169)													---	---	---	---
PRKAG3	53632	broad.mit.edu	37	2	219692362	219692362	+	Intron	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219692362G>T	uc002vjb.1	-						PRKAG3_uc010zkn.1_Intron|PRKAG3_uc010fvy.1_Intron	NM_017431	NP_059127			AMP-activated protein kinase, non-catalytic						cell cycle arrest|fatty acid biosynthetic process|insulin receptor signaling pathway|intracellular protein kinase cascade|regulation of fatty acid oxidation	cytosol	AMP-activated protein kinase activity|protein kinase binding			ovary(1)|lung(1)	2		Renal(207;0.0474)		Epithelial(149;4.35e-07)|all cancers(144;8.96e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)														---	---	---	---
CCDC108	255101	broad.mit.edu	37	2	219893035	219893035	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219893035C>T	uc002vjl.1	-	12	1823	c.1739G>A	c.(1738-1740)CGC>CAC	p.R580H	CCDC108_uc010fwa.1_Missense_Mutation_p.R23H|CCDC108_uc010zkp.1_Missense_Mutation_p.R569H|CCDC108_uc010zkq.1_Missense_Mutation_p.R515H	NM_194302	NP_919278	Q6ZU64	CC108_HUMAN	coiled-coil domain containing 108 isoform 1	580						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)														---	---	---	---
ABCB6	10058	broad.mit.edu	37	2	220074986	220074986	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220074986C>T	uc002vkc.1	-	18	2663	c.2386G>A	c.(2386-2388)GTC>ATC	p.V796I	ABCB6_uc010fwe.1_Missense_Mutation_p.V750I	NM_005689	NP_005680	Q9NP58	ABCB6_HUMAN	ATP-binding cassette, sub-family B, member 6	796	ABC transporter.				cadmium ion transmembrane transport|cellular iron ion homeostasis|detoxification of cadmium ion|porphyrin biosynthetic process	ATP-binding cassette (ABC) transporter complex|Golgi apparatus|integral to mitochondrial outer membrane|plasma membrane|vacuolar membrane	ATP binding|efflux transmembrane transporter activity|heme binding|heme-transporting ATPase activity			breast(1)|central_nervous_system(1)	2		Renal(207;0.0474)		Epithelial(149;1.22e-06)|all cancers(144;0.000201)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)														---	---	---	---
DNPEP	23549	broad.mit.edu	37	2	220251602	220251602	+	Intron	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220251602C>A	uc010zlg.1	-						DNPEP_uc010zlf.1_5'Flank|DNPEP_uc002vle.2_Intron|DNPEP_uc002vlf.1_Intron|DNPEP_uc002vlh.2_Intron|DNPEP_uc002vli.1_Intron|DNPEP_uc002vlj.2_Intron|uc002vlk.1_5'Flank	NM_012100	NP_036232			aspartyl aminopeptidase						peptide metabolic process|proteolysis	cytoplasm	aminopeptidase activity|metallopeptidase activity|protein binding|zinc ion binding				0		Renal(207;0.0474)		Epithelial(149;1.09e-06)|all cancers(144;0.000179)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)	L-Glutamic Acid(DB00142)													---	---	---	---
INHA	3623	broad.mit.edu	37	2	220440169	220440169	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220440169G>A	uc002vmk.1	+	2	1166	c.1022G>A	c.(1021-1023)CGC>CAC	p.R341H		NM_002191	NP_002182	P05111	INHA_HUMAN	inhibin alpha subunit precursor	341					cell cycle arrest|cell surface receptor linked signaling pathway|cell-cell signaling|erythrocyte differentiation|hemoglobin biosynthetic process|induction of apoptosis|negative regulation of B cell differentiation|negative regulation of follicle-stimulating hormone secretion|negative regulation of interferon-gamma biosynthetic process|negative regulation of macrophage differentiation|negative regulation of phosphorylation|nervous system development|ovarian follicle development|positive regulation of follicle-stimulating hormone secretion|regulation of cell proliferation|response to external stimulus|skeletal system development	inhibin A complex|inhibin-betaglycan-ActRII complex	cytokine activity|growth factor activity|hormone activity|signal transducer activity			ovary(1)	1		Renal(207;0.0183)		Epithelial(149;4.58e-07)|all cancers(144;4.31e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00802)														---	---	---	---
WDFY1	57590	broad.mit.edu	37	2	224758993	224758993	+	Silent	SNP	G	A	A	rs145535635		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:224758993G>A	uc002vnq.2	-	8	840	c.789C>T	c.(787-789)GAC>GAT	p.D263D		NM_020830	NP_065881	Q8IWB7	WDFY1_HUMAN	WD repeat and FYVE domain containing 1	263	WD 6.					cytosol|early endosome|nucleus	1-phosphatidylinositol binding|zinc ion binding			lung(1)	1		all_lung(227;0.00682)|Lung NSC(271;0.00859)|Renal(207;0.0112)|all_hematologic(139;0.189)		Epithelial(121;5.34e-10)|all cancers(144;1.67e-07)|Lung(261;0.00807)|LUSC - Lung squamous cell carcinoma(224;0.00843)														---	---	---	---
DOCK10	55619	broad.mit.edu	37	2	225637874	225637874	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225637874C>A	uc010fwz.1	-	53	6443	c.6204G>T	c.(6202-6204)AAG>AAT	p.K2068N	DOCK10_uc002vob.2_Missense_Mutation_p.K2062N|DOCK10_uc002voa.2_Missense_Mutation_p.K724N	NM_014689	NP_055504	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	2068	DHR-2.						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)														---	---	---	---
IRS1	3667	broad.mit.edu	37	2	227662652	227662652	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:227662652C>A	uc002voh.3	-	1	855	c.803G>T	c.(802-804)AGC>ATC	p.S268I		NM_005544	NP_005535	P35568	IRS1_HUMAN	insulin receptor substrate 1	268	Ser-rich.				fibroblast growth factor receptor signaling pathway|glucose homeostasis|insulin receptor signaling pathway|negative regulation of insulin receptor signaling pathway|negative regulation of insulin secretion|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol-mediated signaling|positive regulation of fatty acid beta-oxidation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of insulin receptor signaling pathway|positive regulation of phosphatidylinositol 3-kinase activity	caveola|cytosol|insulin receptor complex|microsome|nucleus	insulin receptor binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase binding|protein kinase C binding|SH2 domain binding|transmembrane receptor protein tyrosine kinase adaptor activity			lung(5)|central_nervous_system(4)|ovary(2)|pancreas(1)	12		Renal(207;0.023)|all_lung(227;0.0994)|all_hematologic(139;0.118)|Esophageal squamous(248;0.23)		Epithelial(121;3.03e-11)|all cancers(144;2.42e-08)|Lung(261;0.00712)|LUSC - Lung squamous cell carcinoma(224;0.0137)												OREG0015248	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
SPHKAP	80309	broad.mit.edu	37	2	228883406	228883406	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228883406T>C	uc002vpq.2	-	7	2211	c.2164A>G	c.(2164-2166)AAG>GAG	p.K722E	SPHKAP_uc002vpp.2_Missense_Mutation_p.K722E|SPHKAP_uc010zlx.1_Missense_Mutation_p.K722E	NM_001142644	NP_001136116	Q2M3C7	SPKAP_HUMAN	sphingosine kinase type 1-interacting protein	722						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)														---	---	---	---
TRIP12	9320	broad.mit.edu	37	2	230668827	230668827	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230668827A>T	uc002vpw.1	-	18	2651	c.2542T>A	c.(2542-2544)TCC>ACC	p.S848T	TRIP12_uc002vpx.1_Missense_Mutation_p.S896T|TRIP12_uc002vpy.1_Missense_Mutation_p.S578T|TRIP12_uc010zlz.1_Intron	NM_004238	NP_004229	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12	848					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	230923861	230923861	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230923861C>T	uc002vqd.1	-	2	571	c.208G>A	c.(208-210)GGC>AGC	p.G70S	FBXO36_uc010fxi.1_Intron|SLC16A14_uc002vqe.2_Missense_Mutation_p.G70S|SLC16A14_uc002vqf.2_Missense_Mutation_p.G70S	NM_152527	NP_689740	Q7RTX9	MOT14_HUMAN	solute carrier family 16 (monocarboxylic acid	70	Cytoplasmic (Potential).					integral to membrane|plasma membrane	symporter activity			ovary(4)|skin(2)	6		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.149)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;7.31e-13)|all cancers(144;5.1e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00948)														---	---	---	---
SP110	3431	broad.mit.edu	37	2	231077056	231077056	+	Intron	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231077056T>C	uc002vqh.3	-						SP110_uc002vqg.3_Intron|SP110_uc002vqi.3_Intron|SP110_uc010fxk.2_Intron	NM_004509	NP_004500			SP110 nuclear body protein isoform a						interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|signal transducer activity|zinc ion binding			ovary(2)|breast(2)	4		Renal(207;0.0112)|all_lung(227;0.0223)|Lung NSC(271;0.0983)|all_hematologic(139;0.104)|Acute lymphoblastic leukemia(138;0.169)		Epithelial(121;2.61e-12)|all cancers(144;6.39e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.0097)														---	---	---	---
ALPI	248	broad.mit.edu	37	2	233322294	233322294	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233322294G>A	uc002vst.3	+	6	745	c.668G>A	c.(667-669)CGC>CAC	p.R223H	ALPI_uc002vsu.3_Missense_Mutation_p.R134H	NM_001631	NP_001622	P09923	PPBI_HUMAN	intestinal alkaline phosphatase precursor	223					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)														---	---	---	---
HJURP	55355	broad.mit.edu	37	2	234750556	234750556	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234750556C>T	uc002vvg.2	-	8	936	c.870G>A	c.(868-870)ATG>ATA	p.M290I	HJURP_uc010znd.1_Missense_Mutation_p.M229I|HJURP_uc010zne.1_Missense_Mutation_p.M198I	NM_018410	NP_060880	Q8NCD3	HJURP_HUMAN	Holliday junction recognition protein	290					cell cycle|CenH3-containing nucleosome assembly at centromere|centromeric core chromatin assembly|chromosome segregation|regulation of DNA binding|regulation of protein complex assembly	condensed chromosome kinetochore|cytoplasm|nucleolus|nucleoplasm	DNA binding|histone binding			ovary(1)	1		Breast(86;0.00204)|all_lung(227;0.00433)|Renal(207;0.00685)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0719)|Lung SC(224;0.128)		Epithelial(121;2.01e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000186)|Lung(119;0.00521)|LUSC - Lung squamous cell carcinoma(224;0.00829)														---	---	---	---
COL6A3	1293	broad.mit.edu	37	2	238245163	238245163	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238245163A>G	uc002vwl.2	-	40	8865	c.8580T>C	c.(8578-8580)AAT>AAC	p.N2860N	COL6A3_uc002vwo.2_Silent_p.N2654N|COL6A3_uc010znj.1_Silent_p.N2253N|COL6A3_uc002vwj.2_Silent_p.N241N	NM_004369	NP_004360	P12111	CO6A3_HUMAN	alpha 3 type VI collagen isoform 1 precursor	2860	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)														---	---	---	---
MLPH	79083	broad.mit.edu	37	2	238462236	238462236	+	3'UTR	SNP	C	T	T	rs139145016		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238462236C>T	uc002vwt.2	+	16					MLPH_uc002vws.2_3'UTR|MLPH_uc002vwu.2_3'UTR|MLPH_uc002vwv.2_3'UTR|MLPH_uc002vww.2_3'UTR|MLPH_uc002vwx.2_3'UTR|MLPH_uc010fyu.2_3'UTR	NM_024101	NP_077006			melanophilin isoform 1								metal ion binding			ovary(1)	1		Breast(86;0.000381)|Renal(207;0.000966)|Ovarian(221;0.0695)|all_hematologic(139;0.095)|all_lung(227;0.17)|Melanoma(123;0.203)		Epithelial(121;1.17e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.02e-10)|Kidney(56;4.23e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.15e-07)|BRCA - Breast invasive adenocarcinoma(100;0.000439)|Lung(119;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0316)														---	---	---	---
LRRFIP1	9208	broad.mit.edu	37	2	238666181	238666181	+	Intron	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238666181A>G	uc002vxe.2	+						LRRFIP1_uc002vxc.2_Missense_Mutation_p.K405R|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)														---	---	---	---
ILKAP	80895	broad.mit.edu	37	2	239090722	239090722	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239090722C>T	uc002vxv.2	-	9	950	c.820G>A	c.(820-822)GCT>ACT	p.A274T	ILKAP_uc010zns.1_Missense_Mutation_p.A206T|ILKAP_uc002vxw.2_Missense_Mutation_p.A154T|ILKAP_uc010znt.1_Missense_Mutation_p.A154T	NM_030768	NP_110395	Q9H0C8	ILKAP_HUMAN	integrin-linked kinase-associated protein	274	PP2C-like.					cytoplasm|protein serine/threonine phosphatase complex	metal ion binding|protein binding			ovary(3)	3		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_lung(227;0.152)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;5.49e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.93e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.82e-08)|BRCA - Breast invasive adenocarcinoma(100;0.00012)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.0163)														---	---	---	---
PER2	8864	broad.mit.edu	37	2	239161605	239161605	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239161605G>A	uc002vyc.2	-	19	3296	c.3059C>T	c.(3058-3060)GCG>GTG	p.A1020V	PER2_uc010znv.1_Missense_Mutation_p.A1020V	NM_022817	NP_073728	O15055	PER2_HUMAN	period 2	1020					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)														---	---	---	---
PRR21	643905	broad.mit.edu	37	2	240981288	240981288	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240981288G>C	uc010zod.1	-	1	1112	c.1112C>G	c.(1111-1113)GCC>GGC	p.A371G		NM_001080835	NP_001074304	Q8WXC7	PRR21_HUMAN	proline rich 21	371										ovary(1)|skin(1)	2																		---	---	---	---
ANKMY1	51281	broad.mit.edu	37	2	241463615	241463615	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241463615C>T	uc002vyz.1	-	7	1481	c.1252G>A	c.(1252-1254)GGG>AGG	p.G418R	ANKMY1_uc002vza.1_Missense_Mutation_p.G277R|ANKMY1_uc010fzd.1_Missense_Mutation_p.G507R|ANKMY1_uc002vzb.1_Intron|ANKMY1_uc002vzc.1_Missense_Mutation_p.G277R|ANKMY1_uc002vzd.1_Missense_Mutation_p.G277R|ANKMY1_uc010fze.1_Missense_Mutation_p.G87R|ANKMY1_uc002vze.2_Missense_Mutation_p.G179R	NM_016552	NP_057636	Q9P2S6	ANKY1_HUMAN	ankyrin repeat and MYND domain containing 1	418							zinc ion binding			central_nervous_system(1)	1		all_epithelial(40;2.79e-15)|Breast(86;2.41e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0335)|Lung NSC(271;0.106)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;1.03e-30)|all cancers(36;4.78e-28)|OV - Ovarian serous cystadenocarcinoma(60;1.45e-14)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.8e-06)|Lung(119;0.00271)|LUSC - Lung squamous cell carcinoma(224;0.01)|Colorectal(34;0.0101)|COAD - Colon adenocarcinoma(134;0.0476)														---	---	---	---
KIF1A	547	broad.mit.edu	37	2	241712648	241712648	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241712648G>A	uc002vzy.2	-	13	1209	c.1063C>T	c.(1063-1065)CGC>TGC	p.R355C	KIF1A_uc010fzk.2_Missense_Mutation_p.R355C|KIF1A_uc002vzz.1_Missense_Mutation_p.R355C	NM_004321	NP_004312	Q12756	KIF1A_HUMAN	axonal transport of synaptic vesicles	355	Kinesin-motor.				anterograde axon cargo transport	cytoplasm|microtubule|nucleus	ATP binding|microtubule motor activity			lung(1)	1		all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;6.12e-30)|all cancers(36;3.46e-27)|OV - Ovarian serous cystadenocarcinoma(60;1.38e-14)|Kidney(56;5e-09)|KIRC - Kidney renal clear cell carcinoma(57;5e-08)|BRCA - Breast invasive adenocarcinoma(100;5.87e-06)|Lung(119;0.00209)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Colorectal(34;0.0282)|COAD - Colon adenocarcinoma(134;0.176)														---	---	---	---
KIF1A	547	broad.mit.edu	37	2	241726674	241726674	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241726674G>A	uc002vzy.2	-	5	569	c.423C>T	c.(421-423)TCC>TCT	p.S141S	KIF1A_uc010fzk.2_Silent_p.S141S|KIF1A_uc002vzz.1_Silent_p.S141S	NM_004321	NP_004312	Q12756	KIF1A_HUMAN	axonal transport of synaptic vesicles	141	Kinesin-motor.				anterograde axon cargo transport	cytoplasm|microtubule|nucleus	ATP binding|microtubule motor activity			lung(1)	1		all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;6.12e-30)|all cancers(36;3.46e-27)|OV - Ovarian serous cystadenocarcinoma(60;1.38e-14)|Kidney(56;5e-09)|KIRC - Kidney renal clear cell carcinoma(57;5e-08)|BRCA - Breast invasive adenocarcinoma(100;5.87e-06)|Lung(119;0.00209)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Colorectal(34;0.0282)|COAD - Colon adenocarcinoma(134;0.176)														---	---	---	---
MTERFD2	130916	broad.mit.edu	37	2	242039193	242039193	+	Silent	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242039193G>T	uc002wan.1	-	1	718	c.225C>A	c.(223-225)GCC>GCA	p.A75A	MTERFD2_uc010zoj.1_Intron|MTERFD2_uc010zok.1_Silent_p.A46A	NM_182501	NP_872307	Q7Z6M4	MTER2_HUMAN	MTERF domain containing 2	46										ovary(1)	1		all_cancers(19;4.67e-31)|all_epithelial(40;8.67e-13)|Breast(86;0.000141)|Renal(207;0.00528)|Ovarian(221;0.104)|Esophageal squamous(248;0.131)|all_lung(227;0.17)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;2.47e-32)|all cancers(36;1.79e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.59e-14)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;2.81e-06)|Lung(119;0.000509)|LUSC - Lung squamous cell carcinoma(224;0.00442)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0886)														---	---	---	---
PASK	23178	broad.mit.edu	37	2	242066171	242066171	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242066171G>A	uc002wao.1	-	10	2251	c.2159C>T	c.(2158-2160)ACG>ATG	p.T720M	PASK_uc010zol.1_Missense_Mutation_p.T534M|PASK_uc010zom.1_Missense_Mutation_p.T685M|PASK_uc010fzl.1_Missense_Mutation_p.T720M|PASK_uc010zon.1_Missense_Mutation_p.T501M|PASK_uc002wap.2_Missense_Mutation_p.T263M|PASK_uc002waq.2_Missense_Mutation_p.T720M	NM_015148	NP_055963	Q96RG2	PASK_HUMAN	PAS domain containing serine/threonine kinase	720					regulation of transcription, DNA-dependent	Golgi apparatus	ATP binding|identical protein binding|protein serine/threonine kinase activity|signal transducer activity			ovary(4)|lung(1)|skin(1)	6		all_cancers(19;4.46e-39)|all_epithelial(40;1.34e-17)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00481)|Lung NSC(271;0.017)|Ovarian(221;0.0228)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.34e-31)|all cancers(36;1e-28)|OV - Ovarian serous cystadenocarcinoma(60;3.53e-14)|Kidney(56;4.31e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.35e-08)|BRCA - Breast invasive adenocarcinoma(100;5.64e-06)|Lung(119;0.000596)|LUSC - Lung squamous cell carcinoma(224;0.00481)|Colorectal(34;0.014)|COAD - Colon adenocarcinoma(134;0.0968)														---	---	---	---
PASK	23178	broad.mit.edu	37	2	242066359	242066359	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242066359C>T	uc002wao.1	-	10	2063	c.1971G>A	c.(1969-1971)CTG>CTA	p.L657L	PASK_uc010zol.1_Silent_p.L471L|PASK_uc010zom.1_Silent_p.L622L|PASK_uc010fzl.1_Silent_p.L657L|PASK_uc010zon.1_Silent_p.L438L|PASK_uc002wap.2_Silent_p.L200L|PASK_uc002waq.2_Silent_p.L657L	NM_015148	NP_055963	Q96RG2	PASK_HUMAN	PAS domain containing serine/threonine kinase	657					regulation of transcription, DNA-dependent	Golgi apparatus	ATP binding|identical protein binding|protein serine/threonine kinase activity|signal transducer activity			ovary(4)|lung(1)|skin(1)	6		all_cancers(19;4.46e-39)|all_epithelial(40;1.34e-17)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00481)|Lung NSC(271;0.017)|Ovarian(221;0.0228)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.34e-31)|all cancers(36;1e-28)|OV - Ovarian serous cystadenocarcinoma(60;3.53e-14)|Kidney(56;4.31e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.35e-08)|BRCA - Breast invasive adenocarcinoma(100;5.64e-06)|Lung(119;0.000596)|LUSC - Lung squamous cell carcinoma(224;0.00481)|Colorectal(34;0.014)|COAD - Colon adenocarcinoma(134;0.0968)														---	---	---	---
ANO7	50636	broad.mit.edu	37	2	242163537	242163537	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242163537C>T	uc002wax.2	+	25	2874	c.2771C>T	c.(2770-2772)ACG>ATG	p.T924M		NM_001001891	NP_001001891	Q6IWH7	ANO7_HUMAN	transmembrane protein 16G isoform NGEP long	924	Cytoplasmic (Potential).					cell junction|chloride channel complex|cytosol	chloride channel activity			pancreas(2)|central_nervous_system(1)	3																		---	---	---	---
HDLBP	3069	broad.mit.edu	37	2	242174626	242174626	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242174626G>A	uc002waz.2	-	23	3282	c.3054C>T	c.(3052-3054)ATC>ATT	p.I1018I	HDLBP_uc002wba.2_Silent_p.I1018I|HDLBP_uc002wbb.2_Silent_p.I970I	NM_203346	NP_976221	Q00341	VIGLN_HUMAN	high density lipoprotein binding protein	1018	KH 12.				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)														---	---	---	---
ITPR1	3708	broad.mit.edu	37	3	4856237	4856237	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:4856237G>A	uc003bqa.2	+	55	7896	c.7548G>A	c.(7546-7548)CCG>CCA	p.P2516P	ITPR1_uc010hca.1_Silent_p.P2501P|ITPR1_uc011asu.1_Silent_p.P527P|ITPR1_uc003bqc.2_Silent_p.P1486P|ITPR1_uc010hcc.1_Silent_p.P284P|ITPR1_uc011asv.1_Silent_p.P240P	NM_001099952	NP_001093422	Q14643	ITPR1_HUMAN	inositol 1,4,5-triphosphate receptor, type 1	2564	Lumenal (Potential).				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)														---	---	---	---
GRM7	2917	broad.mit.edu	37	3	7620434	7620434	+	Missense_Mutation	SNP	G	A	A	rs150165030	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:7620434G>A	uc003bqm.2	+	8	2115	c.1841G>A	c.(1840-1842)CGC>CAC	p.R614H	GRM7_uc011ata.1_RNA|GRM7_uc011atb.1_RNA|GRM7_uc010hcf.2_RNA|GRM7_uc011atc.1_RNA|GRM7_uc010hcg.2_Missense_Mutation_p.R614H|GRM7_uc003bql.2_Missense_Mutation_p.R614H|GRM7_uc003bqn.1_Missense_Mutation_p.R197H|GRM7_uc010hch.1_Missense_Mutation_p.R125H	NM_000844	NP_000835	Q14831	GRM7_HUMAN	glutamate receptor, metabotropic 7 isoform a	614	Helical; Name=1; (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)													---	---	---	---
C3orf32	51066	broad.mit.edu	37	3	8669394	8669394	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:8669394C>T	uc003bqu.2	-	8	844	c.598G>A	c.(598-600)GGC>AGC	p.G200S	C3orf32_uc003bqz.2_Missense_Mutation_p.G200S|C3orf32_uc003bqt.2_Missense_Mutation_p.G149S|C3orf32_uc011atg.1_Missense_Mutation_p.G222S|C3orf32_uc003bqv.2_Missense_Mutation_p.G149S|C3orf32_uc003bqw.2_RNA|C3orf32_uc003bqx.2_RNA|C3orf32_uc003bqy.2_Missense_Mutation_p.G200S	NM_015931	NP_057015	Q9Y2M2	CC032_HUMAN	hypothetical protein LOC51066	200	Cys-rich.									skin(1)	1																		---	---	---	---
BRPF1	7862	broad.mit.edu	37	3	9784848	9784848	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9784848A>G	uc003bse.2	+	7	2603	c.2204A>G	c.(2203-2205)CAG>CGG	p.Q735R	BRPF1_uc003bsf.2_Missense_Mutation_p.Q741R|BRPF1_uc003bsg.2_Missense_Mutation_p.Q735R|BRPF1_uc011ati.1_Missense_Mutation_p.Q735R	NM_004634	NP_004625	P55201	BRPF1_HUMAN	bromodomain and PHD finger-containing protein 1	735	Required for RUNX1 and RUNX2 transcriptional activation.|Interaction with MEAF6 and ING5.				histone H3 acetylation|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|MOZ/MORF histone acetyltransferase complex|plasma membrane	DNA binding|zinc ion binding			ovary(2)|central_nervous_system(1)	3	Medulloblastoma(99;0.227)																	---	---	---	---
BRPF1	7862	broad.mit.edu	37	3	9788862	9788862	+	Silent	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9788862C>A	uc003bse.2	+	14	3873	c.3474C>A	c.(3472-3474)CCC>CCA	p.P1158P	BRPF1_uc003bsf.2_Silent_p.P1164P|BRPF1_uc003bsg.2_Silent_p.P1157P|BRPF1_uc011ati.1_Silent_p.P1063P|OGG1_uc003bsh.2_5'Flank|OGG1_uc003bsi.2_5'Flank|OGG1_uc003bsj.2_5'Flank|OGG1_uc003bsk.2_5'Flank|OGG1_uc003bsl.2_5'Flank|OGG1_uc003bsm.2_5'Flank|OGG1_uc003bsn.2_5'Flank|OGG1_uc003bso.2_5'Flank	NM_004634	NP_004625	P55201	BRPF1_HUMAN	bromodomain and PHD finger-containing protein 1	1158	PWWP.				histone H3 acetylation|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|MOZ/MORF histone acetyltransferase complex|plasma membrane	DNA binding|zinc ion binding			ovary(2)|central_nervous_system(1)	3	Medulloblastoma(99;0.227)																	---	---	---	---
RPUSD3	285367	broad.mit.edu	37	3	9882226	9882226	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9882226C>A	uc011atk.1	-	6	594	c.590G>T	c.(589-591)GGG>GTG	p.G197V	ARPC4_uc003btc.1_Intron|RPUSD3_uc011atl.1_Missense_Mutation_p.G182V|RPUSD3_uc011atm.1_Missense_Mutation_p.G189V|RPUSD3_uc003btn.2_3'UTR	NM_173659	NP_775930	Q6P087	RUSD3_HUMAN	RNA pseudouridylate synthase domain containing 3	197					pseudouridine synthesis		pseudouridine synthase activity|RNA binding			central_nervous_system(1)	1	Medulloblastoma(99;0.227)																	---	---	---	---
CRELD1	78987	broad.mit.edu	37	3	9986201	9986201	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9986201A>G	uc003bug.2	+	11	1319	c.1201A>G	c.(1201-1203)ACT>GCT	p.T401A	CIDEC_uc003bto.2_Intron|CRELD1_uc003buf.2_3'UTR|CRELD1_uc003buh.2_Missense_Mutation_p.T401A|CRELD1_uc003bui.2_Missense_Mutation_p.T401A|CRELD1_uc003buj.2_RNA	NM_001077415	NP_001070883	Q96HD1	CREL1_HUMAN	cysteine-rich with EGF-like domains 1 isoform 3	401	Helical; (Potential).				cardiac septum development|endocardial cushion development	integral to membrane	calcium ion binding			ovary(1)	1																		---	---	---	---
NUP210	23225	broad.mit.edu	37	3	13372050	13372050	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:13372050T>C	uc003bxv.1	-	30	4103	c.4020A>G	c.(4018-4020)CTA>CTG	p.L1340L		NM_024923	NP_079199	Q8TEM1	PO210_HUMAN	nucleoporin 210 precursor	1340	Lumenal (Probable).				carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	endoplasmic reticulum membrane|nuclear membrane|nuclear pore				ovary(3)|large_intestine(3)|skin(3)|pancreas(1)|liver(1)	11	all_neural(104;0.187)																	---	---	---	---
XPC	7508	broad.mit.edu	37	3	14199997	14199997	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14199997A>G	uc011ave.1	-	9	1490	c.1386T>C	c.(1384-1386)CCT>CCC	p.P462P	XPC_uc011avf.1_Silent_p.P269P|XPC_uc011avg.1_Silent_p.P425P	NM_004628	NP_004619	Q01831	XPC_HUMAN	xeroderma pigmentosum, complementation group C	462					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				---	---	---	---
ZFYVE20	64145	broad.mit.edu	37	3	15126293	15126293	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15126293C>A	uc003bzm.1	-	8	1161	c.547G>T	c.(547-549)GGG>TGG	p.G183W	ZFYVE20_uc010hek.1_Missense_Mutation_p.G183W|ZFYVE20_uc011avn.1_Missense_Mutation_p.G183W	NM_022340	NP_071735	Q9H1K0	RBNS5_HUMAN	FYVE-finger-containing Rab5 effector protein	183	FYVE-type.|Necessary for the correct targeting to endosomes.				blood coagulation|endosome transport|protein transport	early endosome membrane|plasma membrane	protein binding|zinc ion binding			skin(2)	2																		---	---	---	---
GALNTL2	117248	broad.mit.edu	37	3	16254150	16254150	+	Silent	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:16254150C>A	uc003car.3	+	6	1747	c.1272C>A	c.(1270-1272)TCC>TCA	p.S424S	GALNTL2_uc003caq.3_Silent_p.S157S	NM_054110	NP_473451	Q8N3T1	GLTL2_HUMAN	UDP-N-acetyl-alpha-D-galactosamine:polypeptide	424	Lumenal (Potential).					Golgi membrane|integral to membrane|transport vesicle	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			breast(1)	1																		---	---	---	---
RFTN1	23180	broad.mit.edu	37	3	16358435	16358435	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:16358435G>A	uc003cay.2	-	10	1919	c.1637C>T	c.(1636-1638)GCC>GTC	p.A546V	RFTN1_uc010hes.2_Missense_Mutation_p.A510V|OXNAD1_uc003cax.2_Intron|OXNAD1_uc011awb.1_Intron	NM_015150	NP_055965	Q14699	RFTN1_HUMAN	raft-linking protein	546						plasma membrane				ovary(3)|central_nervous_system(1)	4																		---	---	---	---
PLCL2	23228	broad.mit.edu	37	3	17052707	17052707	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:17052707C>T	uc011awc.1	+	5	1950	c.1845C>T	c.(1843-1845)AGC>AGT	p.S615S	PLCL2_uc011awd.1_Silent_p.S497S	NM_001144382	NP_001137854	Q9UPR0	PLCL2_HUMAN	phospholipase C-like 2 isoform 1	623	PI-PLC Y-box.				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	17415970	17415970	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:17415970C>T	uc003cbf.2	-	12	2480	c.815G>A	c.(814-816)GGT>GAT	p.G272D	TBC1D5_uc010hev.2_Missense_Mutation_p.G272D|TBC1D5_uc003cbe.2_Missense_Mutation_p.G272D|TBC1D5_uc010hew.1_Missense_Mutation_p.G224D	NM_014744	NP_055559	Q92609	TBCD5_HUMAN	TBC1 domain family, member 5 isoform b	272	Rab-GAP TBC.					intracellular	protein binding|Rab GTPase activator activity			ovary(1)	1																		---	---	---	---
RARB	5915	broad.mit.edu	37	3	25622154	25622154	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:25622154A>G	uc011awl.1	+	5	814	c.748A>G	c.(748-750)ACT>GCT	p.T250A	RARB_uc003cdi.1_Missense_Mutation_p.T131A|RARB_uc003cdh.2_Missense_Mutation_p.T243A	NM_016152	NP_057236	P10826	RARB_HUMAN	retinoic acid receptor, beta isoform 2	250	Ligand-binding.				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)													---	---	---	---
EOMES	8320	broad.mit.edu	37	3	27759084	27759084	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27759084T>C	uc003cdx.2	-	6	1538	c.1538A>G	c.(1537-1539)AAC>AGC	p.N513S	EOMES_uc003cdy.3_Missense_Mutation_p.N532S|EOMES_uc010hfn.2_3'UTR|EOMES_uc011axc.1_Missense_Mutation_p.N237S	NM_005442	NP_005433	O95936	EOMES_HUMAN	eomesodermin	513					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																		---	---	---	---
CMTM7	112616	broad.mit.edu	37	3	32493946	32493946	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32493946G>A	uc003cey.1	+	4	731	c.495G>A	c.(493-495)TCG>TCA	p.S165S	CMTM7_uc003cez.1_Silent_p.S132S	NM_138410	NP_612419	Q96FZ5	CKLF7_HUMAN	CKLF-like MARVEL transmembrane domain containing	165	MARVEL.				chemotaxis	extracellular space|integral to membrane	cytokine activity				0																		---	---	---	---
CCR4	1233	broad.mit.edu	37	3	32995805	32995805	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32995805C>T	uc003cfg.1	+	2	1059	c.891C>T	c.(889-891)TGC>TGT	p.C297C		NM_005508	NP_005499	P51679	CCR4_HUMAN	chemokine (C-C motif) receptor 4	297	Helical; Name=7; (Potential).				chemotaxis|elevation of cytosolic calcium ion concentration|immune response|inflammatory response	integral to plasma membrane				lung(1)	1																		---	---	---	---
MLH1	4292	broad.mit.edu	37	3	37092047	37092047	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37092047G>A	uc003cgl.2	+	19	2234	c.2174G>A	c.(2173-2175)CGC>CAC	p.R725H	MLH1_uc011aye.1_Intron|MLH1_uc011ayb.1_Missense_Mutation_p.R484H|MLH1_uc010hge.2_Missense_Mutation_p.R656H|MLH1_uc003cgn.3_Missense_Mutation_p.R484H|MLH1_uc011ayc.1_Missense_Mutation_p.R627H|MLH1_uc011ayd.1_Missense_Mutation_p.R484H|MLH1_uc003cgo.2_Missense_Mutation_p.R484H|MLH1_uc010hgk.2_Missense_Mutation_p.R312H|MLH1_uc010hgn.2_Missense_Mutation_p.A222T|MLH1_uc010hgm.2_RNA|MLH1_uc010hgo.2_3'UTR|MLH1_uc010hgp.2_Missense_Mutation_p.R108H|MLH1_uc010hgq.2_RNA	NM_000249	NP_000240	P40692	MLH1_HUMAN	MutL protein homolog 1	725					mismatch repair|somatic hypermutation of immunoglobulin genes	chiasma|MutLalpha complex|MutLbeta complex|synaptonemal complex	ATP binding|ATPase activity|protein binding	p.0?(1)		large_intestine(40)|haematopoietic_and_lymphoid_tissue(8)|ovary(6)|pancreas(5)|stomach(3)|central_nervous_system(3)|endometrium(3)|breast(3)|prostate(3)|skin(2)|NS(1)	77							1	D|Mis|N|F|S		colorectal|endometrial|ovarian|CNS	colorectal|endometrial|ovarian|CNS		MMR	Lynch_syndrome|Muir-Torre_syndrome|Turcot_syndrome|Constitutional_Mismatch_Repair_Deficiency_Syndrome				---	---	---	---
MYD88	4615	broad.mit.edu	37	3	38182330	38182330	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38182330C>T	uc003chx.2	+	4	974	c.790C>T	c.(790-792)CTC>TTC	p.L264F	MYD88_uc011ayi.1_Missense_Mutation_p.L256F|MYD88_uc011ayj.1_Silent_p.A195A|MYD88_uc011ayk.1_Silent_p.A150A|MYD88_uc011ayl.1_Missense_Mutation_p.L211F	NM_002468	NP_002459	Q99836	MYD88_HUMAN	myeloid differentiation primary response gene	243	TIR.				3'-UTR-mediated mRNA stabilization|anti-apoptosis|cellular response to mechanical stimulus|inflammatory response|innate immune response|MyD88-dependent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-17 production|positive regulation of interleukin-23 production|positive regulation of interleukin-6 production|regulation of inflammatory response|response to interleukin-1|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|endosome membrane|intrinsic to membrane|plasma membrane	death receptor binding|TIR domain binding|transmembrane receptor activity			haematopoietic_and_lymphoid_tissue(93)|breast(1)	94				KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065)				Mis 		ABC-DLBCL								---	---	---	---
EXOG	9941	broad.mit.edu	37	3	38565416	38565416	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38565416G>A	uc003cih.2	+	6	766	c.670G>A	c.(670-672)GTC>ATC	p.V224I	EXOG_uc010hhg.2_RNA|EXOG_uc011ayq.1_Missense_Mutation_p.V174I|EXOG_uc003cij.2_Missense_Mutation_p.V84I|EXOG_uc010hhd.2_Missense_Mutation_p.V84I|EXOG_uc010hhe.2_Missense_Mutation_p.V84I|EXOG_uc003cik.2_Missense_Mutation_p.V84I|EXOG_uc010hhf.2_Missense_Mutation_p.V84I|EXOG_uc003cii.2_Missense_Mutation_p.V84I	NM_005107	NP_005098	Q9Y2C4	EXOG_HUMAN	endo/exonuclease (5'-3'), endonuclease G-like	224						mitochondrial inner membrane	endonuclease activity|metal ion binding|nucleic acid binding				0																		---	---	---	---
SCN11A	11280	broad.mit.edu	37	3	38936340	38936340	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38936340C>T	uc011ays.1	-	15	2718	c.2519G>A	c.(2518-2520)CGC>CAC	p.R840H	SCN11A_uc010hhn.1_5'UTR	NM_014139	NP_054858	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha	840					response to drug	voltage-gated sodium channel complex	voltage-gated sodium channel activity			skin(6)|ovary(1)|haematopoietic_and_lymphoid_tissue(1)|pancreas(1)	9				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)													---	---	---	---
WDR48	57599	broad.mit.edu	37	3	39119656	39119656	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39119656C>T	uc003cit.2	+	10	1011	c.1001C>T	c.(1000-1002)GCC>GTC	p.A334V	WDR48_uc011ayt.1_Missense_Mutation_p.A325V|WDR48_uc011ayu.1_Missense_Mutation_p.A252V|WDR48_uc011ayv.1_Intron|WDR48_uc003ciu.2_RNA	NM_020839	NP_065890	Q8TAF3	WDR48_HUMAN	WD repeat domain 48	334	WD 7.				interspecies interaction between organisms|protein deubiquitination	lysosome|nucleus	protein binding			ovary(1)|breast(1)	2				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)														---	---	---	---
CX3CR1	1524	broad.mit.edu	37	3	39307048	39307048	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39307048C>T	uc003cjl.2	-	2	1045	c.953G>A	c.(952-954)CGC>CAC	p.R318H		NM_001337	NP_001328	P49238	CX3C1_HUMAN	chemokine (C-X3-C motif) receptor 1	318	Cytoplasmic (Potential).				cell adhesion|cellular defense response|chemotaxis|interspecies interaction between organisms|response to wounding	integral to plasma membrane	chemokine receptor activity			lung(3)	3				KIRC - Kidney renal clear cell carcinoma(284;0.0557)|Kidney(284;0.0699)														---	---	---	---
MYRIP	25924	broad.mit.edu	37	3	39942428	39942428	+	Intron	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39942428T>C	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)														---	---	---	---
ZNF445	353274	broad.mit.edu	37	3	44489280	44489280	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44489280G>A	uc003cnf.2	-	8	2231	c.1883C>T	c.(1882-1884)ACC>ATC	p.T628I	ZNF445_uc011azv.1_Missense_Mutation_p.T616I|ZNF445_uc011azw.1_Missense_Mutation_p.T628I	NM_181489	NP_852466	P59923	ZN445_HUMAN	zinc finger protein 445	628	C2H2-type 5.				viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(197;0.0514)|Kidney(197;0.0646)														---	---	---	---
LARS2	23395	broad.mit.edu	37	3	45527238	45527238	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45527238T>A	uc003cop.1	+	11	1258	c.1073T>A	c.(1072-1074)GTC>GAC	p.V358D	LARS2_uc010hit.1_Missense_Mutation_p.V315D	NM_015340	NP_056155	Q15031	SYLM_HUMAN	leucyl-tRNA synthetase 2, mitochondrial	358					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)													---	---	---	---
ALS2CL	259173	broad.mit.edu	37	3	46718370	46718370	+	Missense_Mutation	SNP	G	A	A	rs140829916	byFrequency	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46718370G>A	uc003cqa.1	-	17	2090	c.1900C>T	c.(1900-1902)CGT>TGT	p.R634C	ALS2CL_uc003cpx.1_5'UTR|ALS2CL_uc003cpy.1_RNA|ALS2CL_uc003cpz.1_Missense_Mutation_p.R149C|ALS2CL_uc003cqb.1_Missense_Mutation_p.R634C|ALS2CL_uc003cqc.1_RNA	NM_147129	NP_667340	Q60I27	AL2CL_HUMAN	ALS2 C-terminal like isoform 1	634					endosome organization|regulation of Rho protein signal transduction		GTPase activator activity|identical protein binding|Rho guanyl-nucleotide exchange factor activity			breast(2)|central_nervous_system(2)|skin(1)	5				BRCA - Breast invasive adenocarcinoma(193;0.000726)|KIRC - Kidney renal clear cell carcinoma(197;0.0171)|Kidney(197;0.0202)														---	---	---	---
PRSS45	377047	broad.mit.edu	37	3	46783906	46783906	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46783906T>C	uc010hjl.2	-	4	621	c.621A>G	c.(619-621)TCA>TCG	p.S207S	PRSS45_uc011bam.1_RNA	NM_199183	NP_954652	Q7RTY3	PRS45_HUMAN	testis serine protease 5	239					proteolysis		serine-type endopeptidase activity				0																		---	---	---	---
SMARCC1	6599	broad.mit.edu	37	3	47719763	47719763	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47719763C>T	uc003crq.2	-	16	1614	c.1496G>A	c.(1495-1497)CGT>CAT	p.R499H	SMARCC1_uc011bbc.1_RNA|SMARCC1_uc011bbd.1_Missense_Mutation_p.R390H	NM_003074	NP_003065	Q92922	SMRC1_HUMAN	SWI/SNF-related matrix-associated	499	SWIRM.				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	p.R499C(1)		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)														---	---	---	---
ZNF589	51385	broad.mit.edu	37	3	48302376	48302376	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48302376G>T	uc003csl.3	+	3	236	c.170G>T	c.(169-171)AGG>ATG	p.R57M	ZNF589_uc010hjt.1_Missense_Mutation_p.R55M|ZNF589_uc003csn.2_RNA|ZNF589_uc011bbg.1_Missense_Mutation_p.R57M|ZNF589_uc003csm.2_RNA	NM_016089	NP_057173	Q86UQ0	ZN589_HUMAN	zinc finger protein 589	57	KRAB.				regulation of transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000649)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)														---	---	---	---
NDUFAF3	25915	broad.mit.edu	37	3	49059972	49059972	+	Splice_Site	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49059972G>A	uc003cvq.2	+	2	774	c.270_splice	c.e2+1	p.N90_splice	DALRD3_uc003cvm.1_5'Flank|DALRD3_uc010hko.1_5'Flank|uc011bcb.1_5'Flank|MIR425_hsa-mir-425|MI0001448_5'Flank|NDUFAF3_uc003cvn.2_Splice_Site_p.N33_splice|uc003cvo.1_5'Flank|MIR191_hsa-mir-191|MI0000465_5'Flank|NDUFAF3_uc003cvp.2_Splice_Site_p.N33_splice|NDUFAF3_uc003cvr.2_Splice_Site_p.N33_splice|NDUFAF3_uc003cvs.2_Splice_Site_p.N33_splice	NM_199069	NP_951032			NADH dehydrogenase (ubiquinone) 1 alpha						mitochondrial respiratory chain complex I assembly	mitochondrial inner membrane|nucleus	protein binding				0																		---	---	---	---
USP19	10869	broad.mit.edu	37	3	49149019	49149019	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49149019G>T	uc003cwd.1	-	20	2983	c.2822C>A	c.(2821-2823)ACC>AAC	p.T941N	USP19_uc003cwa.2_Missense_Mutation_p.T749N|USP19_uc003cvz.3_Missense_Mutation_p.T1044N|USP19_uc011bcg.1_Missense_Mutation_p.T1032N|USP19_uc003cwb.2_Intron|USP19_uc003cwc.1_Missense_Mutation_p.T699N|USP19_uc011bch.1_Missense_Mutation_p.T1042N	NM_006677	NP_006668	O94966	UBP19_HUMAN	ubiquitin thioesterase 19	941	Cytoplasmic (Potential).				ER-associated protein catabolic process|positive regulation of cell cycle process|protein deubiquitination|regulation of protein stability|response to endoplasmic reticulum stress|skeletal muscle atrophy	endoplasmic reticulum membrane|integral to membrane	ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			ovary(4)|breast(2)|lung(1)	7				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)														---	---	---	---
BSN	8927	broad.mit.edu	37	3	49690236	49690236	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49690236G>T	uc003cxe.3	+	5	3361	c.3247G>T	c.(3247-3249)GCC>TCC	p.A1083S		NM_003458	NP_003449	Q9UPA5	BSN_HUMAN	bassoon protein	1083	Potential.				synaptic transmission	cell junction|cytoplasm|cytoskeleton|nucleus|synaptosome	metal ion binding			ovary(5)|pancreas(1)|central_nervous_system(1)|skin(1)	8				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)														---	---	---	---
MST1R	4486	broad.mit.edu	37	3	49933705	49933705	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49933705G>A	uc003cxy.3	-	10	2836	c.2572C>T	c.(2572-2574)CGC>TGC	p.R858C	MST1R_uc011bdd.1_Missense_Mutation_p.R859C|MST1R_uc011bdc.1_5'UTR	NM_002447	NP_002438	Q04912	RON_HUMAN	macrophage stimulating 1 receptor precursor	858	IPT/TIG 3.|Extracellular (Potential).				cellular component movement|defense response|multicellular organismal development|positive regulation of cell proliferation|single fertilization|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|macrophage colony-stimulating factor receptor activity|protein binding			ovary(5)|lung(1)	6				BRCA - Breast invasive adenocarcinoma(193;4.65e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00553)|Kidney(197;0.00625)														---	---	---	---
NAT6	24142	broad.mit.edu	37	3	50334066	50334066	+	Missense_Mutation	SNP	G	A	A	rs74426485	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50334066G>A	uc003czi.2	-	2	932	c.829C>T	c.(829-831)CGC>TGC	p.R277C	HYAL3_uc003czc.1_Intron|HYAL3_uc003czd.1_Intron|HYAL3_uc003cze.1_Intron|HYAL3_uc003czf.1_Intron|HYAL3_uc003czg.1_Intron|NAT6_uc003czj.2_Missense_Mutation_p.R299C|NAT6_uc003czk.3_Missense_Mutation_p.R277C|NAT6_uc003czl.1_Missense_Mutation_p.R277C	NM_012191	NP_036323	Q93015	NAT6_HUMAN	N-acetyltransferase 6	277						cytoplasm	N-acetyltransferase activity			lung(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605)														---	---	---	---
RASSF1	11186	broad.mit.edu	37	3	50369149	50369149	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50369149G>A	uc003dad.1	-	4	744	c.613C>T	c.(613-615)CGC>TGC	p.R205C	RASSF1_uc003daa.1_Missense_Mutation_p.R50C|RASSF1_uc003dab.1_Missense_Mutation_p.R131C|RASSF1_uc003dac.2_Missense_Mutation_p.R50C|RASSF1_uc003dae.1_Missense_Mutation_p.R201C|RASSF1_uc010hlk.1_RNA|RASSF1_uc003daf.1_Missense_Mutation_p.R50C	NM_170714	NP_733832	Q9NS23	RASF1_HUMAN	Ras association domain family 1 isoform D	205	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)														---	---	---	---
ZMYND10	51364	broad.mit.edu	37	3	50381230	50381230	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50381230C>A	uc003dag.1	-	3	399	c.253G>T	c.(253-255)GTG>TTG	p.V85L	RASSF1_uc003dad.1_5'Flank|RASSF1_uc003dae.1_5'Flank|RASSF1_uc010hlk.1_5'Flank|RASSF1_uc003daf.1_5'Flank|RASSF1_uc011bdq.1_5'Flank|ZMYND10_uc010hll.1_Missense_Mutation_p.V85L|ZMYND10_uc003dah.1_Missense_Mutation_p.V6L|ZMYND10_uc010hlm.1_Missense_Mutation_p.V42L	NM_015896	NP_056980	O75800	ZMY10_HUMAN	zinc finger, MYND domain-containing 10	85						cytoplasm	protein binding|zinc ion binding			lung(4)|ovary(1)	5				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)											TSP Lung(30;0.18)			---	---	---	---
GRM2	2912	broad.mit.edu	37	3	51746888	51746888	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51746888C>T	uc010hlv.2	+	3	1089	c.850C>T	c.(850-852)CGC>TGC	p.R284C	GRM2_uc003dbo.3_Intron|GRM2_uc010hlu.2_RNA	NM_000839	NP_000830	Q14416	GRM2_HUMAN	glutamate receptor, metabotropic 2 isoform a	284	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)													---	---	---	---
ABHD14A	25864	broad.mit.edu	37	3	52014951	52014951	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52014951C>T	uc003dco.2	+	5	843	c.733C>T	c.(733-735)CGC>TGC	p.R245C	ABHD14B_uc003dcn.2_Intron|ACY1_uc011bea.1_Intron|ACY1_uc011beb.1_5'Flank|ACY1_uc003dcp.2_5'Flank|ACY1_uc003dcq.2_5'Flank	NM_015407	NP_056222	Q9BUJ0	ABHEA_HUMAN	abhydrolase domain containing 14A	245						cytoplasm|integral to membrane	hydrolase activity				0				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000541)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)														---	---	---	---
DNAH1	25981	broad.mit.edu	37	3	52400871	52400871	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52400871G>A	uc011bef.1	+	36	5994	c.5733G>A	c.(5731-5733)CTG>CTA	p.L1911L		NM_015512	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	1911	AAA 2 (By similarity).				ciliary or flagellar motility|microtubule-based movement|response to mechanical stimulus	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			large_intestine(3)	3				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)														---	---	---	---
BAP1	8314	broad.mit.edu	37	3	52437234	52437234	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52437234C>T	uc003ddx.2	-	14	1925	c.1810G>A	c.(1810-1812)GTG>ATG	p.V604M	BAP1_uc003ddw.2_RNA|BAP1_uc010hmg.2_RNA|BAP1_uc010hmh.2_Intron	NM_004656	NP_004647	Q92560	BAP1_HUMAN	BRCA1 associated protein-1	604	Interaction with BRCA1.				monoubiquitinated histone H2A deubiquitination|negative regulation of cell proliferation|protein K48-linked deubiquitination|regulation of cell cycle|regulation of cell growth|ubiquitin-dependent protein catabolic process	cytoplasm|nucleolus|PR-DUB complex	chromatin binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			pleura(32)|eye(28)|lung(2)|ovary(2)|breast(1)	65				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)				N|Mis|F|S|O		uveal melanoma|breast|NSCLC								---	---	---	---
GLT8D1	55830	broad.mit.edu	37	3	52729486	52729486	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52729486G>A	uc003dfi.3	-	8	902	c.763C>T	c.(763-765)CGA>TGA	p.R255*	GLT8D1_uc003dfj.2_Nonsense_Mutation_p.R255*|GLT8D1_uc003dfk.2_Nonsense_Mutation_p.R255*|GLT8D1_uc003dfl.2_Nonsense_Mutation_p.R255*|GLT8D1_uc003dfm.2_Nonsense_Mutation_p.R255*|GLT8D1_uc003dfn.2_Nonsense_Mutation_p.R255*|GLT8D1_uc003dfo.1_Nonsense_Mutation_p.R255*	NM_152932	NP_690909	Q68CQ7	GL8D1_HUMAN	glycosyltransferase 8 domain containing 1	255	Lumenal (Potential).					integral to membrane|mitochondrion	transferase activity, transferring glycosyl groups				0				BRCA - Breast invasive adenocarcinoma(193;6.78e-05)|Kidney(197;0.000618)|KIRC - Kidney renal clear cell carcinoma(197;0.000779)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)														---	---	---	---
ITIH4	3700	broad.mit.edu	37	3	52858944	52858944	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52858944C>T	uc003dfz.2	-	7	826	c.790G>A	c.(790-792)GCC>ACC	p.A264T	ITIH4_uc011bel.1_5'UTR|ITIH4_uc003dfy.2_Missense_Mutation_p.A128T|ITIH4_uc011bem.1_Missense_Mutation_p.A264T|ITIH4_uc011ben.1_Missense_Mutation_p.A264T	NM_002218	NP_002209	Q14624	ITIH4_HUMAN	inter-alpha (globulin) inhibitor H4	264					acute-phase response|hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			ovary(2)|central_nervous_system(1)	3				BRCA - Breast invasive adenocarcinoma(193;7e-05)|Kidney(197;0.000656)|KIRC - Kidney renal clear cell carcinoma(197;0.000794)|OV - Ovarian serous cystadenocarcinoma(275;0.0496)														---	---	---	---
IL17RD	54756	broad.mit.edu	37	3	57132279	57132279	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57132279G>T	uc003dil.2	-	12	1541	c.1452C>A	c.(1450-1452)TGC>TGA	p.C484*	IL17RD_uc003dik.2_Nonsense_Mutation_p.C460*|IL17RD_uc010hna.2_Nonsense_Mutation_p.C340*|IL17RD_uc011bex.1_Nonsense_Mutation_p.C340*	NM_017563	NP_060033	Q8NFM7	I17RD_HUMAN	interleukin 17 receptor D precursor	484	SEFIR.|Cytoplasmic (Potential).					Golgi membrane|integral to membrane|plasma membrane	receptor activity				0				KIRC - Kidney renal clear cell carcinoma(284;0.0173)|Kidney(284;0.0204)														---	---	---	---
FAM3D	131177	broad.mit.edu	37	3	58625897	58625897	+	Silent	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58625897C>A	uc003dkq.2	-	7	627	c.330G>T	c.(328-330)ACG>ACT	p.T110T		NM_138805	NP_620160	Q96BQ1	FAM3D_HUMAN	family with sequence similarity 3, member D	110					negative regulation of insulin secretion	extracellular region	cytokine activity				0				BRCA - Breast invasive adenocarcinoma(55;0.000225)|Kidney(10;0.000667)|KIRC - Kidney renal clear cell carcinoma(10;0.000802)|OV - Ovarian serous cystadenocarcinoma(275;0.169)														---	---	---	---
PTPRG	5793	broad.mit.edu	37	3	62253473	62253473	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:62253473G>A	uc003dlb.2	+	19	3572	c.2853G>A	c.(2851-2853)ACG>ACA	p.T951T	PTPRG_uc003dlc.2_Silent_p.T922T|PTPRG_uc011bfi.1_Silent_p.T197T|uc010hno.2_Intron|uc003dld.3_Intron|uc010hnp.2_Intron|uc003dle.3_Intron	NM_002841	NP_002832	P23470	PTPRG_HUMAN	protein tyrosine phosphatase, receptor type, G	951	Cytoplasmic (Potential).|Tyrosine-protein phosphatase 1.				transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	identical protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(5)|lung(2)	7				BRCA - Breast invasive adenocarcinoma(55;0.000376)|KIRC - Kidney renal clear cell carcinoma(10;0.0499)|Kidney(10;0.065)														---	---	---	---
FEZF2	55079	broad.mit.edu	37	3	62355818	62355818	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:62355818G>A	uc003dlh.2	-	4	1527	c.1320C>T	c.(1318-1320)CAC>CAT	p.H440H	FEZF2_uc003dli.2_Silent_p.H440H	NM_018008	NP_060478	Q8TBJ5	FEZF2_HUMAN	FEZ family zinc finger 2	440	C2H2-type 6.				transcription, DNA-dependent	nucleus	zinc ion binding			lung(1)	1		Lung SC(41;0.0262)		BRCA - Breast invasive adenocarcinoma(55;0.000221)|KIRC - Kidney renal clear cell carcinoma(15;0.00834)|Kidney(15;0.00957)														---	---	---	---
SYNPR	132204	broad.mit.edu	37	3	63466538	63466538	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:63466538G>A	uc003dlq.2	+	2	424	c.55G>A	c.(55-57)GGT>AGT	p.G19S	SYNPR_uc003dlp.2_Missense_Mutation_p.G39S|SYNPR_uc011bfk.1_Intron|SYNPR_uc011bfl.1_RNA|SYNPR_uc010hnt.2_Missense_Mutation_p.G28S|SYNPR_uc011bfm.1_RNA	NM_144642	NP_653243	Q8TBG9	SYNPR_HUMAN	synaptoporin isoform 2	19	MARVEL.|Helical; (Potential).					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	64005127	64005127	+	Intron	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:64005127A>G	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)														---	---	---	---
ADAMTS9	56999	broad.mit.edu	37	3	64547403	64547403	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:64547403C>T	uc003dmg.2	-	30	4581	c.4549G>A	c.(4549-4551)GTA>ATA	p.V1517I	ADAMTS9_uc011bfo.1_Missense_Mutation_p.V1489I|ADAMTS9_uc003dmh.1_Missense_Mutation_p.V1346I|ADAMTS9_uc011bfp.1_Missense_Mutation_p.V428I|uc003dmi.1_RNA	NM_182920	NP_891550	Q9P2N4	ATS9_HUMAN	ADAM metallopeptidase with thrombospondin type 1	1517	TSP type-1 12.				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)														---	---	---	---
LMOD3	56203	broad.mit.edu	37	3	69167997	69167997	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:69167997T>C	uc003dns.2	-	2	1718	c.1509A>G	c.(1507-1509)AGA>AGG	p.R503R	LMOD3_uc003dnt.2_Silent_p.R503R	NM_198271	NP_938012	Q0VAK6	LMOD3_HUMAN	leiomodin 3 (fetal)	503						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)														---	---	---	---
MINA	84864	broad.mit.edu	37	3	97686163	97686163	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97686163C>A	uc003drz.1	-	2	781	c.275G>T	c.(274-276)CGG>CTG	p.R92L	MINA_uc003dsa.1_Missense_Mutation_p.R92L|MINA_uc003dsb.1_Missense_Mutation_p.R92L|MINA_uc003dsc.1_Missense_Mutation_p.R92L|MINA_uc010hpa.1_RNA|MINA_uc010hpb.1_Intron	NM_001042533	NP_001035998	Q8IUF8	MINA_HUMAN	MYC induced nuclear antigen isoform a	92					ribosome biogenesis	cytoplasm|nucleolus				ovary(1)	1																		---	---	---	---
OR5H2	79310	broad.mit.edu	37	3	98001806	98001806	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98001806G>A	uc003dsj.1	+	1	75	c.75G>A	c.(73-75)CAG>CAA	p.Q25Q		NM_001005482	NP_001005482	Q8NGV7	OR5H2_HUMAN	olfactory receptor, family 5, subfamily H,	25	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(3)	3																		---	---	---	---
CEP97	79598	broad.mit.edu	37	3	101451389	101451389	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:101451389T>C	uc003dvk.1	+	6	646	c.619T>C	c.(619-621)TGT>CGT	p.C207R	CEP97_uc010hpm.1_Missense_Mutation_p.C173R|CEP97_uc011bhf.1_Missense_Mutation_p.C207R|CEP97_uc003dvl.1_5'UTR|CEP97_uc003dvm.1_Missense_Mutation_p.C45R	NM_024548	NP_078824	Q8IW35	CEP97_HUMAN	centrosomal protein 97kDa	207						centrosome|nucleus	protein binding			ovary(2)	2																		---	---	---	---
BBX	56987	broad.mit.edu	37	3	107491891	107491891	+	Silent	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:107491891C>A	uc010hpr.2	+	11	1650	c.1323C>A	c.(1321-1323)CCC>CCA	p.P441P	BBX_uc003dwk.3_Silent_p.P441P|BBX_uc003dwl.3_Intron|BBX_uc010hps.1_Silent_p.P462P|BBX_uc003dwm.3_Silent_p.P441P|BBX_uc003dwo.3_5'Flank	NM_001142568	NP_001136040	Q8WY36	BBX_HUMAN	HMG-BOX transcription factor BBX isoform 1	441					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(3)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(3;0.112)															---	---	---	---
CD96	10225	broad.mit.edu	37	3	111319601	111319601	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111319601A>G	uc003dxw.2	+	8	1145	c.975A>G	c.(973-975)AAA>AAG	p.K325K	CD96_uc003dxv.2_Silent_p.K309K|CD96_uc003dxx.2_Silent_p.K309K|CD96_uc010hpy.1_Silent_p.K309K	NM_198196	NP_937839	P40200	TACT_HUMAN	CD96 antigen isoform 1 precursor	325	Extracellular (Potential).|Ig-like C2-type.				cell adhesion|immune response|regulation of immune response	integral to plasma membrane				skin(2)|central_nervous_system(1)	3														Opitz_Trigonocephaly_syndrome				---	---	---	---
BOC	91653	broad.mit.edu	37	3	112999994	112999994	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112999994A>G	uc003dzx.2	+	15	3046	c.2425A>G	c.(2425-2427)ACC>GCC	p.T809A	BOC_uc003dzy.2_Missense_Mutation_p.T809A|BOC_uc003dzz.2_Missense_Mutation_p.T810A|BOC_uc003eab.2_Missense_Mutation_p.T510A|BOC_uc003eac.2_Missense_Mutation_p.T124A	NM_033254	NP_150279	Q9BWV1	BOC_HUMAN	brother of CDO precursor	809	Fibronectin type-III 3.|Extracellular (Potential).				cell adhesion|muscle cell differentiation|positive regulation of myoblast differentiation	integral to membrane|plasma membrane	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|pancreas(1)	6			Epithelial(53;0.227)															---	---	---	---
GRAMD1C	54762	broad.mit.edu	37	3	113627946	113627946	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113627946A>G	uc003eaq.3	+	9	1007	c.931A>G	c.(931-933)ACT>GCT	p.T311A	GRAMD1C_uc011bil.1_RNA|GRAMD1C_uc011bim.1_RNA|GRAMD1C_uc003ear.2_Missense_Mutation_p.T144A|GRAMD1C_uc003eas.2_Missense_Mutation_p.T106A	NM_017577	NP_060047	Q8IYS0	GRM1C_HUMAN	GRAM domain containing 1C	311						integral to membrane				ovary(2)|skin(1)	3																		---	---	---	---
ZBTB20	26137	broad.mit.edu	37	3	114069597	114069597	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:114069597C>T	uc003ebi.2	-	4	1508	c.1328G>A	c.(1327-1329)AGC>AAC	p.S443N	ZBTB20_uc003ebj.2_Missense_Mutation_p.S370N|ZBTB20_uc010hqp.2_Missense_Mutation_p.S370N|ZBTB20_uc003ebk.2_Missense_Mutation_p.S370N|ZBTB20_uc003ebl.2_Missense_Mutation_p.S370N|ZBTB20_uc003ebm.2_Missense_Mutation_p.S370N|ZBTB20_uc003ebn.2_Missense_Mutation_p.S370N|uc003ebo.1_5'Flank	NM_015642	NP_056457	Q9HC78	ZBT20_HUMAN	zinc finger and BTB domain containing 20 isoform	443					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)|skin(1)	5				LUSC - Lung squamous cell carcinoma(41;0.0581)|Lung(219;0.191)														---	---	---	---
ZBTB20	26137	broad.mit.edu	37	3	114070442	114070442	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:114070442G>A	uc003ebi.2	-	4	663	c.483C>T	c.(481-483)GGC>GGT	p.G161G	ZBTB20_uc003ebj.2_Silent_p.G88G|ZBTB20_uc010hqp.2_Silent_p.G88G|ZBTB20_uc003ebk.2_Silent_p.G88G|ZBTB20_uc003ebl.2_Silent_p.G88G|ZBTB20_uc003ebm.2_Silent_p.G88G|ZBTB20_uc003ebn.2_Silent_p.G88G|uc003ebo.1_5'Flank	NM_015642	NP_056457	Q9HC78	ZBT20_HUMAN	zinc finger and BTB domain containing 20 isoform	161	BTB.				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)														---	---	---	---
GAP43	2596	broad.mit.edu	37	3	115395025	115395025	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:115395025G>A	uc003ebq.2	+	2	582	c.196G>A	c.(196-198)GCT>ACT	p.A66T	GAP43_uc003ebr.2_Missense_Mutation_p.A102T	NM_002045	NP_002036	P17677	NEUM_HUMAN	growth associated protein 43 isoform 2	66					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)														---	---	---	---
IGSF11	152404	broad.mit.edu	37	3	118621438	118621438	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:118621438C>T	uc003ebw.2	-	7	1472	c.1225G>A	c.(1225-1227)GCA>ACA	p.A409T	IGSF11_uc011biv.1_Missense_Mutation_p.A381T|IGSF11_uc003ebx.2_Missense_Mutation_p.A385T|IGSF11_uc003eby.2_Missense_Mutation_p.A408T|IGSF11_uc003ebz.2_Missense_Mutation_p.A384T|IGSF11_uc010hqs.2_Missense_Mutation_p.A408T	NM_001015887	NP_001015887	Q5DX21	IGS11_HUMAN	immunoglobulin superfamily, member 11 isoform b	409	Cytoplasmic (Potential).				cell adhesion|regulation of growth	integral to membrane|plasma membrane	receptor activity				0																		---	---	---	---
B4GALT4	8702	broad.mit.edu	37	3	118931514	118931514	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:118931514T>C	uc003ecg.2	-	8	1558	c.917A>G	c.(916-918)CAC>CGC	p.H306R	B4GALT4_uc003ece.1_3'UTR|B4GALT4_uc003ecf.2_RNA|B4GALT4_uc003ech.2_Missense_Mutation_p.H306R|B4GALT4_uc003eci.2_Missense_Mutation_p.H306R	NM_212543	NP_997708	O60513	B4GT4_HUMAN	UDP-Gal:betaGlcNAc beta 1,4-	306	Lumenal (Potential).				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)													---	---	---	---
CASR	846	broad.mit.edu	37	3	122003470	122003470	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122003470G>A	uc003eev.3	+	7	3041	c.2669G>A	c.(2668-2670)CGC>CAC	p.R890H	CASR_uc003eew.3_Missense_Mutation_p.R900H	NM_000388	NP_000379	P41180	CASR_HUMAN	calcium-sensing receptor precursor	890	Cytoplasmic (Potential).|Interaction with RNF19A.				anatomical structure morphogenesis|calcium ion import|cellular calcium ion homeostasis|chemosensory behavior|detection of calcium ion|ossification	integral to plasma membrane	G-protein coupled receptor activity|phosphatidylinositol phospholipase C activity			ovary(4)|skin(2)|upper_aerodigestive_tract(1)	7				GBM - Glioblastoma multiforme(114;0.226)	Cinacalcet(DB01012)													---	---	---	---
SEMA5B	54437	broad.mit.edu	37	3	122629836	122629836	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122629836G>A	uc003efz.1	-	22	3452	c.3148C>T	c.(3148-3150)CTC>TTC	p.L1050F	SEMA5B_uc011bju.1_Missense_Mutation_p.L956F|SEMA5B_uc003ega.1_RNA|SEMA5B_uc003egb.1_Missense_Mutation_p.L1050F|SEMA5B_uc003efy.1_Missense_Mutation_p.L28F	NM_001031702	NP_001026872	Q9P283	SEM5B_HUMAN	semaphorin 5B isoform 1	1050	Helical; Signal-anchor for type III membrane protein; (Potential).				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)														---	---	---	---
KALRN	8997	broad.mit.edu	37	3	124149556	124149556	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124149556T>C	uc003ehg.2	+	16	2884	c.2757T>C	c.(2755-2757)AAT>AAC	p.N919N	KALRN_uc010hrv.1_Silent_p.N919N|KALRN_uc003ehf.1_Silent_p.N919N|KALRN_uc011bjy.1_Silent_p.N919N|KALRN_uc003ehh.1_Silent_p.N265N	NM_001024660	NP_001019831	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase isoform 1	919	Spectrin 4.				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																		---	---	---	---
KLF15	28999	broad.mit.edu	37	3	126070789	126070789	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126070789G>T	uc011bkk.1	-	2	1159	c.977C>A	c.(976-978)CCT>CAT	p.P326H		NM_014079	NP_054798	Q9UIH9	KLF15_HUMAN	Kruppel-like factor 15	326	C2H2-type 1.					nucleus	DNA binding|zinc ion binding			lung(1)	1				GBM - Glioblastoma multiforme(114;0.147)														---	---	---	---
ZXDC	79364	broad.mit.edu	37	3	126190875	126190875	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126190875A>G	uc003eiv.2	-	3	1134	c.1080T>C	c.(1078-1080)TGT>TGC	p.C360C	ZXDC_uc010hsh.2_RNA|ZXDC_uc003eix.2_Silent_p.C360C	NM_025112	NP_079388	Q2QGD7	ZXDC_HUMAN	ZXD family zinc finger C isoform 1	360	C2H2-type 7.				positive regulation of transcription, DNA-dependent	nucleus	C2H2 zinc finger domain binding|identical protein binding|LRR domain binding|nucleic acid binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.155)														---	---	---	---
SEC61A1	29927	broad.mit.edu	37	3	127786377	127786377	+	Silent	SNP	A	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127786377A>T	uc003ekb.2	+	10	1273	c.1089A>T	c.(1087-1089)GTA>GTT	p.V363V	RUVBL1_uc003eke.2_Intron|RUVBL1_uc003ekf.2_Intron|SEC61A1_uc003ekc.2_Silent_p.V310V|SEC61A1_uc003ekd.2_Silent_p.V243V|SEC61A1_uc003ekg.2_Silent_p.V57V	NM_013336	NP_037468	P61619	S61A1_HUMAN	Sec61 alpha 1 subunit	363	Helical; (Potential).				protein targeting to ER	integral to endoplasmic reticulum membrane	P-P-bond-hydrolysis-driven protein transmembrane transporter activity|protein binding|ribosome binding			ovary(1)	1																		---	---	---	---
MBD4	8930	broad.mit.edu	37	3	129152936	129152936	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129152936G>A	uc003emh.1	-	4	1421	c.1245C>T	c.(1243-1245)AGC>AGT	p.S415S	MBD4_uc003emi.1_Silent_p.S415S|MBD4_uc003emj.1_Silent_p.S409S|MBD4_uc003emk.1_Silent_p.S97S|MBD4_uc011bkw.1_Silent_p.S415S	NM_003925	NP_003916	O95243	MBD4_HUMAN	methyl-CpG binding domain protein 4	415					depyrimidination	nucleoplasm	DNA N-glycosylase activity|endodeoxyribonuclease activity|protein binding|satellite DNA binding			ovary(1)|lung(1)	2													BER_DNA_glycosylases					---	---	---	---
COL6A6	131873	broad.mit.edu	37	3	130354562	130354562	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130354562G>T	uc010htl.2	+	27	5079	c.5048G>T	c.(5047-5049)GGT>GTT	p.G1683V	COL6A6_uc003eni.3_5'UTR	NM_001102608	NP_001096078	A6NMZ7	CO6A6_HUMAN	collagen type VI alpha 6 precursor	1683	Triple-helical region.				axon guidance|cell adhesion	collagen				ovary(6)|central_nervous_system(1)|pancreas(1)	8																		---	---	---	---
COL6A6	131873	broad.mit.edu	37	3	130380888	130380888	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130380888A>G	uc010htl.2	+	34	6269	c.6238A>G	c.(6238-6240)AGA>GGA	p.R2080G	COL6A6_uc003eni.3_Missense_Mutation_p.R179G	NM_001102608	NP_001096078	A6NMZ7	CO6A6_HUMAN	collagen type VI alpha 6 precursor	2080	VWFA 9.|Nonhelical region.				axon guidance|cell adhesion	collagen				ovary(6)|central_nervous_system(1)|pancreas(1)	8																		---	---	---	---
PIK3R4	30849	broad.mit.edu	37	3	130422673	130422673	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130422673G>A	uc003enj.2	-	13	3573	c.2992C>T	c.(2992-2994)CGA>TGA	p.R998*		NM_014602	NP_055417	Q99570	PI3R4_HUMAN	phosphoinositide-3-kinase, regulatory subunit 4	998	WD 1.				fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway	cytosol	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1)	12																		---	---	---	---
CPNE4	131034	broad.mit.edu	37	3	131283121	131283121	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:131283121G>A	uc003eok.2	-	11	1435	c.1000C>T	c.(1000-1002)CAA>TAA	p.Q334*	CPNE4_uc011blq.1_Nonsense_Mutation_p.Q352*|CPNE4_uc003eol.2_Nonsense_Mutation_p.Q352*|CPNE4_uc003eom.2_Nonsense_Mutation_p.Q334*	NM_130808	NP_570720	Q96A23	CPNE4_HUMAN	copine IV	334	VWFA.									upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
PPP2R3A	5523	broad.mit.edu	37	3	135721928	135721928	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:135721928C>T	uc003eqv.1	+	2	2153	c.1588C>T	c.(1588-1590)CCA>TCA	p.P530S	PPP2R3A_uc011blz.1_Intron	NM_002718	NP_002709	Q06190	P2R3A_HUMAN	protein phosphatase 2, regulatory subunit B'',	530					protein dephosphorylation	protein phosphatase type 2A complex	calcium ion binding|protein binding|protein phosphatase type 2A regulator activity			ovary(3)|pancreas(1)|lung(1)|breast(1)|skin(1)	7																		---	---	---	---
STAG1	10274	broad.mit.edu	37	3	136059352	136059352	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136059352T>C	uc003era.1	-	32	3945	c.3653A>G	c.(3652-3654)GAC>GGC	p.D1218G	STAG1_uc003erb.1_Missense_Mutation_p.D1181G	NM_005862	NP_005853	Q8WVM7	STAG1_HUMAN	stromal antigen 1	1218					cell division|chromosome segregation|mitotic metaphase/anaphase transition|mitotic prometaphase	cell junction|chromatin|chromosome, centromeric region|nucleoplasm	protein binding			ovary(2)	2																		---	---	---	---
SOX14	8403	broad.mit.edu	37	3	137484306	137484306	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137484306C>T	uc003erm.1	+	1	728	c.680C>T	c.(679-681)ACT>ATT	p.T227I		NM_004189	NP_004180	O95416	SOX14_HUMAN	SRY-box 14	227					negative regulation of transcription from RNA polymerase II promoter|nervous system development|transcription, DNA-dependent	nucleus	sequence-specific DNA binding				0																		---	---	---	---
COPB2	9276	broad.mit.edu	37	3	139080026	139080026	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:139080026C>T	uc003etf.3	-	17	2237	c.2107G>A	c.(2107-2109)GCC>ACC	p.A703T	COPB2_uc011bmv.1_Missense_Mutation_p.A674T|COPB2_uc010hui.2_Missense_Mutation_p.A674T	NM_004766	NP_004757	P35606	COPB2_HUMAN	coatomer protein complex, subunit beta 2 (beta	703					COPI coating of Golgi vesicle|intra-Golgi vesicle-mediated transport|intracellular protein transport|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat|cytosol	protein binding|structural molecule activity			ovary(2)	2																		---	---	---	---
ATR	545	broad.mit.edu	37	3	142176461	142176461	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142176461C>T	uc003eux.3	-	45	7762	c.7640G>A	c.(7639-7641)CGA>CAA	p.R2547Q	ATR_uc003euy.1_Missense_Mutation_p.R433Q	NM_001184	NP_001175	Q13535	ATR_HUMAN	ataxia telangiectasia and Rad3 related protein	2547	PI3K/PI4K.				cell cycle|cellular response to gamma radiation|cellular response to UV|DNA damage checkpoint|DNA repair|DNA replication|multicellular organismal development|negative regulation of DNA replication|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|protein autophosphorylation|replicative senescence	PML body	ATP binding|DNA binding|MutLalpha complex binding|MutSalpha complex binding|protein serine/threonine kinase activity			lung(5)|skin(5)|breast(4)|ovary(3)|stomach(1)|central_nervous_system(1)|liver(1)	20													Other_conserved_DNA_damage_response_genes					---	---	---	---
TRPC1	7220	broad.mit.edu	37	3	142521156	142521156	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142521156G>A	uc003evc.2	+	10	1863	c.1727G>A	c.(1726-1728)TGT>TAT	p.C576Y	TRPC1_uc003evb.2_Missense_Mutation_p.C542Y|TRPC1_uc011bni.1_Missense_Mutation_p.C95Y	NM_003304	NP_003295	P48995	TRPC1_HUMAN	transient receptor potential cation channel,	576	Cytoplasmic (Potential).				axon guidance|cytosolic calcium ion homeostasis|positive regulation of release of sequestered calcium ion into cytosol|response to calcium ion	cytosol|integral to plasma membrane	protein binding|store-operated calcium channel activity			ovary(2)	2																		---	---	---	---
PAQR9	344838	broad.mit.edu	37	3	142681261	142681261	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142681261A>G	uc003evg.2	-	1	918	c.918T>C	c.(916-918)ATT>ATC	p.I306I	PAQR9_uc003evf.1_RNA	NM_198504	NP_940906	Q6ZVX9	PAQR9_HUMAN	progestin and adipoQ receptor family member IX	306	Helical; (Potential).					integral to membrane	receptor activity				0																		---	---	---	---
IGSF10	285313	broad.mit.edu	37	3	151164676	151164676	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151164676C>T	uc011bod.1	-	4	3093	c.3093G>A	c.(3091-3093)CTG>CTA	p.L1031L		NM_178822	NP_849144	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10 precursor	1031					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)															---	---	---	---
SUCNR1	56670	broad.mit.edu	37	3	151598580	151598580	+	Nonsense_Mutation	SNP	T	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151598580T>A	uc003ezf.1	+	3	348	c.249T>A	c.(247-249)TAT>TAA	p.Y83*		NM_033050	NP_149039	Q9BXA5	SUCR1_HUMAN	succinate receptor 1	83	Extracellular (Potential).					integral to membrane|plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			ovary(1)	1			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)		Succinic acid(DB00139)													---	---	---	---
P2RY1	5028	broad.mit.edu	37	3	152553661	152553661	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:152553661C>T	uc003ezq.2	+	1	926	c.90C>T	c.(88-90)GTC>GTT	p.V30V		NM_002563	NP_002554	P47900	P2RY1_HUMAN	purinergic receptor P2Y1	30	Extracellular (Potential).				activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|platelet activation	integral to plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			lung(1)	1			LUSC - Lung squamous cell carcinoma(72;0.0628)|Lung(72;0.11)															---	---	---	---
MYNN	55892	broad.mit.edu	37	3	169497257	169497257	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169497257T>A	uc003fft.2	+	3	1397	c.968T>A	c.(967-969)ATA>AAA	p.I323K	MYNN_uc011bpm.1_Missense_Mutation_p.I209K|MYNN_uc003ffu.2_Missense_Mutation_p.I323K|MYNN_uc003ffv.2_Missense_Mutation_p.I50K|MYNN_uc010hwo.2_Missense_Mutation_p.I323K|MYNN_uc003ffw.1_RNA	NM_018657	NP_061127	Q9NPC7	MYNN_HUMAN	myoneurin	323	C2H2-type 1.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(1)	1	all_cancers(22;9.55e-22)|all_epithelial(15;2.04e-26)|all_lung(20;5.05e-16)|Lung NSC(18;2.19e-15)|Ovarian(172;0.000223)|Breast(254;0.197)		Epithelial(2;4.03e-64)|all cancers(2;2.19e-58)|Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.00676)															---	---	---	---
USP13	8975	broad.mit.edu	37	3	179499615	179499615	+	Intron	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179499615A>G	uc003fkh.2	+							NM_003940	NP_003931			ubiquitin thiolesterase 13						ubiquitin-dependent protein catabolic process		cysteine-type endopeptidase activity|omega peptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			ovary(1)	1	all_cancers(143;7.79e-15)|Ovarian(172;0.0338)|Breast(254;0.148)		OV - Ovarian serous cystadenocarcinoma(80;1e-25)|GBM - Glioblastoma multiforme(14;0.0169)															---	---	---	---
ABCC5	10057	broad.mit.edu	37	3	183682976	183682976	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183682976C>T	uc003fmg.2	-	14	2193	c.2028G>A	c.(2026-2028)ACG>ACA	p.T676T	ABCC5_uc011bqt.1_Silent_p.T204T|ABCC5_uc010hxl.2_Silent_p.T676T	NM_005688	NP_005679	O15440	MRP5_HUMAN	ATP-binding cassette, sub-family C, member 5	676	ABC transporter 1.					integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of substances|organic anion transmembrane transporter activity			ovary(2)|large_intestine(1)|central_nervous_system(1)	4	all_cancers(143;1.85e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)															---	---	---	---
EIF4G1	1981	broad.mit.edu	37	3	184040373	184040373	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184040373A>G	uc003fnp.2	+	12	1848	c.1650A>G	c.(1648-1650)GCA>GCG	p.A550A	EIF4G1_uc003fno.1_Silent_p.A491A|EIF4G1_uc010hxw.1_Silent_p.A386A|EIF4G1_uc003fnt.2_Silent_p.A261A|EIF4G1_uc003fnq.2_Silent_p.A463A|EIF4G1_uc003fnr.2_Silent_p.A386A|EIF4G1_uc010hxx.2_Silent_p.A557A|EIF4G1_uc003fns.2_Silent_p.A510A|EIF4G1_uc010hxy.2_Silent_p.A557A|EIF4G1_uc003fnv.3_Silent_p.A550A|EIF4G1_uc003fnu.3_Silent_p.A550A|EIF4G1_uc003fnw.2_Silent_p.A557A|EIF4G1_uc003fnx.2_Silent_p.A354A|EIF4G1_uc003fny.3_Silent_p.A354A	NM_198241	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4	550					insulin receptor signaling pathway|interspecies interaction between organisms|nuclear-transcribed mRNA poly(A) tail shortening|regulation of translational initiation	cytosol|eukaryotic translation initiation factor 4F complex	protein binding|translation initiation factor activity			lung(2)|ovary(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	7	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)															---	---	---	---
EPHB3	2049	broad.mit.edu	37	3	184299146	184299146	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184299146C>T	uc003foz.2	+	15	3275	c.2838C>T	c.(2836-2838)TTC>TTT	p.F946F		NM_004443	NP_004434	P54753	EPHB3_HUMAN	ephrin receptor EphB3 precursor	946	Cytoplasmic (Potential).|SAM.					integral to plasma membrane	ATP binding|ephrin receptor activity			lung(5)|breast(2)|upper_aerodigestive_tract(1)|stomach(1)|skin(1)|ovary(1)	11	all_cancers(143;1.89e-10)|Ovarian(172;0.0339)		Epithelial(37;1.27e-34)|OV - Ovarian serous cystadenocarcinoma(80;3.8e-22)															---	---	---	---
IGF2BP2	10644	broad.mit.edu	37	3	185363401	185363401	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185363401C>T	uc003fpo.2	-	16	1797	c.1718G>A	c.(1717-1719)CGC>CAC	p.R573H	IGF2BP2_uc010hyi.2_Missense_Mutation_p.R516H|IGF2BP2_uc010hyj.2_Missense_Mutation_p.R510H|IGF2BP2_uc010hyk.2_Missense_Mutation_p.R437H|IGF2BP2_uc010hyl.2_Missense_Mutation_p.R467H|IGF2BP2_uc003fpp.2_Missense_Mutation_p.R530H|IGF2BP2_uc003fpq.2_Missense_Mutation_p.R578H	NM_006548	NP_006539	Q9Y6M1	IF2B2_HUMAN	insulin-like growth factor 2 mRNA binding	573	KH 4.				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	185797681	185797681	+	Missense_Mutation	SNP	G	A	A	rs141531791		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185797681G>A	uc003fpz.2	-	7	822	c.575C>T	c.(574-576)GCG>GTG	p.A192V	ETV5_uc003fpy.2_Missense_Mutation_p.A234V	NM_004454	NP_004445	P41161	ETV5_HUMAN	ets variant gene 5 (ets-related molecule)	192					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 								---	---	---	---
EIF4A2	1974	broad.mit.edu	37	3	186504931	186504931	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186504931A>G	uc003fqs.2	+	8	826	c.787A>G	c.(787-789)ACA>GCA	p.T263A	EIF4A2_uc003fqt.2_RNA|EIF4A2_uc003fqu.2_Missense_Mutation_p.T264A|EIF4A2_uc003fqv.2_Missense_Mutation_p.T168A|EIF4A2_uc003fqw.2_Missense_Mutation_p.T168A|EIF4A2_uc011bsb.1_Missense_Mutation_p.T136A|SNORA63_uc010hyw.1_5'Flank|SNORA4_uc010hyx.1_5'Flank	NM_001967	NP_001958	Q14240	IF4A2_HUMAN	eukaryotic translation initiation factor 4A2	263	Helicase C-terminal.				interspecies interaction between organisms|nuclear-transcribed mRNA poly(A) tail shortening|regulation of translational initiation	cytosol|eukaryotic translation initiation factor 4F complex	ATP binding|ATP-dependent helicase activity|protein binding|translation initiation factor activity			ovary(2)|breast(2)	4	all_cancers(143;2.68e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.07e-20)	GBM - Glioblastoma multiforme(93;0.0704)				T	BCL6	NHL								---	---	---	---
MASP1	5648	broad.mit.edu	37	3	186954151	186954151	+	Intron	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186954151C>T	uc003frh.1	-						MASP1_uc003fri.2_Missense_Mutation_p.R503H|MASP1_uc003frj.2_Missense_Mutation_p.R472H	NM_001879	NP_001870			mannan-binding lectin serine protease 1 isoform						complement activation, lectin pathway|negative regulation of complement activation|proteolysis	extracellular space	calcium ion binding|calcium-dependent protein binding|protein binding|protein homodimerization activity|serine-type endopeptidase activity			ovary(2)|breast(1)|liver(1)	4	all_cancers(143;5.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;3.49e-18)	GBM - Glioblastoma multiforme(93;0.0366)														---	---	---	---
TNK2	10188	broad.mit.edu	37	3	195594482	195594482	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195594482C>A	uc003fvu.1	-	12	3185	c.2642G>T	c.(2641-2643)AGC>ATC	p.S881I	TNK2_uc003fvq.1_Missense_Mutation_p.S288I|TNK2_uc003fvr.1_Missense_Mutation_p.S406I|TNK2_uc003fvs.1_Missense_Mutation_p.S913I|TNK2_uc003fvt.1_Missense_Mutation_p.S959I|TNK2_uc010hzw.1_RNA	NM_005781	NP_005772	Q07912	ACK1_HUMAN	tyrosine kinase, non-receptor, 2 isoform 1	881	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)													---	---	---	---
PIGX	54965	broad.mit.edu	37	3	196454970	196454970	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196454970G>A	uc010iaj.2	+	4	653	c.372G>A	c.(370-372)GTG>GTA	p.V124V	PIGX_uc003fwx.3_Silent_p.V124V|PIGX_uc011btx.1_RNA	NM_017861	NP_060331	Q8TBF5	PIGX_HUMAN	phosphatidylinositol glycan anchor biosynthesis,	165	Lumenal (Potential).				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)														---	---	---	---
PAK2	5062	broad.mit.edu	37	3	196509566	196509566	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196509566C>T	uc003fwy.3	+	2	371	c.49C>T	c.(49-51)CGA>TGA	p.R17*		NM_002577	NP_002568	Q13177	PAK2_HUMAN	p21-activated kinase 2	17					axon guidance|cellular component disassembly involved in apoptosis|interspecies interaction between organisms|negative regulation of protein kinase activity|peptidyl-serine phosphorylation|positive regulation of peptidyl-tyrosine phosphorylation|protein autophosphorylation|regulation of apoptosis|regulation of defense response to virus by virus|regulation of growth|T cell costimulation|T cell receptor signaling pathway|viral reproduction	cytosol|nucleus|perinuclear region of cytoplasm|plasma membrane	ATP binding|identical protein binding|protein kinase binding|protein serine/threonine kinase activity|protein tyrosine kinase activator activity			ovary(1)|lung(1)	2	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;1.07e-23)|all cancers(36;6.38e-22)|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;0.00405)														---	---	---	---
GAK	2580	broad.mit.edu	37	4	860918	860918	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:860918C>G	uc003gbm.3	-	21	2897	c.2698G>C	c.(2698-2700)GCC>CCC	p.A900P	GAK_uc003gbn.3_Missense_Mutation_p.A821P|GAK_uc010ibk.1_Missense_Mutation_p.A794P|GAK_uc010ibi.2_Missense_Mutation_p.A81P|GAK_uc010ibj.2_RNA|GAK_uc003gbl.3_Missense_Mutation_p.A764P	NM_005255	NP_005246	O14976	GAK_HUMAN	cyclin G associated kinase	900					cell cycle	focal adhesion|Golgi apparatus|perinuclear region of cytoplasm	ATP binding|heat shock protein binding|protein serine/threonine kinase activity			lung(2)|central_nervous_system(1)|skin(1)	4				Colorectal(103;0.219)														---	---	---	---
GAK	2580	broad.mit.edu	37	4	861151	861151	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:861151T>C	uc003gbm.3	-	21	2664	c.2465A>G	c.(2464-2466)GAC>GGC	p.D822G	GAK_uc003gbn.3_Missense_Mutation_p.D743G|GAK_uc010ibk.1_Missense_Mutation_p.D716G|GAK_uc010ibi.2_Missense_Mutation_p.D3G|GAK_uc010ibj.2_RNA|GAK_uc003gbl.3_Missense_Mutation_p.D686G	NM_005255	NP_005246	O14976	GAK_HUMAN	cyclin G associated kinase	822					cell cycle	focal adhesion|Golgi apparatus|perinuclear region of cytoplasm	ATP binding|heat shock protein binding|protein serine/threonine kinase activity			lung(2)|central_nervous_system(1)|skin(1)	4				Colorectal(103;0.219)														---	---	---	---
FAM193A	8603	broad.mit.edu	37	4	2673877	2673877	+	Nonsense_Mutation	SNP	T	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2673877T>A	uc010icl.2	+	11	1587	c.1236T>A	c.(1234-1236)TGT>TGA	p.C412*	FAM193A_uc010ick.2_Nonsense_Mutation_p.C612*|FAM193A_uc003gfd.2_Nonsense_Mutation_p.C412*|FAM193A_uc011bvm.1_Nonsense_Mutation_p.C434*|FAM193A_uc011bvn.1_Nonsense_Mutation_p.C412*|FAM193A_uc011bvo.1_RNA|FAM193A_uc010icm.2_RNA|FAM193A_uc003gfe.2_Nonsense_Mutation_p.C266*	NM_003704	NP_003695	P78312	F193A_HUMAN	hypothetical protein LOC8603	412										ovary(3)	3																		---	---	---	---
ADD1	118	broad.mit.edu	37	4	2906508	2906508	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2906508C>T	uc003gfr.2	+	10	1367	c.1179C>T	c.(1177-1179)TAC>TAT	p.Y393Y	ADD1_uc003gfn.2_Intron|ADD1_uc003gfo.2_Silent_p.Y393Y|ADD1_uc003gfp.2_Silent_p.Y393Y|ADD1_uc003gfq.2_Silent_p.Y393Y|ADD1_uc003gfs.2_Silent_p.Y393Y|ADD1_uc003gft.3_Silent_p.Y393Y	NM_001119	NP_001110	P35611	ADDA_HUMAN	adducin 1 (alpha) isoform a	393					actin filament bundle assembly|barbed-end actin filament capping|cellular component disassembly involved in apoptosis|positive regulation of protein binding	cytosol|F-actin capping protein complex|nucleus|plasma membrane	actin filament binding|calmodulin binding|metal ion binding|protein heterodimerization activity|protein homodimerization activity|spectrin binding|transcription factor binding			ovary(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)														---	---	---	---
ADD1	118	broad.mit.edu	37	4	2916624	2916624	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2916624C>T	uc003gfr.2	+	13	1807	c.1619C>T	c.(1618-1620)ACG>ATG	p.T540M	ADD1_uc003gfn.2_Intron|ADD1_uc003gfo.2_Missense_Mutation_p.T571M|ADD1_uc003gfp.2_Missense_Mutation_p.T540M|ADD1_uc003gfq.2_Missense_Mutation_p.T571M|ADD1_uc003gfs.2_Missense_Mutation_p.T571M	NM_001119	NP_001110	P35611	ADDA_HUMAN	adducin 1 (alpha) isoform a	540					actin filament bundle assembly|barbed-end actin filament capping|cellular component disassembly involved in apoptosis|positive regulation of protein binding	cytosol|F-actin capping protein complex|nucleus|plasma membrane	actin filament binding|calmodulin binding|metal ion binding|protein heterodimerization activity|protein homodimerization activity|spectrin binding|transcription factor binding			ovary(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)														---	---	---	---
LYAR	55646	broad.mit.edu	37	4	4283520	4283520	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:4283520G>T	uc011bvy.1	-	4	370	c.227C>A	c.(226-228)GCG>GAG	p.A76E	LYAR_uc011bvx.1_5'Flank|LYAR_uc003ght.2_Missense_Mutation_p.A76E	NM_001145725	NP_001139197	Q9NX58	LYAR_HUMAN	Ly1 antibody reactive homolog	76						nucleolus	metal ion binding|protein binding				0				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)														---	---	---	---
STK32B	55351	broad.mit.edu	37	4	5468447	5468447	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5468447C>T	uc003gih.1	+	10	991	c.927C>T	c.(925-927)TGC>TGT	p.C309C	STK32B_uc010ida.1_Silent_p.C262C	NM_018401	NP_060871	Q9NY57	ST32B_HUMAN	serine/threonine kinase 32B	309							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	5624508	5624508	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5624508G>A	uc003gij.2	-	14	2311	c.2257C>T	c.(2257-2259)CGC>TGC	p.R753C	EVC2_uc011bwb.1_Missense_Mutation_p.R193C|EVC2_uc003gik.2_Missense_Mutation_p.R673C	NM_147127	NP_667338	Q86UK5	LBN_HUMAN	limbin	753	Potential.					integral to membrane				large_intestine(3)|ovary(2)	5																		---	---	---	---
EVC	2121	broad.mit.edu	37	4	5754686	5754686	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5754686G>A	uc003gil.1	+	9	1406	c.1222G>A	c.(1222-1224)GCT>ACT	p.A408T	EVC_uc003gim.1_RNA|CRMP1_uc003gin.1_Intron	NM_153717	NP_714928	P57679	EVC_HUMAN	Ellis van Creveld syndrome protein	408					muscle organ development	integral to membrane				ovary(1)|skin(1)	2		Myeloproliferative disorder(84;0.117)																---	---	---	---
PPP2R2C	5522	broad.mit.edu	37	4	6377649	6377649	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6377649A>G	uc003gjc.2	-	4	714	c.344T>C	c.(343-345)ATC>ACC	p.I115T	PPP2R2C_uc003gjb.2_Missense_Mutation_p.I98T|PPP2R2C_uc011bwd.1_Missense_Mutation_p.I108T|PPP2R2C_uc011bwe.1_Missense_Mutation_p.I108T|PPP2R2C_uc003gja.2_Missense_Mutation_p.I115T|PPP2R2C_uc003gjd.1_Missense_Mutation_p.I203T	NM_020416	NP_065149	Q9Y2T4	2ABG_HUMAN	gamma isoform of regulatory subunit B55, protein	115	WD 2.				signal transduction	protein phosphatase type 2A complex	protein phosphatase type 2A regulator activity			ovary(1)|kidney(1)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
KIAA0232	9778	broad.mit.edu	37	4	6865064	6865064	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6865064G>A	uc003gjr.3	+	7	3418	c.2955G>A	c.(2953-2955)GGG>GGA	p.G985G	KIAA0232_uc003gjq.3_Silent_p.G985G	NM_014743	NP_055558	Q92628	K0232_HUMAN	hypothetical protein LOC9778	985							ATP binding			ovary(2)	2																		---	---	---	---
AFAP1	60312	broad.mit.edu	37	4	7820796	7820796	+	Intron	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7820796C>T	uc003gkg.1	-						AFAP1_uc011bwk.1_Intron	NM_198595	NP_940997			actin filament associated protein 1							actin cytoskeleton|cytoplasm|focal adhesion	actin binding				0																		---	---	---	---
BOD1L	259282	broad.mit.edu	37	4	13597501	13597501	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13597501C>T	uc003gmz.1	-	12	8204	c.8087G>A	c.(8086-8088)GGA>GAA	p.G2696E		NM_148894	NP_683692	Q8NFC6	BOD1L_HUMAN	biorientation of chromosomes in cell division	2696							DNA binding			ovary(5)|breast(1)	6																		---	---	---	---
BOD1L	259282	broad.mit.edu	37	4	13603238	13603238	+	Silent	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13603238C>A	uc003gmz.1	-	10	5403	c.5286G>T	c.(5284-5286)CTG>CTT	p.L1762L	BOD1L_uc010idr.1_Silent_p.L1099L	NM_148894	NP_683692	Q8NFC6	BOD1L_HUMAN	biorientation of chromosomes in cell division	1762							DNA binding			ovary(5)|breast(1)	6																		---	---	---	---
PROM1	8842	broad.mit.edu	37	4	15982050	15982050	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15982050G>A	uc003goo.2	-	23	2696	c.2484C>T	c.(2482-2484)TAC>TAT	p.Y828Y	PROM1_uc003gor.2_Silent_p.Y828Y|PROM1_uc003gos.2_Silent_p.Y819Y|PROM1_uc003got.2_Silent_p.Y828Y|PROM1_uc003gou.2_Silent_p.Y819Y|PROM1_uc003gop.2_Silent_p.Y819Y|PROM1_uc003goq.3_Silent_p.Y819Y	NM_006017	NP_006008	O43490	PROM1_HUMAN	prominin 1 isoform 1	828	Cytoplasmic (Potential).				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																		---	---	---	---
STIM2	57620	broad.mit.edu	37	4	27024459	27024459	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:27024459C>T	uc003gsh.3	+	13	2583	c.2367C>T	c.(2365-2367)CGC>CGT	p.R789R	STIM2_uc003gsg.3_Silent_p.R781R|STIM2_uc010iex.2_3'UTR|STIM2_uc010iey.2_3'UTR	NM_020860	NP_065911	Q9P246	STIM2_HUMAN	stromal interaction molecule 2	694	Cytoplasmic (Potential).				activation of store-operated calcium channel activity|calcium ion transport|cellular calcium ion homeostasis|negative regulation of calcium ion transport via store-operated calcium channel activity	endoplasmic reticulum membrane|integral to membrane|plasma membrane	calcium channel regulator activity|calcium ion binding|protein binding			central_nervous_system(1)|skin(1)	2		Breast(46;0.0503)																---	---	---	---
PCDH7	5099	broad.mit.edu	37	4	30723234	30723234	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:30723234G>A	uc003gsk.1	+	1	1198	c.190G>A	c.(190-192)GTG>ATG	p.V64M	PCDH7_uc011bxw.1_Missense_Mutation_p.V64M|PCDH7_uc011bxx.1_Missense_Mutation_p.V64M	NM_002589	NP_002580	O60245	PCDH7_HUMAN	protocadherin 7 isoform a precursor	64	Extracellular (Potential).|Cadherin 1.				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	30724012	30724012	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:30724012C>T	uc003gsk.1	+	1	1976	c.968C>T	c.(967-969)CCG>CTG	p.P323L	PCDH7_uc011bxw.1_Missense_Mutation_p.P276L|PCDH7_uc011bxx.1_Missense_Mutation_p.P323L	NM_002589	NP_002580	O60245	PCDH7_HUMAN	protocadherin 7 isoform a precursor	323	Cadherin 3.|Extracellular (Potential).				homophilic cell adhesion	integral to plasma membrane	calcium ion binding			upper_aerodigestive_tract(1)|ovary(1)|liver(1)|skin(1)	4																		---	---	---	---
APBB2	323	broad.mit.edu	37	4	41016202	41016202	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:41016202G>A	uc003gvl.2	-	6	863	c.233C>T	c.(232-234)GCC>GTC	p.A78V	APBB2_uc003gvm.2_Missense_Mutation_p.A78V|APBB2_uc003gvn.2_Missense_Mutation_p.A78V|APBB2_uc011byt.1_Missense_Mutation_p.A61V	NM_173075	NP_775098	Q92870	APBB2_HUMAN	amyloid beta A4 precursor protein-binding,	78					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																		---	---	---	---
GABRA4	2557	broad.mit.edu	37	4	46976326	46976326	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:46976326G>A	uc003gxg.2	-	6	783	c.644C>T	c.(643-645)CCG>CTG	p.P215L		NM_000809	NP_000800	P48169	GBRA4_HUMAN	gamma-aminobutyric acid A receptor, alpha 4	215	Extracellular (Probable).				gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	benzodiazepine receptor activity|chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			ovary(2)|upper_aerodigestive_tract(1)|breast(1)	4					Alprazolam(DB00404)|Ethchlorvynol(DB00189)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Lorazepam(DB00186)|Meprobamate(DB00371)|Midazolam(DB00683)													---	---	---	---
SCFD2	152579	broad.mit.edu	37	4	54231634	54231634	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:54231634A>C	uc003gzu.2	-	1	609	c.475T>G	c.(475-477)TTG>GTG	p.L159V	SCFD2_uc010igm.2_Missense_Mutation_p.L159V	NM_152540	NP_689753	Q8WU76	SCFD2_HUMAN	sec1 family domain containing 2	159					protein transport|vesicle docking involved in exocytosis					ovary(2)|pancreas(1)	3			GBM - Glioblastoma multiforme(3;1.07e-26)|LUSC - Lung squamous cell carcinoma(32;0.0134)															---	---	---	---
CENPC1	1060	broad.mit.edu	37	4	68380266	68380266	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68380266C>T	uc003hdd.1	-	8	1153	c.970G>A	c.(970-972)GCA>ACA	p.A324T	CENPC1_uc010ihj.1_RNA|CENPC1_uc010ihk.1_RNA|CENPC1_uc010ihm.1_Missense_Mutation_p.A324T	NM_001812	NP_001803	Q03188	CENPC_HUMAN	centromere protein C 1	324					mitotic prometaphase	condensed chromosome kinetochore|condensed nuclear chromosome, centromeric region|cytosol	DNA binding			urinary_tract(1)|lung(1)	2																		---	---	---	---
CSN3	1448	broad.mit.edu	37	4	71114881	71114881	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71114881C>T	uc003hfe.3	+	4	312	c.254C>T	c.(253-255)GCT>GTT	p.A85V		NM_005212	NP_005203	P07498	CASK_HUMAN	casein kappa precursor	85						extracellular region	protein binding			ovary(2)|kidney(1)|central_nervous_system(1)	4																		---	---	---	---
PPEF2	5470	broad.mit.edu	37	4	76787346	76787346	+	Missense_Mutation	SNP	C	T	T	rs138384094	byFrequency;by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76787346C>T	uc003hix.2	-	15	2273	c.1916G>A	c.(1915-1917)CGC>CAC	p.R639H	PPEF2_uc003hiy.2_RNA|PPEF2_uc003hiz.1_3'UTR	NM_006239	NP_006230	O14830	PPE2_HUMAN	serine/threonine protein phosphatase with	639					detection of stimulus involved in sensory perception|negative regulation of MAPKKK cascade|negative regulation of peptidyl-threonine phosphorylation|protein dephosphorylation|visual perception	cytoplasm|photoreceptor inner segment|photoreceptor outer segment	calcium ion binding|Hsp70 protein binding|Hsp90 protein binding|iron ion binding|manganese ion binding|mitogen-activated protein kinase kinase kinase binding|protein serine/threonine phosphatase activity			ovary(2)|lung(1)|central_nervous_system(1)	4			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)															---	---	---	---
FRAS1	80144	broad.mit.edu	37	4	79437097	79437097	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79437097C>A	uc003hlb.2	+	66	10759	c.10319C>A	c.(10318-10320)ACC>AAC	p.T3440N		NM_025074	NP_079350	Q86XX4	FRAS1_HUMAN	Fraser syndrome 1	3435	Extracellular (Potential).				cell communication	integral to membrane|plasma membrane	metal ion binding			large_intestine(5)	5																		---	---	---	---
ARHGAP24	83478	broad.mit.edu	37	4	86898809	86898809	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:86898809G>A	uc003hpk.2	+	8	1342	c.893G>A	c.(892-894)CGC>CAC	p.R298H	ARHGAP24_uc003hpl.2_Missense_Mutation_p.R203H|ARHGAP24_uc010ikf.2_Missense_Mutation_p.R213H|ARHGAP24_uc003hpm.2_Missense_Mutation_p.R205H	NM_001025616	NP_001020787	Q8N264	RHG24_HUMAN	Rho GTPase activating protein 24 isoform 1	298	Rho-GAP.				angiogenesis|cell differentiation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cell projection|cytoskeleton|cytosol|focal adhesion	GTPase activator activity|protein binding				0		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000571)														---	---	---	---
SPP1	6696	broad.mit.edu	37	4	88903760	88903760	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88903760C>T	uc003hra.2	+	7	822	c.657C>T	c.(655-657)AGC>AGT	p.S219S	SPP1_uc003hrb.2_Silent_p.S192S|SPP1_uc003hrc.2_Silent_p.S205S|SPP1_uc011cde.1_Silent_p.S232S|SPP1_uc003hrd.2_Silent_p.S178S	NM_001040058	NP_001035147	P10451	OSTP_HUMAN	secreted phosphoprotein 1 isoform a	219					biomineral tissue development|cell adhesion|decidualization|embryo implantation|ossification|response to vitamin D	extracellular space	cytokine activity			ovary(1)	1		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;9.87e-05)														---	---	---	---
RAP1GDS1	5910	broad.mit.edu	37	4	99313170	99313170	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99313170C>T	uc003htx.3	+	6	766	c.576C>T	c.(574-576)CAC>CAT	p.H192H	RAP1GDS1_uc003htu.2_Silent_p.H192H|RAP1GDS1_uc003htw.3_Silent_p.H193H|RAP1GDS1_uc003htv.3_Silent_p.H193H|RAP1GDS1_uc003htz.3_Silent_p.H143H|RAP1GDS1_uc003hty.3_Silent_p.H144H|RAP1GDS1_uc003hua.3_Intron	NM_001100427	NP_001093897	P52306	GDS1_HUMAN	RAP1, GTP-GDP dissociation stimulator 1 isoform	192	ARM 2.						binding|GTPase activator activity			ovary(1)|lung(1)|breast(1)	3				OV - Ovarian serous cystadenocarcinoma(123;2.9e-07)|LUSC - Lung squamous cell carcinoma(1;0.0253)|Lung(1;0.0576)				T	NUP98	T-ALL								---	---	---	---
TET2	54790	broad.mit.edu	37	4	106157341	106157341	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:106157341T>A	uc003hxk.2	+	3	2628	c.2242T>A	c.(2242-2244)TTA>ATA	p.L748I	TET2_uc011cez.1_Missense_Mutation_p.L769I|TET2_uc003hxj.2_RNA|TET2_uc010ilp.1_Missense_Mutation_p.L748I|TET2_uc003hxi.1_Missense_Mutation_p.L748I	NM_001127208	NP_001120680	Q6N021	TET2_HUMAN	tet oncogene family member 2 isoform a	748	Gln-rich.				cell cycle|myeloid cell differentiation		metal ion binding|methylcytosine dioxygenase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			haematopoietic_and_lymphoid_tissue(732)|pancreas(1)	733		Myeloproliferative disorder(5;0.0393)		OV - Ovarian serous cystadenocarcinoma(123;7.18e-08)				Mis N|F		MDS								---	---	---	---
SYNPO2	171024	broad.mit.edu	37	4	119952870	119952870	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119952870A>G	uc003icm.3	+	4	3136	c.2940A>G	c.(2938-2940)CAA>CAG	p.Q980Q	SYNPO2_uc010ina.2_Silent_p.Q980Q|SYNPO2_uc010inb.2_Silent_p.Q980Q|SYNPO2_uc011cgh.1_Intron|SYNPO2_uc010inc.2_Silent_p.Q908Q	NM_001128933	NP_001122405	Q9UMS6	SYNP2_HUMAN	synaptopodin 2 isoform b	980						nucleus|Z disc	14-3-3 protein binding|actin binding|muscle alpha-actinin binding			ovary(2)	2																		---	---	---	---
MAD2L1	4085	broad.mit.edu	37	4	120983144	120983144	+	Silent	SNP	A	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:120983144A>C	uc003idl.2	-	3	451	c.327T>G	c.(325-327)ACT>ACG	p.T109T	MAD2L1_uc003idm.2_Intron	NM_002358	NP_002349	Q13257	MD2L1_HUMAN	MAD2-like 1	109	HORMA.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|negative regulation of apoptosis|negative regulation of mitotic anaphase-promoting complex activity|positive regulation of mitotic cell cycle spindle assembly checkpoint	condensed chromosome kinetochore|cytosol|nucleus|perinuclear region of cytoplasm	protein homodimerization activity				0																		---	---	---	---
BBS7	55212	broad.mit.edu	37	4	122770069	122770069	+	Silent	SNP	G	A	A	rs142376157		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:122770069G>A	uc003ied.2	-	9	1038	c.864C>T	c.(862-864)AGC>AGT	p.S288S	BBS7_uc003iee.1_Silent_p.S288S	NM_176824	NP_789794	Q8IWZ6	BBS7_HUMAN	Bardet-Biedl syndrome 7 protein isoform a	288					cilium morphogenesis|digestive tract morphogenesis|fat cell differentiation|heart looping|melanosome transport|pigment granule aggregation in cell center|response to stimulus|visual perception	BBSome|centrosome|cilium membrane	protein binding			ovary(1)	1														Bardet-Biedl_syndrome				---	---	---	---
SPRY1	10252	broad.mit.edu	37	4	124323363	124323363	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:124323363G>A	uc003ifa.2	+	2	805	c.617G>A	c.(616-618)CGG>CAG	p.R206Q	SPRY1_uc003ifb.2_Missense_Mutation_p.R206Q	NM_199327	NP_955359	O43609	SPY1_HUMAN	sprouty homolog 1, antagonist of FGF signaling	206	Cys-rich.|SPR.				epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway	cytosol|lamellipodium|plasma membrane				skin(2)|ovary(1)	3																		---	---	---	---
FAT4	79633	broad.mit.edu	37	4	126370353	126370353	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:126370353G>A	uc003ifj.3	+	9	8182	c.8182G>A	c.(8182-8184)GTT>ATT	p.V2728I	FAT4_uc011cgp.1_Missense_Mutation_p.V1026I|FAT4_uc003ifi.1_Missense_Mutation_p.V206I	NM_024582	NP_078858	Q6V0I7	FAT4_HUMAN	FAT tumor suppressor homolog 4 precursor	2728	Cadherin 26.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(9)|skin(5)|upper_aerodigestive_tract(2)|pancreas(2)	18																		---	---	---	---
FAT4	79633	broad.mit.edu	37	4	126398366	126398366	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:126398366C>T	uc003ifj.3	+	13	12350	c.12350C>T	c.(12349-12351)CCA>CTA	p.P4117L	FAT4_uc011cgp.1_Missense_Mutation_p.P2380L|FAT4_uc003ifi.1_Missense_Mutation_p.P1595L	NM_024582	NP_078858	Q6V0I7	FAT4_HUMAN	FAT tumor suppressor homolog 4 precursor	4117	Laminin G-like 1.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(9)|skin(5)|upper_aerodigestive_tract(2)|pancreas(2)	18																		---	---	---	---
FAT4	79633	broad.mit.edu	37	4	126411789	126411789	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:126411789C>T	uc003ifj.3	+	17	13812	c.13812C>T	c.(13810-13812)ACC>ACT	p.T4604T	FAT4_uc011cgp.1_Silent_p.T2845T|FAT4_uc003ifi.1_Silent_p.T2081T	NM_024582	NP_078858	Q6V0I7	FAT4_HUMAN	FAT tumor suppressor homolog 4 precursor	4604	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(9)|skin(5)|upper_aerodigestive_tract(2)|pancreas(2)	18																		---	---	---	---
PCDH10	57575	broad.mit.edu	37	4	134071537	134071537	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:134071537G>A	uc003iha.2	+	1	1068	c.242G>A	c.(241-243)CGC>CAC	p.R81H	uc003igy.2_5'Flank|PCDH10_uc003igz.2_Missense_Mutation_p.R81H	NM_032961	NP_116586	Q9P2E7	PCD10_HUMAN	protocadherin 10 isoform 1 precursor	81	Cadherin 1.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2				LUSC - Lung squamous cell carcinoma(193;0.227)														---	---	---	---
PCDH10	57575	broad.mit.edu	37	4	134072675	134072675	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:134072675G>A	uc003iha.2	+	1	2206	c.1380G>A	c.(1378-1380)GCG>GCA	p.A460A	uc003igy.2_5'Flank|PCDH10_uc003igz.2_Silent_p.A460A	NM_032961	NP_116586	Q9P2E7	PCD10_HUMAN	protocadherin 10 isoform 1 precursor	460	Cadherin 4.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2				LUSC - Lung squamous cell carcinoma(193;0.227)														---	---	---	---
LRBA	987	broad.mit.edu	37	4	151773292	151773292	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151773292C>T	uc010ipj.2	-	23	4044	c.3570G>A	c.(3568-3570)ATG>ATA	p.M1190I	LRBA_uc003ilt.3_5'Flank|LRBA_uc003ilu.3_Missense_Mutation_p.M1190I	NM_006726	NP_006717	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and	1190						endoplasmic reticulum|Golgi apparatus|integral to membrane|lysosome|plasma membrane	protein binding			ovary(3)|breast(3)|skin(1)	7	all_hematologic(180;0.151)																	---	---	---	---
FBXW7	55294	broad.mit.edu	37	4	153271192	153271192	+	Splice_Site	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:153271192A>G	uc003ims.2	-	3	733	c.584_splice	c.e3+1	p.S195_splice	FBXW7_uc011cii.1_Splice_Site_p.S195_splice|FBXW7_uc003imt.2_Splice_Site_p.S195_splice|FBXW7_uc011cih.1_5'Flank|FBXW7_uc003imq.2_Splice_Site_p.S115_splice|FBXW7_uc003imr.2_Splice_Site_p.S77_splice	NM_033632	NP_361014			F-box and WD repeat domain containing 7 isoform						interspecies interaction between organisms|lipid homeostasis|negative regulation of DNA endoreduplication|negative regulation of hepatocyte proliferation|negative regulation of Notch signaling pathway|negative regulation of triglyceride biosynthetic process|positive regulation of epidermal growth factor receptor activity|positive regulation of ERK1 and ERK2 cascade|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|protein stabilization|protein ubiquitination|regulation of lipid storage|regulation of protein localization|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process|sister chromatid cohesion|vasculature development	nucleolus|nucleolus|nucleoplasm|nucleoplasm|SCF ubiquitin ligase complex	protein binding|protein binding			haematopoietic_and_lymphoid_tissue(125)|large_intestine(99)|stomach(16)|lung(14)|endometrium(13)|ovary(9)|biliary_tract(8)|upper_aerodigestive_tract(5)|central_nervous_system(3)|kidney(3)|skin(3)|pancreas(3)|breast(2)|prostate(2)|cervix(1)|NS(1)|bone(1)	308	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)						Mis|N|D|F		colorectal|endometrial|T-ALL								---	---	---	---
FHDC1	85462	broad.mit.edu	37	4	153897150	153897150	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:153897150C>T	uc003inf.2	+	11	2782	c.2707C>T	c.(2707-2709)CGC>TGC	p.R903C		NM_033393	NP_203751	Q9C0D6	FHDC1_HUMAN	FH2 domain containing 1	903					actin cytoskeleton organization		actin binding			large_intestine(1)|ovary(1)	2	all_hematologic(180;0.093)																	---	---	---	---
TRIM2	23321	broad.mit.edu	37	4	154243896	154243896	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154243896T>C	uc003ing.2	+	9	1999	c.1798T>C	c.(1798-1800)TTT>CTT	p.F600L	TRIM2_uc003inh.2_Missense_Mutation_p.F627L	NM_001130067	NP_001123539	Q9C040	TRIM2_HUMAN	tripartite motif-containing 2 isoform 2	600	NHL 3.					cytoplasm	zinc ion binding			central_nervous_system(1)	1	all_hematologic(180;0.093)	Medulloblastoma(177;0.00225)		GBM - Glioblastoma multiforme(119;0.0102)|LUSC - Lung squamous cell carcinoma(193;0.0703)														---	---	---	---
DCHS2	54798	broad.mit.edu	37	4	155253791	155253791	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155253791G>A	uc003inw.2	-	9	2072	c.2072C>T	c.(2071-2073)ACC>ATC	p.T691I	DCHS2_uc003inx.2_Missense_Mutation_p.T1190I	NM_017639	NP_060109	Q6V1P9	PCD23_HUMAN	dachsous 2 isoform 1	691	Cadherin 5.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|pancreas(1)	4	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)														---	---	---	---
MAP9	79884	broad.mit.edu	37	4	156289916	156289916	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:156289916C>T	uc003ios.2	-	5	794	c.530G>A	c.(529-531)CGG>CAG	p.R177Q	MAP9_uc011cin.1_Missense_Mutation_p.R176Q|MAP9_uc010iqa.1_RNA|MAP9_uc003iot.1_Missense_Mutation_p.R176Q|MAP9_uc010iqb.1_Missense_Mutation_p.R104Q	NM_001039580	NP_001034669	Q49MG5	MAP9_HUMAN	aster-associated protein	177					cell division|mitosis	cytoplasm|microtubule|spindle				ovary(1)|central_nervous_system(1)	2	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.143)														---	---	---	---
GLRB	2743	broad.mit.edu	37	4	158074033	158074033	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:158074033C>G	uc003ipj.2	+	9	1270	c.1068C>G	c.(1066-1068)AAC>AAG	p.N356K		NM_000824	NP_000815	P48167	GLRB_HUMAN	glycine receptor, beta isoform A precursor	356	Cytoplasmic (Probable).				nervous system development|neuropeptide signaling pathway|startle response	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	extracellular-glycine-gated chloride channel activity|protein binding|receptor activity			skin(2)	2	all_hematologic(180;0.24)	Renal(120;0.0458)		KIRC - Kidney renal clear cell carcinoma(143;0.0564)|COAD - Colon adenocarcinoma(41;0.0642)|Kidney(143;0.0707)	Glycine(DB00145)													---	---	---	---
FAM198B	51313	broad.mit.edu	37	4	159092395	159092395	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159092395C>T	uc003ipp.3	-	2	585	c.133G>A	c.(133-135)GCC>ACC	p.A45T	uc003ipu.1_5'Flank|FAM198B_uc003ipq.3_Missense_Mutation_p.A45T|FAM198B_uc003ipr.3_Missense_Mutation_p.A45T|FAM198B_uc003ips.2_Missense_Mutation_p.A45T|uc003ipt.1_RNA	NM_016613	NP_057697	Q6UWH4	F198B_HUMAN	hypothetical protein LOC51313 isoform 2	45	Helical; Signal-anchor for type II membrane protein; (Potential).					Golgi membrane|integral to membrane					0																		---	---	---	---
KLHL2	11275	broad.mit.edu	37	4	166215608	166215608	+	Silent	SNP	T	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166215608T>G	uc003irb.2	+	6	901	c.642T>G	c.(640-642)TCT>TCG	p.S214S	KLHL2_uc011cjm.1_Silent_p.S218S|KLHL2_uc003irc.2_Silent_p.S126S|KLHL2_uc010ira.2_5'UTR	NM_007246	NP_009177	O95198	KLHL2_HUMAN	kelch-like 2, Mayven isoform 1	214					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)														---	---	---	---
DDX60	55601	broad.mit.edu	37	4	169194431	169194431	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169194431T>C	uc003irp.2	-	18	2865	c.2573A>G	c.(2572-2574)CAG>CGG	p.Q858R		NM_017631	NP_060101	Q8IY21	DDX60_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	858	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)														---	---	---	---
KIAA1712	80817	broad.mit.edu	37	4	175231102	175231102	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:175231102T>C	uc003itr.2	+	8	1194	c.780T>C	c.(778-780)TGT>TGC	p.C260C	KIAA1712_uc010iro.2_Silent_p.C260C|KIAA1712_uc003its.2_RNA	NM_001040157	NP_001035247	Q9C0F1	CEP44_HUMAN	HBV PreS1-transactivated protein 3 isoform a	260	Potential.					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	175598374	175598374	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:175598374T>C	uc003ity.1	-	7	1285	c.782A>G	c.(781-783)TAC>TGC	p.Y261C	GLRA3_uc003itz.1_Missense_Mutation_p.Y261C	NM_006529	NP_006520	O75311	GLRA3_HUMAN	glycine receptor, alpha 3 isoform a	261	Helical; (Probable).				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)													---	---	---	---
ASB5	140458	broad.mit.edu	37	4	177142368	177142368	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:177142368G>A	uc003iuq.1	-	5	624	c.608C>T	c.(607-609)ACT>ATT	p.T203I	ASB5_uc003iup.1_Missense_Mutation_p.T150I	NM_080874	NP_543150	Q8WWX0	ASB5_HUMAN	ankyrin repeat and SOCS box-containing protein	203	ANK 5.				intracellular signal transduction					skin(2)	2		Breast(14;0.00015)|Melanoma(52;0.00886)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;2.13e-20)|Epithelial(43;9.94e-18)|OV - Ovarian serous cystadenocarcinoma(60;2e-09)|GBM - Glioblastoma multiforme(59;0.000254)|STAD - Stomach adenocarcinoma(60;0.000653)|LUSC - Lung squamous cell carcinoma(193;0.0393)														---	---	---	---
VEGFC	7424	broad.mit.edu	37	4	177648991	177648991	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:177648991A>G	uc003ius.1	-	3	923	c.493T>C	c.(493-495)TGC>CGC	p.C165R		NM_005429	NP_005420	P49767	VEGFC_HUMAN	vascular endothelial growth factor C	165					angiogenesis|induction of positive chemotaxis|platelet activation|platelet degranulation|positive regulation of cell division|positive regulation of mast cell chemotaxis|substrate-dependent cell migration|vascular endothelial growth factor receptor signaling pathway	membrane|platelet alpha granule lumen	chemoattractant activity|growth factor activity			lung(5)	5		Breast(14;0.000223)|Renal(120;0.00988)|Prostate(90;0.00996)|Melanoma(52;0.0101)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;1.59e-18)|Epithelial(43;3.68e-16)|OV - Ovarian serous cystadenocarcinoma(60;8.52e-09)|GBM - Glioblastoma multiforme(59;0.000546)|STAD - Stomach adenocarcinoma(60;0.00308)|Colorectal(24;0.025)|COAD - Colon adenocarcinoma(29;0.0359)|LUSC - Lung squamous cell carcinoma(193;0.0397)														---	---	---	---
CDKN2AIP	55602	broad.mit.edu	37	4	184368553	184368553	+	Silent	SNP	A	G	G	rs143559678		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184368553A>G	uc003ivp.1	+	3	1878	c.1716A>G	c.(1714-1716)GCA>GCG	p.A572A	CDKN2AIP_uc003ivq.1_Silent_p.A317A	NM_017632	NP_060102	Q9NXV6	CARF_HUMAN	CDKN2A interacting protein	572					negative regulation of cell growth|positive regulation of signal transduction|regulation of protein stability	granular component|nucleoplasm	double-stranded RNA binding|p53 binding				0		all_lung(41;6.9e-12)|Lung NSC(41;1.28e-11)|Colorectal(36;0.00435)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_hematologic(60;0.0749)		all cancers(43;1.15e-26)|Epithelial(43;2.98e-22)|OV - Ovarian serous cystadenocarcinoma(60;7.64e-10)|GBM - Glioblastoma multiforme(59;4.22e-06)|Colorectal(24;5.87e-06)|STAD - Stomach adenocarcinoma(60;2.09e-05)|COAD - Colon adenocarcinoma(29;5.15e-05)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.155)														---	---	---	---
C4orf41	60684	broad.mit.edu	37	4	184585026	184585026	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184585026C>T	uc003ivx.2	+	2	182	c.6C>T	c.(4-6)AGC>AGT	p.S2S	C4orf41_uc003ivw.2_Silent_p.S2S|C4orf41_uc010isc.2_5'UTR	NM_021942	NP_068761	Q7Z392	CD041_HUMAN	hypothetical protein LOC60684 isoform a	2											0		all_lung(41;4.4e-14)|Lung NSC(41;1.03e-13)|Colorectal(36;0.00139)|all_hematologic(60;0.00756)|Hepatocellular(41;0.00826)|Renal(120;0.00988)|Prostate(90;0.0235)|all_neural(102;0.202)		all cancers(43;1.39e-26)|Epithelial(43;2.42e-22)|OV - Ovarian serous cystadenocarcinoma(60;6.85e-10)|GBM - Glioblastoma multiforme(59;6.71e-06)|Colorectal(24;9.67e-06)|STAD - Stomach adenocarcinoma(60;2.36e-05)|COAD - Colon adenocarcinoma(29;7.07e-05)|LUSC - Lung squamous cell carcinoma(40;0.00984)|READ - Rectum adenocarcinoma(43;0.171)														---	---	---	---
CCDC111	201973	broad.mit.edu	37	4	185593391	185593391	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:185593391C>T	uc003iwk.2	+	7	1054	c.621C>T	c.(619-621)AGC>AGT	p.S207S	CCDC111_uc010isd.1_RNA|CCDC111_uc003iwj.2_Silent_p.S207S|CCDC111_uc003iwl.2_Silent_p.S207S|CCDC111_uc003iwm.2_Silent_p.S78S|CCDC111_uc003iwn.2_Silent_p.S32S	NM_152683	NP_689896	Q96LW4	CC111_HUMAN	coiled-coil domain containing 111	207					DNA replication, synthesis of RNA primer		DNA primase activity			central_nervous_system(1)	1		all_lung(41;9.65e-12)|Lung NSC(41;1.64e-11)|Colorectal(36;0.00531)|Hepatocellular(41;0.00932)|Renal(120;0.0246)|Prostate(90;0.0283)|all_hematologic(60;0.0749)|all_neural(102;0.131)		all cancers(43;5.84e-27)|Epithelial(43;2.2e-23)|OV - Ovarian serous cystadenocarcinoma(60;4.28e-11)|STAD - Stomach adenocarcinoma(60;2.66e-05)|GBM - Glioblastoma multiforme(59;3.03e-05)|Colorectal(24;7.57e-05)|BRCA - Breast invasive adenocarcinoma(30;0.000249)|COAD - Colon adenocarcinoma(29;0.000502)|LUSC - Lung squamous cell carcinoma(40;0.00995)|READ - Rectum adenocarcinoma(43;0.173)														---	---	---	---
CCDC110	256309	broad.mit.edu	37	4	186381064	186381064	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186381064G>T	uc003ixu.3	-	6	753	c.677C>A	c.(676-678)ACT>AAT	p.T226N	CCDC110_uc003ixv.3_Missense_Mutation_p.T189N|CCDC110_uc011ckt.1_Missense_Mutation_p.T226N	NM_152775	NP_689988	Q8TBZ0	CC110_HUMAN	coiled-coil domain containing 110 isoform a	226						nucleus				central_nervous_system(1)	1		all_lung(41;1.3e-11)|Lung NSC(41;2.25e-11)|Melanoma(20;7.86e-05)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|Colorectal(36;0.0381)|all_hematologic(60;0.0749)		OV - Ovarian serous cystadenocarcinoma(60;1.13e-10)|BRCA - Breast invasive adenocarcinoma(30;8.01e-05)|GBM - Glioblastoma multiforme(59;0.00014)|STAD - Stomach adenocarcinoma(60;0.000777)|LUSC - Lung squamous cell carcinoma(40;0.00921)|COAD - Colon adenocarcinoma(29;0.0105)|READ - Rectum adenocarcinoma(43;0.164)														---	---	---	---
F11	2160	broad.mit.edu	37	4	187195296	187195296	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187195296C>A	uc003iza.1	+	5	685	c.352C>A	c.(352-354)CTA>ATA	p.L118I	F11_uc003iyz.2_Missense_Mutation_p.L118I	NM_000128	NP_000119	P03951	FA11_HUMAN	coagulation factor XI precursor	118	Apple 2.				blood coagulation, intrinsic pathway|plasminogen activation|positive regulation of fibrinolysis	extracellular space|plasma membrane	heparin binding|serine-type endopeptidase activity				0		all_cancers(14;6.2e-52)|all_epithelial(14;1.62e-38)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|Colorectal(36;0.0161)|all_neural(102;0.202)		OV - Ovarian serous cystadenocarcinoma(60;2.13e-11)|BRCA - Breast invasive adenocarcinoma(30;4.59e-06)|GBM - Glioblastoma multiforme(59;0.000149)|STAD - Stomach adenocarcinoma(60;0.000314)|LUSC - Lung squamous cell carcinoma(40;0.00112)|READ - Rectum adenocarcinoma(43;0.176)	Coagulation Factor IX(DB00100)													---	---	---	---
FAM173B	134145	broad.mit.edu	37	5	10239183	10239183	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10239183C>T	uc003jeo.2	-	2	331	c.302G>A	c.(301-303)CGC>CAC	p.R101H	FAM173B_uc003jep.2_RNA|FAM173B_uc010itr.2_Missense_Mutation_p.R101H	NM_199133	NP_954584	Q6P4H8	F173B_HUMAN	hypothetical protein LOC134145	101						integral to membrane				kidney(1)|central_nervous_system(1)	2																		---	---	---	---
DNAH5	1767	broad.mit.edu	37	5	13845019	13845019	+	Missense_Mutation	SNP	G	A	A	rs146087064		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13845019G>A	uc003jfd.2	-	32	5240	c.5198C>T	c.(5197-5199)TCG>TTG	p.S1733L		NM_001369	NP_001360	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	1733	Stem (By similarity).				microtubule-based movement	cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(14)|skin(13)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|pancreas(1)	31	Lung NSC(4;0.00476)													Kartagener_syndrome				---	---	---	---
MYO10	4651	broad.mit.edu	37	5	16699619	16699619	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16699619G>A	uc003jft.3	-	26	3964	c.3496C>T	c.(3496-3498)CGT>TGT	p.R1166C	MYO10_uc011cnc.1_Missense_Mutation_p.R45C|MYO10_uc011cnd.1_Missense_Mutation_p.R523C|MYO10_uc011cne.1_Missense_Mutation_p.R523C|MYO10_uc010itx.2_Missense_Mutation_p.R789C	NM_012334	NP_036466	Q9HD67	MYO10_HUMAN	myosin X	1166					axon guidance|signal transduction	myosin complex	actin binding|ATP binding|motor activity			ovary(2)|pancreas(1)	3																		---	---	---	---
MYO10	4651	broad.mit.edu	37	5	16764481	16764481	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16764481C>T	uc003jft.3	-	12	1672	c.1204G>A	c.(1204-1206)GCC>ACC	p.A402T	MYO10_uc010itx.2_Missense_Mutation_p.A25T	NM_012334	NP_036466	Q9HD67	MYO10_HUMAN	myosin X	402	Myosin head-like.				axon guidance|signal transduction	myosin complex	actin binding|ATP binding|motor activity			ovary(2)|pancreas(1)	3																		---	---	---	---
RNASEN	29102	broad.mit.edu	37	5	31515179	31515179	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31515179C>T	uc003jhg.2	-	7	1565	c.1206G>A	c.(1204-1206)GAG>GAA	p.E402E	RNASEN_uc003jhh.2_Silent_p.E365E|RNASEN_uc003jhi.2_Silent_p.E365E|RNASEN_uc010iui.1_Silent_p.E325E	NM_013235	NP_037367	Q9NRR4	RNC_HUMAN	ribonuclease III, nuclear isoform 1	402					gene silencing by RNA|ribosome biogenesis|RNA processing	nucleolus|nucleoplasm	double-stranded RNA binding|metal ion binding|protein binding|ribonuclease III activity				0																		---	---	---	---
PDZD2	23037	broad.mit.edu	37	5	32069705	32069705	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32069705G>A	uc003jhl.2	+	15	2870	c.2482G>A	c.(2482-2484)GCA>ACA	p.A828T	PDZD2_uc003jhm.2_Missense_Mutation_p.A828T|PDZD2_uc011cnx.1_Missense_Mutation_p.A654T	NM_178140	NP_835260	O15018	PDZD2_HUMAN	PDZ domain containing 2	828					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	32088835	32088835	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32088835A>G	uc003jhl.2	+	20	5669	c.5281A>G	c.(5281-5283)AGT>GGT	p.S1761G	PDZD2_uc003jhm.2_Missense_Mutation_p.S1761G	NM_178140	NP_835260	O15018	PDZD2_HUMAN	PDZ domain containing 2	1761					cell adhesion	cell-cell junction|endoplasmic reticulum|extracellular region|nucleus				central_nervous_system(4)|ovary(2)|skin(2)|large_intestine(1)	9																		---	---	---	---
ADAMTS12	81792	broad.mit.edu	37	5	33576232	33576232	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33576232A>G	uc003jia.1	-	19	4062	c.3899T>C	c.(3898-3900)CTA>CCA	p.L1300P	ADAMTS12_uc010iuq.1_Missense_Mutation_p.L1215P	NM_030955	NP_112217	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1	1300	Spacer 2.				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)			---	---	---	---
NIPBL	25836	broad.mit.edu	37	5	36976272	36976272	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36976272G>A	uc003jkl.3	+	9	1762	c.1263G>A	c.(1261-1263)TCG>TCA	p.S421S	NIPBL_uc003jkk.3_Silent_p.S421S|NIPBL_uc003jkm.1_Silent_p.S300S	NM_133433	NP_597677	Q6KC79	NIPBL_HUMAN	delangin isoform A	421	Gln-rich.				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	37022373	37022373	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37022373C>T	uc003jkl.3	+	29	5954	c.5455C>T	c.(5455-5457)CGA>TGA	p.R1819*	NIPBL_uc003jkk.3_Nonsense_Mutation_p.R1819*	NM_133433	NP_597677	Q6KC79	NIPBL_HUMAN	delangin isoform A	1819					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)															---	---	---	---
LIFR	3977	broad.mit.edu	37	5	38506042	38506042	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38506042G>A	uc010ive.1	-	9	1588	c.1256C>T	c.(1255-1257)TCA>TTA	p.S419L	LIFR_uc003jli.2_Missense_Mutation_p.S419L	NM_001127671	NP_001121143	P42702	LIFR_HUMAN	leukemia inhibitory factor receptor precursor	419	Fibronectin type-III 2.|Extracellular (Potential).				positive regulation of cell proliferation	extracellular region|integral to plasma membrane	ciliary neurotrophic factor receptor binding|growth factor binding|leukemia inhibitory factor receptor activity			ovary(3)|large_intestine(1)	4	all_lung(31;0.00021)							T	PLAG1	salivary adenoma								---	---	---	---
PLCXD3	345557	broad.mit.edu	37	5	41382224	41382224	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41382224T>C	uc003jmm.1	-	2	618	c.516A>G	c.(514-516)CCA>CCG	p.P172P		NM_001005473	NP_001005473	Q63HM9	PLCX3_HUMAN	phosphatidylinositol-specific phospholipase C, X	172	PI-PLC X-box.				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																		---	---	---	---
ISL1	3670	broad.mit.edu	37	5	50680484	50680484	+	Silent	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:50680484G>T	uc003jor.2	+	2	686	c.138G>T	c.(136-138)GCG>GCT	p.A46A	uc003joq.1_5'Flank	NM_002202	NP_002193	P61371	ISL1_HUMAN	islet-1	46	LIM zinc-binding 1.				generation of precursor metabolites and energy|multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			central_nervous_system(2)|ovary(1)	3		Lung NSC(810;0.000845)|Breast(144;0.0411)																---	---	---	---
ITGA1	3672	broad.mit.edu	37	5	52214554	52214554	+	Intron	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:52214554G>A	uc003jou.2	+						ITGA1_uc003jov.2_Intron|ITGA1_uc003jow.2_Intron	NM_181501	NP_852478			integrin, alpha 1 precursor						axon guidance|cell-matrix adhesion|integrin-mediated signaling pathway|muscle contraction	integrin complex	collagen binding|receptor activity			ovary(2)|lung(1)	3		Lung NSC(810;5.05e-05)|Breast(144;0.0851)																---	---	---	---
ARL15	54622	broad.mit.edu	37	5	53409092	53409092	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:53409092A>G	uc003jpg.1	-	4	496	c.402T>C	c.(400-402)ACT>ACC	p.T134T	ARL15_uc010ivs.1_RNA	NM_019087	NP_061960	Q9NXU5	ARL15_HUMAN	ADP-ribosylation factor-like 15	134							GTP binding			ovary(1)	1		Lung NSC(810;0.000779)																---	---	---	---
MAP3K1	4214	broad.mit.edu	37	5	56177584	56177584	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56177584C>T	uc003jqw.3	+	14	3058	c.2557C>T	c.(2557-2559)CGT>TGT	p.R853C		NM_005921	NP_005912	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase	853					cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	cytosol	ATP binding|zinc ion binding			ovary(1)|skin(1)	2		Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;6.08e-40)														---	---	---	---
ADAMTS6	11174	broad.mit.edu	37	5	64537967	64537967	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64537967G>A	uc003jtp.2	-	15	2711	c.1897C>T	c.(1897-1899)CGA>TGA	p.R633*	ADAMTS6_uc003jto.2_RNA|ADAMTS6_uc003jtq.2_RNA|ADAMTS6_uc003jtr.1_Nonsense_Mutation_p.R254*	NM_197941	NP_922932	Q9UKP5	ATS6_HUMAN	ADAM metallopeptidase with thrombospondin type 1	633					proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding				0		Lung NSC(167;2.44e-06)|Prostate(74;0.014)|Ovarian(174;0.0549)|Breast(144;0.111)|Colorectal(97;0.235)		Lung(70;0.00942)														---	---	---	---
ADAMTS6	11174	broad.mit.edu	37	5	64556430	64556430	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64556430T>C	uc003jtp.2	-	14	2641	c.1827A>G	c.(1825-1827)ACA>ACG	p.T609T	ADAMTS6_uc003jto.2_RNA|ADAMTS6_uc003jtq.2_RNA|ADAMTS6_uc003jtr.1_Silent_p.T230T	NM_197941	NP_922932	Q9UKP5	ATS6_HUMAN	ADAM metallopeptidase with thrombospondin type 1	609	TSP type-1 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)														---	---	---	---
BDP1	55814	broad.mit.edu	37	5	70840949	70840949	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:70840949C>T	uc003kbp.1	+	32	6910	c.6647C>T	c.(6646-6648)ACA>ATA	p.T2216I	BDP1_uc003kbo.2_Missense_Mutation_p.T2216I|BDP1_uc003kbq.1_RNA|BDP1_uc003kbr.1_RNA	NM_018429	NP_060899	A6H8Y1	BDP1_HUMAN	transcription factor-like nuclear regulator	2216					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)														---	---	---	---
MAP1B	4131	broad.mit.edu	37	5	71495820	71495820	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:71495820G>A	uc003kbw.3	+	5	6879	c.6638G>A	c.(6637-6639)CGC>CAC	p.R2213H	MAP1B_uc010iyw.1_Missense_Mutation_p.R2230H|MAP1B_uc010iyx.1_Missense_Mutation_p.R2087H|MAP1B_uc010iyy.1_Missense_Mutation_p.R2087H	NM_005909	NP_005900	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	2213						microtubule|microtubule associated complex	structural molecule activity			large_intestine(2)|ovary(1)|central_nervous_system(1)|pancreas(1)	5		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)														---	---	---	---
RGNEF	64283	broad.mit.edu	37	5	73188008	73188008	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:73188008G>T	uc011csq.1	+	26	3530	c.3519G>T	c.(3517-3519)AAG>AAT	p.K1173N	RGNEF_uc003kcx.2_Missense_Mutation_p.K1173N|RGNEF_uc010izf.2_Missense_Mutation_p.K1173N|RGNEF_uc011csr.1_Missense_Mutation_p.K860N|RGNEF_uc003kcz.3_Missense_Mutation_p.K137N|RGNEF_uc003kda.3_Missense_Mutation_p.K137N	NM_001080479	NP_001073948	Q8N1W1	RGNEF_HUMAN	Rho-guanine nucleotide exchange factor	1173	PH.				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)														---	---	---	---
HMGCR	3156	broad.mit.edu	37	5	74643146	74643146	+	Intron	SNP	A	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74643146A>T	uc003kdp.2	+						HMGCR_uc011cst.1_Intron|HMGCR_uc003kdq.2_Intron|HMGCR_uc010izn.1_Intron	NM_000859	NP_000850			3-hydroxy-3-methylglutaryl-Coenzyme A reductase						cholesterol biosynthetic process|coenzyme A metabolic process|germ cell migration|gonad development|isoprenoid biosynthetic process	endoplasmic reticulum membrane|integral to membrane|peroxisomal membrane	hydroxymethylglutaryl-CoA reductase (NADPH) activity|NADP binding			ovary(1)	1		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Prostate(461;0.174)		OV - Ovarian serous cystadenocarcinoma(47;2.24e-54)	Atorvastatin(DB01076)|Bezafibrate(DB01393)|Cerivastatin(DB00439)|Fluvastatin(DB01095)|Lovastatin(DB00227)|NADH(DB00157)|Pravastatin(DB00175)|Rosuvastatin(DB01098)|Simvastatin(DB00641)													---	---	---	---
HMGCR	3156	broad.mit.edu	37	5	74655088	74655088	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74655088G>A	uc003kdp.2	+	17	2407	c.2251G>A	c.(2251-2253)GCC>ACC	p.A751T	HMGCR_uc011cst.1_Missense_Mutation_p.A771T|HMGCR_uc003kdq.2_Missense_Mutation_p.A698T|HMGCR_uc010izo.2_Missense_Mutation_p.A74T|HMGCR_uc010izp.2_Intron	NM_000859	NP_000850	P04035	HMDH_HUMAN	3-hydroxy-3-methylglutaryl-Coenzyme A reductase	751	Catalytic.				cholesterol biosynthetic process|coenzyme A metabolic process|germ cell migration|gonad development|isoprenoid biosynthetic process	endoplasmic reticulum membrane|integral to membrane|peroxisomal membrane	hydroxymethylglutaryl-CoA reductase (NADPH) activity|NADP binding			ovary(1)	1		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Prostate(461;0.174)		OV - Ovarian serous cystadenocarcinoma(47;2.24e-54)	Atorvastatin(DB01076)|Bezafibrate(DB01393)|Cerivastatin(DB00439)|Fluvastatin(DB01095)|Lovastatin(DB00227)|NADH(DB00157)|Pravastatin(DB00175)|Rosuvastatin(DB01098)|Simvastatin(DB00641)													---	---	---	---
SV2C	22987	broad.mit.edu	37	5	75596664	75596664	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75596664T>A	uc003kei.1	+	11	1881	c.1747T>A	c.(1747-1749)TAT>AAT	p.Y583N		NM_014979	NP_055794	Q496J9	SV2C_HUMAN	synaptic vesicle glycoprotein 2C	583	Helical; (Potential).				neurotransmitter transport	cell junction|integral to membrane|synaptic vesicle membrane	transmembrane transporter activity			skin(1)	1		all_lung(232;0.007)|Lung NSC(167;0.0148)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;1.16e-50)|all cancers(79;7.25e-40)														---	---	---	---
WDR41	55255	broad.mit.edu	37	5	76788019	76788019	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76788019G>A	uc003kff.1	-	1	314	c.27C>T	c.(25-27)GGC>GGT	p.G9G	WDR41_uc011csy.1_Silent_p.G9G|WDR41_uc011csz.1_Silent_p.G9G|WDR41_uc011cta.1_RNA|WDR41_uc011ctb.1_RNA	NM_018268	NP_060738	Q9HAD4	WDR41_HUMAN	WD repeat domain 41	9											0		all_lung(232;0.000961)|Lung NSC(167;0.0011)|Ovarian(174;0.0105)|Prostate(461;0.059)		OV - Ovarian serous cystadenocarcinoma(54;6.3e-50)|Epithelial(54;2.04e-44)|all cancers(79;6.84e-40)														---	---	---	---
BHMT2	23743	broad.mit.edu	37	5	78379171	78379171	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78379171T>C	uc003kft.2	+	6	778	c.755T>C	c.(754-756)TTT>TCT	p.F252S	BHMT2_uc011cth.1_Missense_Mutation_p.F188S	NM_017614	NP_060084	Q9H2M3	BHMT2_HUMAN	betaine-homocysteine methyltransferase 2	252	Hcy-binding.				methionine biosynthetic process	cytoplasm	betaine-homocysteine S-methyltransferase activity|homocysteine S-methyltransferase activity|zinc ion binding			ovary(1)	1		all_lung(232;0.00063)|Lung NSC(167;0.00171)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;2.09e-45)|Epithelial(54;9.3e-41)|all cancers(79;4.09e-36)	L-Methionine(DB00134)													---	---	---	---
JMY	133746	broad.mit.edu	37	5	78596523	78596523	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78596523A>G	uc003kfx.3	+	6	2238	c.1718A>G	c.(1717-1719)TAT>TGT	p.Y573C	JMY_uc003kfw.1_Missense_Mutation_p.Y219C	NM_152405	NP_689618	Q8N9B5	JMY_HUMAN	junction-mediating and regulatory protein	573					'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)														---	---	---	---
MSH3	4437	broad.mit.edu	37	5	79974921	79974921	+	Intron	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79974921G>A	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					---	---	---	---
RPS23	6228	broad.mit.edu	37	5	81573573	81573573	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:81573573C>T	uc003khu.2	-	2	196	c.103G>A	c.(103-105)GCC>ACC	p.A35T	ATP6AP1L_uc003khv.2_5'Flank	NM_001025	NP_001016	P62266	RS23_HUMAN	ribosomal protein S23	35					endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic small ribosomal subunit	protein binding|structural constituent of ribosome				0		Lung NSC(167;0.0025)|all_lung(232;0.00278)|Ovarian(174;0.0336)		OV - Ovarian serous cystadenocarcinoma(54;1.94e-42)|Epithelial(54;8.38e-37)|all cancers(79;1.42e-31)														---	---	---	---
VCAN	1462	broad.mit.edu	37	5	82833950	82833950	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:82833950G>A	uc003kii.3	+	8	5484	c.5128G>A	c.(5128-5130)GAC>AAC	p.D1710N	VCAN_uc003kij.3_Missense_Mutation_p.D723N|VCAN_uc010jau.2_Intron|VCAN_uc003kik.3_Intron|VCAN_uc003kil.3_Missense_Mutation_p.D374N	NM_004385	NP_004376	P13611	CSPG2_HUMAN	versican isoform 1 precursor	1710	GAG-beta.				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	83402507	83402507	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:83402507G>A	uc003kio.1	-	6	1030	c.611C>T	c.(610-612)GCG>GTG	p.A204V	EDIL3_uc003kip.1_Missense_Mutation_p.A194V	NM_005711	NP_005702	O43854	EDIL3_HUMAN	EGF-like repeats and discoidin I-like	204	F5/8 type C 1.				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)														---	---	---	---
NR2F1	7025	broad.mit.edu	37	5	92923897	92923897	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:92923897C>T	uc003kkj.2	+	2	2425	c.738C>T	c.(736-738)ACC>ACT	p.T246T		NM_005654	NP_005645	P10589	COT1_HUMAN	nuclear receptor subfamily 2, group F, member 1	246					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)														---	---	---	---
SPATA9	83890	broad.mit.edu	37	5	95011143	95011143	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:95011143C>T	uc003klj.1	-	3	507	c.351G>A	c.(349-351)GCG>GCA	p.A117A	SPATA9_uc010jbh.1_RNA|SPATA9_uc003klh.1_RNA|SPATA9_uc003kli.1_Intron	NM_031952	NP_114158	Q9BWV2	SPAT9_HUMAN	spermatogenesis associated 9	117					cell differentiation|multicellular organismal development|spermatogenesis	integral to membrane					0		all_cancers(142;1.28e-06)|all_epithelial(76;1.55e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.00473)|Colorectal(57;0.0846)|Breast(839;0.198)		all cancers(79;8.91e-16)														---	---	---	---
ST8SIA4	7903	broad.mit.edu	37	5	100222222	100222222	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:100222222A>G	uc003knk.2	-	3	656	c.328T>C	c.(328-330)TAT>CAT	p.Y110H	ST8SIA4_uc003knl.2_Missense_Mutation_p.Y110H	NM_005668	NP_005659	Q92187	SIA8D_HUMAN	ST8 alpha-N-acetyl-neuraminide	110	Lumenal (Potential).				axon guidance|N-glycan processing	integral to Golgi membrane	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity			large_intestine(1)|central_nervous_system(1)	2		all_cancers(142;1.5e-07)|all_epithelial(76;1.43e-10)|Prostate(80;0.000644)|Lung NSC(167;0.0059)|all_lung(232;0.00914)|Ovarian(225;0.024)|Colorectal(57;0.09)|Breast(839;0.203)		COAD - Colon adenocarcinoma(37;0.00402)														---	---	---	---
NUDT12	83594	broad.mit.edu	37	5	102890483	102890483	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:102890483G>A	uc003koi.2	-	5	1129	c.1036C>T	c.(1036-1038)CCC>TCC	p.P346S	NUDT12_uc011cvb.1_Missense_Mutation_p.P328S	NM_031438	NP_113626	Q9BQG2	NUD12_HUMAN	nudix-type motif 12	346	Nudix hydrolase.					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)														---	---	---	---
FAM170A	340069	broad.mit.edu	37	5	118965518	118965518	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118965518G>A	uc003ksm.2	+	1	265	c.55G>A	c.(55-57)GCT>ACT	p.A19T	FAM170A_uc003ksl.2_Missense_Mutation_p.A19T|FAM170A_uc003ksn.2_Missense_Mutation_p.A19T|FAM170A_uc003kso.2_Missense_Mutation_p.A19T	NM_182761	NP_877438	A1A519	F170A_HUMAN	family with sequence similarity 170, member A	19						intracellular	zinc ion binding			skin(1)	1																		---	---	---	---
ZNF608	57507	broad.mit.edu	37	5	124036739	124036739	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:124036739A>G	uc003ktq.1	-	2	1253	c.1130T>C	c.(1129-1131)TTG>TCG	p.L377S	ZNF608_uc003ktr.1_RNA|ZNF608_uc003kts.1_Missense_Mutation_p.L377S|ZNF608_uc003ktt.1_Missense_Mutation_p.L377S	NM_020747	NP_065798	Q9ULD9	ZN608_HUMAN	zinc finger protein 608	377						intracellular	zinc ion binding			skin(3)|ovary(2)|lung(1)	6		all_cancers(142;0.186)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.00126)|Epithelial(69;0.00238)|all cancers(49;0.00783)														---	---	---	---
GRAMD3	65983	broad.mit.edu	37	5	125824495	125824495	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:125824495G>A	uc003ktu.2	+	13	1598	c.1168G>A	c.(1168-1170)GCA>ACA	p.A390T	GRAMD3_uc011cwt.1_Missense_Mutation_p.A405T|GRAMD3_uc011cwv.1_Missense_Mutation_p.A398T|GRAMD3_uc011cww.1_Missense_Mutation_p.A286T|GRAMD3_uc011cwx.1_RNA|GRAMD3_uc011cwy.1_Missense_Mutation_p.A281T|GRAMD3_uc011cwz.1_Missense_Mutation_p.A374T	NM_023927	NP_076416	Q96HH9	GRAM3_HUMAN	GRAM domain containing 3 isoform 2	390										central_nervous_system(1)	1		Prostate(80;0.0928)	KIRC - Kidney renal clear cell carcinoma(527;0.0584)|Kidney(363;0.0934)	Epithelial(69;0.0401)|OV - Ovarian serous cystadenocarcinoma(64;0.0604)|all cancers(49;0.108)														---	---	---	---
MEGF10	84466	broad.mit.edu	37	5	126781226	126781226	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:126781226G>A	uc003kuh.3	+	21	2931	c.2569G>A	c.(2569-2571)GGG>AGG	p.G857R	MEGF10_uc003kui.3_Missense_Mutation_p.G857R	NM_032446	NP_115822	Q96KG7	MEG10_HUMAN	multiple EGF-like-domains 10 precursor	857	Extracellular (Potential).|Necessary for interaction with AP2M1, self-assembly and formation of the irregular, mosaic-like adhesion pattern.				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)														---	---	---	---
ADAMTS19	171019	broad.mit.edu	37	5	128983558	128983558	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:128983558G>A	uc003kvb.1	+	12	1955	c.1955G>A	c.(1954-1956)GGG>GAG	p.G652E	ADAMTS19_uc010jdh.1_RNA	NM_133638	NP_598377	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1	652	TSP type-1 1.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(5)|breast(2)|lung(1)|skin(1)	9		all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.222)														---	---	---	---
RAPGEF6	51735	broad.mit.edu	37	5	130846113	130846113	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:130846113G>A	uc003kvn.1	-	8	905	c.699C>T	c.(697-699)GAC>GAT	p.D233D	RAPGEF6_uc003kvp.1_Silent_p.D283D|RAPGEF6_uc003kvo.1_Silent_p.D233D|RAPGEF6_uc010jdi.1_Silent_p.D233D|RAPGEF6_uc010jdj.1_Silent_p.D233D|RAPGEF6_uc003kvq.2_5'Flank|RAPGEF6_uc003kvr.2_Silent_p.D233D|RAPGEF6_uc011cxe.1_RNA|RAPGEF6_uc010jdk.2_Silent_p.D233D	NM_016340	NP_057424	Q8TEU7	RPGF6_HUMAN	PDZ domain-containing guanine nucleotide	233					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)														---	---	---	---
PPP2CA	5515	broad.mit.edu	37	5	133536739	133536739	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133536739C>T	uc003kze.2	-	4	911	c.513G>A	c.(511-513)TCG>TCA	p.S171S		NM_002715	NP_002706	P67775	PP2AA_HUMAN	protein phosphatase 2, catalytic subunit, alpha	171					ceramide metabolic process|inactivation of MAPK activity|induction of apoptosis|meiosis|negative regulation of cell growth|negative regulation of epithelial to mesenchymal transition|negative regulation of tyrosine phosphorylation of Stat3 protein|positive regulation of protein serine/threonine kinase activity|protein dephosphorylation|regulation of cell adhesion|regulation of DNA replication|regulation of transcription, DNA-dependent|regulation of Wnt receptor signaling pathway|response to organic substance|RNA splicing|second-messenger-mediated signaling	chromosome, centromeric region|cytosol|mitochondrion|nucleus|protein phosphatase type 2A complex|soluble fraction|spindle pole	metal ion binding|phosphoprotein phosphatase activity			ovary(2)|lung(1)|skin(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		Vitamin E(DB00163)													---	---	---	---
TXNDC15	79770	broad.mit.edu	37	5	134229174	134229174	+	Intron	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134229174T>C	uc003lac.1	+						TXNDC15_uc010jdy.1_Intron|TXNDC15_uc011cxv.1_Intron	NM_024715	NP_078991			disulfide isomerase precursor						cell redox homeostasis	integral to membrane				ovary(1)|breast(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)															---	---	---	---
LECT2	3950	broad.mit.edu	37	5	135283098	135283098	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:135283098C>T	uc003lbe.1	-	4	579	c.378G>A	c.(376-378)TTG>TTA	p.L126L	FBXL21_uc003lbc.2_Intron	NM_002302	NP_002293	O14960	LECT2_HUMAN	leukocyte cell-derived chemotaxin 2 precursor	126					chemotaxis|skeletal system development	cytoplasm|extracellular space				ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)															---	---	---	---
KLHL3	26249	broad.mit.edu	37	5	136964110	136964110	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:136964110G>A	uc010jek.2	-	13	1911	c.1467C>T	c.(1465-1467)AGC>AGT	p.S489S	KLHL3_uc011cyc.1_Silent_p.S224S|KLHL3_uc003lbr.3_Silent_p.S407S|KLHL3_uc011cyd.1_RNA	NM_017415	NP_059111	Q9UH77	KLHL3_HUMAN	kelch-like 3	489	Kelch 4.					cytoplasm|cytoskeleton	actin binding|structural molecule activity				0		all_hematologic(541;3.67e-07)|Breast(839;7.61e-05)|Prostate(281;0.000825)|Ovarian(839;0.0481)|all_lung(232;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)	GBM - Glioblastoma multiforme(465;0.0223)														---	---	---	---
SLC23A1	9963	broad.mit.edu	37	5	138715412	138715412	+	Missense_Mutation	SNP	C	T	T	rs151281788	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138715412C>T	uc003leh.2	-	8	977	c.880G>A	c.(880-882)GGT>AGT	p.G294S	SLC23A1_uc003leg.2_Missense_Mutation_p.G298S	NM_005847	NP_005838	Q9UHI7	S23A1_HUMAN	solute carrier family 23 (nucleobase	294					brain development|nucleobase, nucleoside, nucleotide and nucleic acid metabolic process|response to toxin|transepithelial L-ascorbic acid transport|water-soluble vitamin metabolic process	apical plasma membrane|cytoplasm|integral to plasma membrane|intracellular organelle|membrane fraction	dehydroascorbic acid transporter activity|L-ascorbate:sodium symporter activity|nucleobase transmembrane transporter activity|protein binding|sodium-dependent L-ascorbate transmembrane transporter activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)		Vitamin C(DB00126)													---	---	---	---
ANKHD1-EIF4EBP3	404734	broad.mit.edu	37	5	139887448	139887448	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139887448C>T	uc003lfs.1	+	20	3754	c.3630C>T	c.(3628-3630)CTC>CTT	p.L1210L	ANKHD1_uc003lfq.1_Silent_p.L1229L|ANKHD1_uc003lfr.2_Silent_p.L1210L|ANKHD1_uc003lft.1_Silent_p.L421L|ANKHD1_uc003lfu.1_Silent_p.L690L|ANKHD1_uc003lfv.1_Silent_p.L287L|ANKHD1-EIF4EBP3_uc011czh.1_5'Flank|ANKHD1_uc003lfw.2_5'Flank	NM_020690	NP_065741	Q8IWZ2	Q8IWZ2_HUMAN	ANKHD1-EIF4EBP3 protein	1210						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	139941176	139941176	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139941176G>A	uc003lgd.1	-	7	1117	c.758C>T	c.(757-759)GCC>GTC	p.A253V	APBB3_uc003lgb.1_Missense_Mutation_p.A25V|APBB3_uc003lgc.1_Missense_Mutation_p.A25V|APBB3_uc003lge.1_Missense_Mutation_p.A246V|APBB3_uc003lgf.1_RNA|APBB3_uc010jfp.1_RNA|APBB3_uc011czi.1_Missense_Mutation_p.A25V|APBB3_uc010jfq.1_Missense_Mutation_p.A25V	NM_133172	NP_573418	O95704	APBB3_HUMAN	amyloid beta precursor protein-binding, family	248	PID 1.					actin cytoskeleton|cytoplasm				ovary(2)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHA2	56146	broad.mit.edu	37	5	140176157	140176157	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140176157C>T	uc003lhd.2	+	1	1714	c.1608C>T	c.(1606-1608)AGC>AGT	p.S536S	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhc.1_Silent_p.S536S|PCDHA2_uc011czy.1_Silent_p.S536S	NM_018905	NP_061728	Q9Y5H9	PCDA2_HUMAN	protocadherin alpha 2 isoform 1 precursor	536	Cadherin 5.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(4)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHA3	56145	broad.mit.edu	37	5	140181571	140181571	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140181571C>T	uc003lhf.2	+	1	789	c.789C>T	c.(787-789)ACC>ACT	p.T263T	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA2_uc011czy.1_Intron|PCDHA3_uc011czz.1_Silent_p.T263T	NM_018906	NP_061729	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3 isoform 1 precursor	263	Cadherin 3.|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)															---	---	---	---
PCDHA3	56145	broad.mit.edu	37	5	140182272	140182272	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140182272G>A	uc003lhf.2	+	1	1490	c.1490G>A	c.(1489-1491)CGG>CAG	p.R497Q	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA2_uc011czy.1_Intron|PCDHA3_uc011czz.1_Missense_Mutation_p.R497Q	NM_018906	NP_061729	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3 isoform 1 precursor	497	Cadherin 5.|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)															---	---	---	---
PCDHA4	56144	broad.mit.edu	37	5	140186905	140186905	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140186905G>A	uc003lhi.2	+	1	234	c.133G>A	c.(133-135)GTG>ATG	p.V45M	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhh.1_Missense_Mutation_p.V45M|PCDHA4_uc011daa.1_Missense_Mutation_p.V45M	NM_018907	NP_061730	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4 isoform 1 precursor	45	Cadherin 1.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding			ovary(4)|skin(2)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHA4	56144	broad.mit.edu	37	5	140188263	140188263	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140188263G>A	uc003lhi.2	+	1	1592	c.1491G>A	c.(1489-1491)CGG>CGA	p.R497R	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhh.1_Silent_p.R497R|PCDHA4_uc011daa.1_Silent_p.R497R	NM_018907	NP_061730	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4 isoform 1 precursor	497	Cadherin 5.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding			ovary(4)|skin(2)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHA5	56143	broad.mit.edu	37	5	140203557	140203557	+	Missense_Mutation	SNP	C	T	T	rs140039635		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140203557C>T	uc003lhl.2	+	1	2197	c.2197C>T	c.(2197-2199)CGG>TGG	p.R733W	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.R733W|PCDHA5_uc003lhj.1_Missense_Mutation_p.R733W	NM_018908	NP_061731	Q9Y5H7	PCDA5_HUMAN	protocadherin alpha 5 isoform 1 precursor	733	Cytoplasmic (Potential).				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	140209209	140209209	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140209209C>T	uc003lho.2	+	1	1560	c.1533C>T	c.(1531-1533)CAC>CAT	p.H511H	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_Silent_p.H511H|PCDHA6_uc011dab.1_Silent_p.H511H	NM_018909	NP_061732	Q9UN73	PCDA6_HUMAN	protocadherin alpha 6 isoform 1 precursor	511	Cadherin 5.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	extracellular region|integral to plasma membrane	calcium ion binding|protein binding			haematopoietic_and_lymphoid_tissue(1)|skin(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHA6	56142	broad.mit.edu	37	5	140209726	140209726	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140209726G>A	uc003lho.2	+	1	2077	c.2050G>A	c.(2050-2052)GTG>ATG	p.V684M	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.V684M	NM_018909	NP_061732	Q9UN73	PCDA6_HUMAN	protocadherin alpha 6 isoform 1 precursor	684	Extracellular (Potential).				homophilic cell adhesion|nervous system development	extracellular region|integral to plasma membrane	calcium ion binding|protein binding			haematopoietic_and_lymphoid_tissue(1)|skin(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHA13	56136	broad.mit.edu	37	5	140263605	140263605	+	Silent	SNP	G	A	A	rs61734917	byFrequency	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140263605G>A	uc003lif.2	+	1	1752	c.1752G>A	c.(1750-1752)TCG>TCA	p.S584S	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.S584S|PCDHA13_uc003lid.2_Silent_p.S584S	NM_018904	NP_061727	Q9Y5I0	PCDAD_HUMAN	protocadherin alpha 13 isoform 1 precursor	584	Cadherin 6.|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	140264042	140264042	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140264042G>A	uc003lif.2	+	1	2189	c.2189G>A	c.(2188-2190)GGC>GAC	p.G730D	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_Missense_Mutation_p.G730D|PCDHA13_uc003lid.2_Missense_Mutation_p.G730D	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)															---	---	---	---
PCDHB11	56125	broad.mit.edu	37	5	140579471	140579471	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140579471G>A	uc003liy.2	+	1	124	c.124G>A	c.(124-126)GGG>AGG	p.G42R	PCDHB11_uc011daj.1_Intron	NM_018931	NP_061754	Q9Y5F2	PCDBB_HUMAN	protocadherin beta 11 precursor	42	Extracellular (Potential).|Cadherin 1.				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to plasma membrane	calcium ion binding			skin(3)|ovary(2)|upper_aerodigestive_tract(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)															---	---	---	---
PCDHB11	56125	broad.mit.edu	37	5	140580614	140580614	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140580614G>A	uc003liy.2	+	1	1267	c.1267G>A	c.(1267-1269)GTC>ATC	p.V423I	PCDHB11_uc011daj.1_Missense_Mutation_p.V58I	NM_018931	NP_061754	Q9Y5F2	PCDBB_HUMAN	protocadherin beta 11 precursor	423	Extracellular (Potential).|Cadherin 4.				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to plasma membrane	calcium ion binding			skin(3)|ovary(2)|upper_aerodigestive_tract(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)															---	---	---	---
PCDHB11	56125	broad.mit.edu	37	5	140581384	140581384	+	Silent	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140581384C>A	uc003liy.2	+	1	2037	c.2037C>A	c.(2035-2037)GCC>GCA	p.A679A	PCDHB11_uc011daj.1_Silent_p.A314A	NM_018931	NP_061754	Q9Y5F2	PCDBB_HUMAN	protocadherin beta 11 precursor	679	Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to plasma membrane	calcium ion binding			skin(3)|ovary(2)|upper_aerodigestive_tract(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)															---	---	---	---
TAF7	6879	broad.mit.edu	37	5	140698866	140698866	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140698866G>A	uc003ljg.2	-	1	1486	c.746C>T	c.(745-747)ACG>ATG	p.T249M		NM_005642	NP_005633	Q15545	TAF7_HUMAN	TATA box-binding protein-associated factor 2F	249	Potential.				negative regulation of histone acetylation|negative regulation of protein kinase activity|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|spermine transport|transcription initiation from RNA polymerase II promoter	Golgi apparatus|MLL1 complex|transcription factor TFIID complex|transcription factor TFTC complex	histone acetyltransferase binding|thyroid hormone receptor binding|transcription coactivator activity|transcription regulatory region DNA binding|vitamin D receptor binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
TAF7	6879	broad.mit.edu	37	5	140699557	140699557	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140699557G>A	uc003ljg.2	-	1	795	c.55C>T	c.(55-57)CGT>TGT	p.R19C		NM_005642	NP_005633	Q15545	TAF7_HUMAN	TATA box-binding protein-associated factor 2F	19					negative regulation of histone acetylation|negative regulation of protein kinase activity|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|spermine transport|transcription initiation from RNA polymerase II promoter	Golgi apparatus|MLL1 complex|transcription factor TFIID complex|transcription factor TFTC complex	histone acetyltransferase binding|thyroid hormone receptor binding|transcription coactivator activity|transcription regulatory region DNA binding|vitamin D receptor binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)													OREG0016852	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
PCDHGA5	56110	broad.mit.edu	37	5	140745350	140745350	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140745350G>A	uc003lju.1	+	1	1453	c.1453G>A	c.(1453-1455)GCT>ACT	p.A485T	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc011das.1_Missense_Mutation_p.A485T	NM_018918	NP_061741	Q9Y5G8	PCDG5_HUMAN	protocadherin gamma subfamily A, 5 isoform 1	485	Extracellular (Potential).|Cadherin 5.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHGA6	56109	broad.mit.edu	37	5	140754322	140754322	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140754322C>T	uc003ljy.1	+	1	672	c.672C>T	c.(670-672)AGC>AGT	p.S224S	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc011dau.1_Silent_p.S224S	NM_018919	NP_061742	Q9Y5G7	PCDG6_HUMAN	protocadherin gamma subfamily A, 6 isoform 1	224	Extracellular (Potential).|Cadherin 2.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHGA11	56105	broad.mit.edu	37	5	140802733	140802733	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140802733G>A	uc003lkq.1	+	1	2197	c.1939G>A	c.(1939-1941)GTC>ATC	p.V647I	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_Missense_Mutation_p.V647I|PCDHGA11_uc003lkp.1_Intron	NM_018914	NP_061737	Q9Y5H2	PCDGB_HUMAN	protocadherin gamma subfamily A, 11 isoform 1	647	Extracellular (Potential).|Cadherin 6.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
GNPDA1	10007	broad.mit.edu	37	5	141385882	141385882	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141385882C>T	uc003lmf.3	-	3	995	c.236G>A	c.(235-237)CGA>CAA	p.R79Q	GNPDA1_uc003lmg.3_Missense_Mutation_p.R79Q|GNPDA1_uc010jgh.2_Missense_Mutation_p.R79Q|GNPDA1_uc003lmh.3_Missense_Mutation_p.R45Q	NM_005471	NP_005462	P46926	GNPI1_HUMAN	glucosamine-6-phosphate deaminase 1	79					generation of precursor metabolites and energy|glucosamine catabolic process|N-acetylglucosamine metabolic process|single fertilization	cytoplasm	glucosamine-6-phosphate deaminase activity|hydrolase activity				0		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
MYOZ3	91977	broad.mit.edu	37	5	150056388	150056388	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150056388G>A	uc003lss.2	+	7	1294	c.707G>A	c.(706-708)AGA>AAA	p.R236K	MYOZ3_uc003lsr.2_Missense_Mutation_p.R236K	NM_001122853	NP_001116325	Q8TDC0	MYOZ3_HUMAN	myozenin 3	236						sarcomere	protein binding			skin(1)	1		Medulloblastoma(196;0.134)|all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
CCDC69	26112	broad.mit.edu	37	5	150564974	150564974	+	Intron	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150564974G>A	uc003ltq.2	-						CCDC69_uc010jhu.2_Intron|CCDC69_uc011dcq.1_Intron	NM_015621	NP_056436			coiled-coil domain containing 69											ovary(2)	2		Medulloblastoma(196;0.091)|all_hematologic(541;0.207)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
FAT2	2196	broad.mit.edu	37	5	150948214	150948214	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150948214G>A	uc003lue.3	-	1	292	c.279C>T	c.(277-279)TGC>TGT	p.C93C	GM2A_uc011dcs.1_Intron|FAT2_uc010jhx.1_Silent_p.C93C	NM_001447	NP_001438	Q9NYQ8	FAT2_HUMAN	FAT tumor suppressor 2 precursor	93	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)															---	---	---	---
G3BP1	10146	broad.mit.edu	37	5	151170562	151170562	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:151170562T>A	uc003lun.2	+	4	461	c.290T>A	c.(289-291)CTT>CAT	p.L97H	G3BP1_uc010jhy.1_Missense_Mutation_p.L97H|G3BP1_uc003lum.2_Missense_Mutation_p.L97H|G3BP1_uc011dcu.1_5'UTR|G3BP1_uc010jhz.2_5'UTR	NM_005754	NP_005745	Q13283	G3BP1_HUMAN	Ras-GTPase-activating protein SH3-domain-binding	97	NTF2.				Ras protein signal transduction|transport	cytosol|nucleus|plasma membrane	ATP binding|ATP-dependent DNA helicase activity|ATP-dependent RNA helicase activity|DNA binding|endonuclease activity|protein binding|RNA binding			skin(3)|ovary(1)	4		all_hematologic(541;0.0338)|Medulloblastoma(196;0.091)	Kidney(363;0.000171)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)															---	---	---	---
GRIA1	2890	broad.mit.edu	37	5	153190682	153190682	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153190682G>T	uc003lva.3	+	16	2983	c.2618G>T	c.(2617-2619)GGA>GTA	p.G873V	GRIA1_uc003luy.3_Missense_Mutation_p.G873V|GRIA1_uc003luz.3_Missense_Mutation_p.G778V|GRIA1_uc011dcv.1_RNA|GRIA1_uc011dcw.1_Missense_Mutation_p.G793V|GRIA1_uc011dcx.1_Missense_Mutation_p.G804V|GRIA1_uc011dcy.1_Missense_Mutation_p.G883V|GRIA1_uc011dcz.1_Missense_Mutation_p.G883V	NM_001114183	NP_001107655	P42261	GRIA1_HUMAN	glutamate receptor, ionotropic, AMPA 1 isoform	873	Cytoplasmic (Potential).				synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|dendritic spine|endocytic vesicle membrane|endoplasmic reticulum membrane|neuronal cell body|postsynaptic density|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity|PDZ domain binding			ovary(4)|skin(2)	6		Medulloblastoma(196;0.0391)|all_neural(177;0.16)|all_hematologic(541;0.21)	Kidney(363;0.000173)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|L-Glutamic Acid(DB00142)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)													---	---	---	---
FAM114A2	10827	broad.mit.edu	37	5	153382396	153382396	+	Intron	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153382396G>A	uc003lvb.2	-						FAM114A2_uc003lvc.2_Intron|FAM114A2_uc003lvd.2_Intron|FAM114A2_uc003lve.2_Intron|FAM114A2_uc011dda.1_Intron	NM_018691	NP_061161			hypothetical protein LOC10827								purine nucleotide binding				0																		---	---	---	---
LARP1	23367	broad.mit.edu	37	5	154183225	154183225	+	Silent	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154183225C>A	uc003lvp.2	+	13	2788	c.2359C>A	c.(2359-2361)CGG>AGG	p.R787R	LARP1_uc003lvo.2_Silent_p.R710R|LARP1_uc010jie.1_Silent_p.R582R	NM_033551	NP_291029	Q6PKG0	LARP1_HUMAN	la related protein isoform 2	787							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	154183749	154183749	+	Intron	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154183749T>C	uc003lvp.2	+						LARP1_uc003lvo.2_Intron	NM_033551	NP_291029			la related protein isoform 2								protein binding|RNA binding			ovary(2)|pancreas(1)|skin(1)	4	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)															---	---	---	---
FAM71B	153745	broad.mit.edu	37	5	156590674	156590674	+	Intron	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156590674A>G	uc003lwn.2	-							NM_130899	NP_570969			family with sequence similarity 71, member B							nucleus				ovary(4)|pancreas(1)|skin(1)	6	Renal(175;0.00212)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)															---	---	---	---
CYFIP2	26999	broad.mit.edu	37	5	156810373	156810373	+	Intron	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156810373A>G	uc003lwq.2	+						CYFIP2_uc011ddn.1_Intron|CYFIP2_uc011ddo.1_Intron|CYFIP2_uc003lwr.2_Intron|CYFIP2_uc003lws.2_Intron|CYFIP2_uc003lwt.2_Intron|CYFIP2_uc011ddp.1_Intron|CYFIP2_uc003lwv.2_Intron	NM_001037333	NP_001032410			cytoplasmic FMR1 interacting protein 2						apoptosis|cell-cell adhesion	cell junction|perinuclear region of cytoplasm|synapse|synaptosome	protein binding				0	Renal(175;0.00212)	Medulloblastoma(196;0.0306)|all_neural(177;0.0897)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)															---	---	---	---
ADAM19	8728	broad.mit.edu	37	5	156920119	156920119	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156920119C>T	uc003lwz.2	-	16	1834	c.1770G>A	c.(1768-1770)GTG>GTA	p.V590V	ADAM19_uc003lww.1_Silent_p.V323V|ADAM19_uc003lwy.2_Silent_p.V189V|ADAM19_uc011ddr.1_Silent_p.V521V	NM_033274	NP_150377	Q9H013	ADA19_HUMAN	ADAM metallopeptidase domain 19 preproprotein	590	Extracellular (Potential).|Cys-rich.				proteolysis	integral to membrane	metalloendopeptidase activity|SH3 domain binding|zinc ion binding			ovary(3)|large_intestine(2)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	8	Renal(175;0.00488)	Medulloblastoma(196;0.0359)|all_neural(177;0.14)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)															---	---	---	---
ATP10B	23120	broad.mit.edu	37	5	160113246	160113246	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160113246A>G	uc003lym.1	-	6	1157	c.310T>C	c.(310-312)TTG>CTG	p.L104L	ATP10B_uc003lyp.2_Silent_p.L104L|ATP10B_uc011deg.1_Silent_p.L148L|ATP10B_uc003lyo.2_5'Flank	NM_025153	NP_079429	O94823	AT10B_HUMAN	ATPase, class V, type 10B	104	Helical; (Potential).				ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(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)															---	---	---	---
GABRB2	2561	broad.mit.edu	37	5	160721153	160721153	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160721153G>A	uc003lys.1	-	11	1692	c.1474C>T	c.(1474-1476)CGC>TGC	p.R492C	GABRB2_uc011deh.1_Missense_Mutation_p.R293C|GABRB2_uc003lyr.1_Missense_Mutation_p.R454C|GABRB2_uc003lyt.1_Missense_Mutation_p.R454C|GABRB2_uc010jiu.1_Missense_Mutation_p.R391C	NM_021911	NP_068711	P47870	GBRB2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta	492	Helical; (Probable).				gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|GABA-A receptor activity				0	Renal(175;0.00259)	Medulloblastoma(196;0.021)|all_neural(177;0.0463)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)													---	---	---	---
GABRG2	2566	broad.mit.edu	37	5	161520894	161520894	+	Silent	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:161520894C>A	uc003lyz.3	+	2	526	c.168C>A	c.(166-168)GTC>GTA	p.V56V	GABRG2_uc010jjc.2_Silent_p.V56V|GABRG2_uc003lyy.3_Silent_p.V56V|GABRG2_uc011dej.1_5'UTR	NM_000816	NP_000807	P18507	GBRG2_HUMAN	gamma-aminobutyric acid A receptor, gamma 2	56	Extracellular (Probable).				gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	benzodiazepine receptor activity|chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity|protein binding			ovary(4)|skin(1)	5	Renal(175;0.000319)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0734)|OV - Ovarian serous cystadenocarcinoma(192;0.135)|Epithelial(171;0.136)														---	---	---	---
NUDCD2	134492	broad.mit.edu	37	5	162880969	162880969	+	3'UTR	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:162880969G>A	uc003lze.2	-	4						NM_145266	NP_660309			NudC domain containing 2							intracellular					0	Renal(175;0.000281)	Medulloblastoma(196;0.0207)|all_neural(177;0.0966)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0981)|OV - Ovarian serous cystadenocarcinoma(192;0.183)|Epithelial(171;0.247)														---	---	---	---
LCP2	3937	broad.mit.edu	37	5	169689854	169689854	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169689854T>C	uc003man.1	-	12	1017	c.810A>G	c.(808-810)CCA>CCG	p.P270P	LCP2_uc011des.1_Silent_p.P65P|LCP2_uc011det.1_Silent_p.P99P|LCP2_uc010jjo.1_Silent_p.P77P	NM_005565	NP_005556	Q13094	LCP2_HUMAN	lymphocyte cytosolic protein 2	270					immune response|platelet activation|T cell receptor signaling pathway|transmembrane receptor protein tyrosine kinase signaling pathway	cytosol	protein binding			ovary(1)	1	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0109)|all_neural(177;0.0146)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	OV - Ovarian serous cystadenocarcinoma(192;0.247)														---	---	---	---
NKX2-5	1482	broad.mit.edu	37	5	172659583	172659583	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172659583G>A	uc003mcm.1	-	2	1140	c.964C>T	c.(964-966)CGA>TGA	p.R322*		NM_004387	NP_004378	P52952	NKX25_HUMAN	NK2 transcription factor related, locus 5	322			R -> Q (in ASD-AVCD; somatic mutation).		adult heart development|atrial cardiac muscle cell development|atrial septum morphogenesis|heart looping|hemopoiesis|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cardiac muscle cell apoptosis|negative regulation of myotube differentiation|negative regulation of transcription from RNA polymerase II promoter|outflow tract septum morphogenesis|pharyngeal system development|positive regulation of calcium ion transport via voltage-gated calcium channel activity|positive regulation of cardioblast differentiation|positive regulation of cell proliferation|positive regulation of heart contraction|positive regulation of neuron differentiation|positive regulation of sodium ion transport|positive regulation of survival gene product expression|positive regulation of transcription initiation from RNA polymerase II promoter|positive regulation of transcription via serum response element binding|regulation of cardiac muscle contraction|right ventricular cardiac muscle tissue morphogenesis|septum secundum development|spleen development|thyroid gland development|vasculogenesis|ventricular septum morphogenesis		chromatin binding|protein heterodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|serum response element binding|transcription factor binding			central_nervous_system(1)	1	Renal(175;0.000159)|Lung NSC(126;0.00229)|all_lung(126;0.004)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)															---	---	---	---
HMP19	51617	broad.mit.edu	37	5	173534316	173534316	+	Splice_Site	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173534316G>A	uc003mcx.2	+	5	470	c.325_splice	c.e5-1	p.H109_splice	HMP19_uc011dfh.1_Splice_Site_p.S12_splice	NM_015980	NP_057064			HMP19 protein						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)															---	---	---	---
UNC5A	90249	broad.mit.edu	37	5	176297387	176297387	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176297387C>T	uc003mey.2	+	6	930	c.738C>T	c.(736-738)AGC>AGT	p.S246S	UNC5A_uc003mex.1_Silent_p.S246S|UNC5A_uc010jkg.1_Silent_p.S206S	NM_133369	NP_588610	Q6ZN44	UNC5A_HUMAN	netrin receptor Unc5h1 precursor	246	TSP type-1.|Extracellular (Potential).				apoptosis|axon guidance|regulation of apoptosis	integral to membrane|plasma membrane				skin(1)	1	all_cancers(89;0.000119)|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	176314232	176314232	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176314232G>A	uc003mfa.2	-	12	1799	c.1707C>T	c.(1705-1707)CCC>CCT	p.P569P	HK3_uc003mez.2_Silent_p.P125P	NM_002115	NP_002106	P52790	HXK3_HUMAN	hexokinase 3	569	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)															---	---	---	---
NSD1	64324	broad.mit.edu	37	5	176678848	176678848	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176678848C>T	uc003mfr.3	+	12	4897	c.4759C>T	c.(4759-4761)CGC>TGC	p.R1587C	NSD1_uc003mft.3_Missense_Mutation_p.R1318C|NSD1_uc003mfs.1_Missense_Mutation_p.R1484C|NSD1_uc011dfx.1_Missense_Mutation_p.R1235C	NM_022455	NP_071900	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	1587	PHD-type 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	176721549	176721549	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176721549A>G	uc003mfr.3	+	23	7318	c.7180A>G	c.(7180-7182)ATT>GTT	p.I2394V	NSD1_uc003mft.3_Missense_Mutation_p.I2125V|NSD1_uc011dfx.1_Missense_Mutation_p.I2042V	NM_022455	NP_071900	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	2394	Pro-rich.				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)			---	---	---	---
GRK6	2870	broad.mit.edu	37	5	176860178	176860178	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176860178T>C	uc011dfz.1	+	6	631	c.471T>C	c.(469-471)CCT>CCC	p.P157P	GRK6_uc003mgp.2_Silent_p.P157P|GRK6_uc003mgq.2_Silent_p.P157P|GRK6_uc003mgs.1_Silent_p.P127P	NM_002082	NP_002073	P43250	GRK6_HUMAN	G protein-coupled receptor kinase 6 isoform B	157	N-terminal.|RGS.				regulation of G-protein coupled receptor protein signaling pathway	membrane	ATP binding|G-protein coupled receptor kinase activity|signal transducer activity			large_intestine(1)|stomach(1)|breast(1)	3	all_cancers(89;1.15e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	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)															---	---	---	---
BTNL9	153579	broad.mit.edu	37	5	180475169	180475169	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180475169C>T	uc003mmt.2	+	3	583	c.352C>T	c.(352-354)CTG>TTG	p.L118L	BTNL9_uc011dhi.1_Silent_p.L49L	NM_152547	NP_689760	Q6UXG8	BTNL9_HUMAN	butyrophilin-like 9 precursor	118	Extracellular (Potential).|Ig-like V-type.					integral to membrane				ovary(1)|central_nervous_system(1)	2	all_cancers(89;2.45e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
CDYL	9425	broad.mit.edu	37	6	4935952	4935952	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:4935952A>G	uc003mwi.2	+	5	1188	c.1057A>G	c.(1057-1059)ACC>GCC	p.T353A	CDYL_uc003mwj.2_Missense_Mutation_p.T299A|CDYL_uc003mwk.2_Missense_Mutation_p.T64A|CDYL_uc011dhx.1_Missense_Mutation_p.T167A|CDYL_uc011dhy.1_Missense_Mutation_p.T167A	NM_001143971	NP_001137443	Q9Y232	CDYL1_HUMAN	chromodomain protein, Y chromosome-like isoform	353					regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	nucleus	histone acetyltransferase activity				0	Ovarian(93;0.11)	all_hematologic(90;0.0901)|Lung NSC(90;0.244)		OV - Ovarian serous cystadenocarcinoma(45;0.182)														---	---	---	---
F13A1	2162	broad.mit.edu	37	6	6197549	6197549	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:6197549A>G	uc003mwv.2	-	9	1246	c.1123T>C	c.(1123-1125)TGC>CGC	p.C375R	F13A1_uc011dib.1_Missense_Mutation_p.C312R	NM_000129	NP_000120	P00488	F13A_HUMAN	coagulation factor XIII A1 subunit precursor	375					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)													---	---	---	---
MYLIP	29116	broad.mit.edu	37	6	16143371	16143371	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:16143371C>T	uc003nbq.2	+	4	822	c.585C>T	c.(583-585)AGC>AGT	p.S195S	MYLIP_uc003nbr.2_Silent_p.S14S	NM_013262	NP_037394	Q8WY64	MYLIP_HUMAN	myosin regulatory light chain interacting	195	FERM.				cellular component movement|nervous system development	cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding|ubiquitin-protein ligase activity|zinc ion binding			pancreas(1)	1	Breast(50;0.0799)|Ovarian(93;0.103)	all_hematologic(90;0.0895)	Epithelial(50;0.241)															---	---	---	---
KIF13A	63971	broad.mit.edu	37	6	17837152	17837152	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17837152C>T	uc003ncg.3	-	11	1217	c.1112G>A	c.(1111-1113)CGG>CAG	p.R371Q	KIF13A_uc003ncf.2_Missense_Mutation_p.R371Q|KIF13A_uc003nch.3_Missense_Mutation_p.R371Q|KIF13A_uc003nci.3_Missense_Mutation_p.R371Q|KIF13A_uc003ncj.2_Missense_Mutation_p.R47Q	NM_022113	NP_071396	Q9H1H9	KI13A_HUMAN	kinesin family member 13A isoform a	371	Potential.				cargo loading into vesicle|cell cycle|cytokinesis|endosome to lysosome transport|Golgi to plasma membrane protein transport|melanosome organization|plus-end-directed vesicle transport along microtubule	centrosome|endosome membrane|microtubule|midbody|trans-Golgi network membrane	ATP binding|microtubule motor activity|protein binding			large_intestine(2)|ovary(2)	4	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)															---	---	---	---
E2F3	1871	broad.mit.edu	37	6	20481645	20481645	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:20481645C>T	uc003nda.2	+	3	1041	c.714C>T	c.(712-714)AAC>AAT	p.N238N	E2F3_uc003ncz.2_Silent_p.N232N	NM_001949	NP_001940	O00716	E2F3_HUMAN	E2F transcription factor 3	238	Potential.|DEF box.				G1 phase of mitotic cell cycle|G2 phase of mitotic cell cycle|transcription initiation from RNA polymerase II promoter	transcription factor complex	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			lung(1)	1	all_cancers(95;0.154)|all_epithelial(95;0.0585)|Breast(50;0.146)|Ovarian(93;0.148)		OV - Ovarian serous cystadenocarcinoma(7;0.0068)|all cancers(50;0.0148)|Epithelial(50;0.0562)															---	---	---	---
CDKAL1	54901	broad.mit.edu	37	6	20758841	20758841	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:20758841C>T	uc003ndc.1	+	7	658	c.484C>T	c.(484-486)CGT>TGT	p.R162C	CDKAL1_uc003ndd.1_Missense_Mutation_p.R162C|CDKAL1_uc003nde.1_Missense_Mutation_p.R92C	NM_017774	NP_060244	Q5VV42	CDKAL_HUMAN	CDK5 regulatory subunit associated protein	162	MTTase N-terminal.				RNA modification	integral to membrane	4 iron, 4 sulfur cluster binding|metal ion binding|transferase activity			ovary(2)	2	all_epithelial(95;0.0708)|Breast(50;0.131)|Ovarian(93;0.227)		OV - Ovarian serous cystadenocarcinoma(7;0.0241)|all cancers(50;0.123)|Epithelial(50;0.248)															---	---	---	---
TDP2	51567	broad.mit.edu	37	6	24653309	24653309	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24653309G>A	uc003nej.2	-	6	734	c.709C>T	c.(709-711)CGA>TGA	p.R237*	TDP2_uc003nei.2_Nonsense_Mutation_p.R125*|TDP2_uc010jpu.1_Nonsense_Mutation_p.R237*	NM_016614	NP_057698	O95551	TYDP2_HUMAN	TRAF and TNF receptor-associated protein	237					cell surface receptor linked signaling pathway|double-strand break repair	PML body	5'-tyrosyl-DNA phosphodiesterase activity|magnesium ion binding|nuclease activity|protein binding|transcription corepressor activity			ovary(1)|lung(1)	2													Direct_reversal_of_damage|Editing_and_processing_nucleases					---	---	---	---
LRRC16A	55604	broad.mit.edu	37	6	25600624	25600624	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25600624A>G	uc011djw.1	+	33	3578	c.3202A>G	c.(3202-3204)AGT>GGT	p.S1068G	LRRC16A_uc010jpx.2_Missense_Mutation_p.S1068G|LRRC16A_uc010jpy.2_Missense_Mutation_p.S1068G	NM_017640	NP_060110	Q5VZK9	LR16A_HUMAN	leucine rich repeat containing 16A	1068	Inhibits capping activity of CAPZA2 (By similarity).				actin filament organization|blood coagulation|cell migration|lamellipodium assembly|ruffle organization|urate metabolic process	cytosol|lamellipodium|nucleus				ovary(1)|breast(1)|central_nervous_system(1)|pancreas(1)	4																		---	---	---	---
HIST1H2BL	8340	broad.mit.edu	37	6	27775557	27775557	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27775557T>C	uc003njl.2	-	1	153	c.128A>G	c.(127-129)TAC>TGC	p.Y43C	HIST1H3H_uc003njm.2_5'Flank	NM_003519	NP_003510	Q99880	H2B1L_HUMAN	histone cluster 1, H2bl	43					nucleosome assembly	nucleosome|nucleus	DNA binding				0																		---	---	---	---
HIST1H2BN	8341	broad.mit.edu	37	6	27806599	27806599	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27806599G>T	uc003njv.2	+	1	160	c.160G>T	c.(160-162)GGT>TGT	p.G54C	HIST1H2AK_uc003njs.2_5'Flank|HIST1H2BN_uc003njt.1_RNA|HIST1H2BN_uc003nju.1_Missense_Mutation_p.G54C	NM_003520	NP_003511	Q99877	H2B1N_HUMAN	histone cluster 1, H2bn	54					nucleosome assembly	nucleosome|nucleus	DNA binding				0																		---	---	---	---
OR2B6	26212	broad.mit.edu	37	6	27925691	27925691	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27925691G>C	uc011dkx.1	+	1	673	c.673G>C	c.(673-675)GTA>CTA	p.V225L		NM_012367	NP_036499	P58173	OR2B6_HUMAN	olfactory receptor, family 2, subfamily B,	225	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1																		---	---	---	---
TRIM15	89870	broad.mit.edu	37	6	30139991	30139991	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30139991C>T	uc010jrx.2	+	7	1742	c.1263C>T	c.(1261-1263)TAC>TAT	p.Y421Y		NM_033229	NP_150232	Q9C019	TRI15_HUMAN	tripartite motif protein 15	421	B30.2/SPRY.				mesodermal cell fate determination	intracellular	zinc ion binding				0																		---	---	---	---
C6orf136	221545	broad.mit.edu	37	6	30617500	30617500	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30617500A>G	uc003nqw.3	+	2	431	c.238A>G	c.(238-240)AGC>GGC	p.S80G	C6orf136_uc003nqx.3_Missense_Mutation_p.S261G|C6orf136_uc011dmn.1_Intron	NM_001109938	NP_001103408	Q5SQH8	CF136_HUMAN	hypothetical protein LOC221545 isoform 1	80											0																		---	---	---	---
DDR1	780	broad.mit.edu	37	6	30859233	30859233	+	Silent	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30859233C>A	uc003nrr.2	+	7	901	c.642C>A	c.(640-642)ACC>ACA	p.T214T	DDR1_uc010jse.2_Silent_p.T214T|DDR1_uc003nrq.2_Silent_p.T214T|DDR1_uc003nrs.2_Silent_p.T214T|DDR1_uc003nrt.2_Silent_p.T214T|DDR1_uc011dms.1_Silent_p.T232T|DDR1_uc003nru.2_Silent_p.T214T|DDR1_uc011dmu.1_Intron|DDR1_uc003nrv.2_Silent_p.T214T|DDR1_uc003nrw.1_Silent_p.T13T|DDR1_uc003nry.1_5'Flank|DDR1_uc003nrx.1_5'Flank	NM_013993	NP_054699	Q08345	DDR1_HUMAN	discoidin domain receptor family, member 1	214	Extracellular (Potential).				cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway	extracellular region|integral to plasma membrane	ATP binding|protein binding|protein binding|transmembrane receptor protein tyrosine kinase activity			lung(4)|central_nervous_system(3)|large_intestine(1)|ovary(1)	9					Imatinib(DB00619)													---	---	---	---
LTA	4049	broad.mit.edu	37	6	31541102	31541102	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31541102G>A	uc011dnu.1	+	4	463	c.250G>A	c.(250-252)GAC>AAC	p.D84N	LTA_uc003nue.1_Missense_Mutation_p.D84N|LTA_uc003nuf.2_Intron|LTA_uc003nuh.2_Missense_Mutation_p.D31N|LTA_uc003nug.2_Missense_Mutation_p.D31N|LTA_uc010jsr.2_Intron|TNF_uc003nui.2_5'Flank	NM_001159740	NP_001153212	P01374	TNFB_HUMAN	lymphotoxin alpha precursor	84					cell-cell signaling|induction of apoptosis|signal transduction	extracellular space|membrane	cytokine activity|tumor necrosis factor receptor binding				0					Etanercept(DB00005)													---	---	---	---
BAT2	7916	broad.mit.edu	37	6	31593069	31593069	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31593069C>T	uc003nvb.3	+	6	834	c.585C>T	c.(583-585)CCC>CCT	p.P195P	BAT2_uc011dnv.1_RNA|BAT2_uc003nvc.3_Silent_p.P195P|BAT2_uc003nve.2_Silent_p.P58P	NM_080686	NP_542417	P48634	PRC2A_HUMAN	HLA-B associated transcript-2	195	4 X 57 AA type A repeats.					cytoplasm|nucleus	protein binding				0																		---	---	---	---
BAT2	7916	broad.mit.edu	37	6	31603453	31603453	+	Missense_Mutation	SNP	C	A	A	rs115028652	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31603453C>A	uc003nvb.3	+	24	5717	c.5468C>A	c.(5467-5469)CCG>CAG	p.P1823Q	BAT2_uc003nvc.3_Missense_Mutation_p.P1823Q	NM_080686	NP_542417	P48634	PRC2A_HUMAN	HLA-B associated transcript-2	1823						cytoplasm|nucleus	protein binding				0																		---	---	---	---
C6orf47	57827	broad.mit.edu	37	6	31627518	31627518	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31627518A>G	uc003nvm.1	-	1	1032	c.207T>C	c.(205-207)GCT>GCC	p.A69A		NM_021184	NP_067007	O95873	CF047_HUMAN	G4 protein	69										ovary(1)	1																		---	---	---	---
VARS	7407	broad.mit.edu	37	6	31760564	31760564	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31760564A>T	uc003nxe.2	-	4	1054	c.631T>A	c.(631-633)TCA>ACA	p.S211T	VARS_uc011doi.1_RNA	NM_006295	NP_006286	P26640	SYVC_HUMAN	valyl-tRNA synthetase	211	GST C-terminal.				translational elongation|valyl-tRNA aminoacylation	cytosol	ATP binding|protein binding|valine-tRNA ligase activity			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3					L-Valine(DB00161)													---	---	---	---
SLC44A4	80736	broad.mit.edu	37	6	31838664	31838664	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31838664C>T	uc010jti.2	-	10	928	c.862G>A	c.(862-864)GCC>ACC	p.A288T	SLC44A4_uc011dol.1_Missense_Mutation_p.A212T|SLC44A4_uc011dom.1_Missense_Mutation_p.A246T	NM_025257	NP_079533	Q53GD3	CTL4_HUMAN	choline transporter-like protein 4	288	Extracellular (Potential).					integral to membrane|plasma membrane	choline transmembrane transporter activity			large_intestine(2)|ovary(1)|central_nervous_system(1)	4					Choline(DB00122)													---	---	---	---
EHMT2	10919	broad.mit.edu	37	6	31852688	31852688	+	Splice_Site	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31852688C>T	uc003nxz.1	-	19	2458	c.2448_splice	c.e19+1	p.N816_splice	EHMT2_uc003nxv.1_5'Flank|EHMT2_uc003nxw.1_5'Flank|EHMT2_uc003nxx.1_Intron|EHMT2_uc003nxy.1_Missense_Mutation_p.V608M|EHMT2_uc011don.1_Splice_Site_p.N839_splice|EHMT2_uc003nya.1_Splice_Site_p.N782_splice	NM_006709	NP_006700			euchromatic histone-lysine N-methyltransferase 2						DNA methylation|peptidyl-lysine dimethylation	chromosome|nucleus	histone methyltransferase activity (H3-K27 specific)|histone methyltransferase activity (H3-K9 specific)|p53 binding|zinc ion binding			ovary(1)	1																		---	---	---	---
STK19	8859	broad.mit.edu	37	6	31939920	31939920	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31939920C>T	uc003nyv.2	+	1	275	c.147C>T	c.(145-147)GTC>GTT	p.V49V	DOM3Z_uc003nyo.1_5'UTR|DOM3Z_uc003nyp.1_5'UTR|DOM3Z_uc003nyq.1_5'UTR|DOM3Z_uc003nyr.1_5'UTR|DOM3Z_uc003nys.1_5'Flank|DOM3Z_uc010jtl.1_5'UTR|STK19_uc003nyt.2_5'UTR|DOM3Z_uc003nyu.1_5'UTR|STK19_uc011dow.1_Silent_p.V49V|STK19_uc011dox.1_5'UTR|STK19_uc003nyw.2_Silent_p.V49V|STK19_uc010jtn.1_5'Flank	NM_032454	NP_115830	P49842	STK19_HUMAN	serine/threonine kinase 19 isoform 2	49						nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			skin(4)	4																		---	---	---	---
TNXB	7148	broad.mit.edu	37	6	32039796	32039796	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32039796C>T	uc003nzl.2	-	13	5163	c.4961G>A	c.(4960-4962)CGC>CAC	p.R1654H		NM_019105	NP_061978	P22105	TENX_HUMAN	tenascin XB isoform 1 precursor	1736	Fibronectin type-III 9.				actin cytoskeleton organization|cell adhesion|collagen metabolic process|elastic fiber assembly|signal transduction	extracellular space|intracellular|proteinaceous extracellular matrix	heparin binding|integrin binding				0																		---	---	---	---
TNXB	7148	broad.mit.edu	37	6	32039876	32039876	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32039876C>A	uc003nzl.2	-	13	5083	c.4881G>T	c.(4879-4881)CAG>CAT	p.Q1627H		NM_019105	NP_061978	P22105	TENX_HUMAN	tenascin XB isoform 1 precursor	1709	Fibronectin type-III 9.				actin cytoskeleton organization|cell adhesion|collagen metabolic process|elastic fiber assembly|signal transduction	extracellular space|intracellular|proteinaceous extracellular matrix	heparin binding|integrin binding				0																		---	---	---	---
TNXB	7148	broad.mit.edu	37	6	32065871	32065871	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32065871T>C	uc003nzl.2	-	2	307	c.105A>G	c.(103-105)CCA>CCG	p.P35P	TNXB_uc010jts.1_Silent_p.P34P|ATF6B_uc003nzm.1_3'UTR	NM_019105	NP_061978	P22105	TENX_HUMAN	tenascin XB isoform 1 precursor	35					actin cytoskeleton organization|cell adhesion|collagen metabolic process|elastic fiber assembly|signal transduction	extracellular space|intracellular|proteinaceous extracellular matrix	heparin binding|integrin binding				0																		---	---	---	---
PPT2	9374	broad.mit.edu	37	6	32123717	32123717	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32123717C>A	uc003nzx.2	+	5	1071	c.503C>A	c.(502-504)CCC>CAC	p.P168H	PRRT1_uc003nzu.2_5'Flank|uc003nzv.3_5'Flank|PPT2_uc003nzw.2_Missense_Mutation_p.P174H|PPT2_uc011dpi.1_RNA|PPT2_uc003nzy.1_RNA|PPT2_uc003nzz.2_Missense_Mutation_p.P168H|PPT2_uc003oaa.2_Missense_Mutation_p.P168H|PPT2_uc010jtu.1_Missense_Mutation_p.P168H	NM_005155	NP_005146	Q9UMR5	PPT2_HUMAN	palmitoyl-protein thioesterase 2 isoform a	168					protein modification process	lysosome	palmitoyl-(protein) hydrolase activity				0																		---	---	---	---
EGFL8	80864	broad.mit.edu	37	6	32135028	32135028	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32135028G>A	uc003oab.1	+	6	653	c.595G>A	c.(595-597)GTG>ATG	p.V199M	PPT2_uc003nzy.1_RNA|EGFL8_uc003oac.1_Missense_Mutation_p.V199M	NM_030652	NP_085155	Q99944	EGFL8_HUMAN	NG3 protein precursor	199	Potential.					extracellular region|integral to membrane	calcium ion binding				0																		---	---	---	---
GPSM3	63940	broad.mit.edu	37	6	32159535	32159535	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32159535C>T	uc003oay.3	-	3	689	c.296G>A	c.(295-297)CGT>CAT	p.R99H	PBX2_uc003oav.1_5'Flank|PBX2_uc003oaw.2_5'Flank|GPSM3_uc003oax.3_Missense_Mutation_p.R76H|GPSM3_uc003oaz.2_Missense_Mutation_p.R99H	NM_022107	NP_071390	Q9Y4H4	GPSM3_HUMAN	G-protein signaling modulator 3 (AGS3-like, C.	99					signal transduction	cytoplasm	GTPase activator activity|protein binding				0																		---	---	---	---
NOTCH4	4855	broad.mit.edu	37	6	32168997	32168997	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32168997G>A	uc003obb.2	-	22	4175	c.4036C>T	c.(4036-4038)CGG>TGG	p.R1346W	NOTCH4_uc003oba.2_Missense_Mutation_p.R9W|NOTCH4_uc011dpu.1_RNA|NOTCH4_uc011dpv.1_RNA	NM_004557	NP_004548	Q99466	NOTC4_HUMAN	notch4 preproprotein	1346	Extracellular (Potential).				cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm	calcium ion binding|protein heterodimerization activity|receptor activity			lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1)	22																		---	---	---	---
PSMB8	5696	broad.mit.edu	37	6	32809478	32809478	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32809478G>T	uc003oce.2	-	5	615	c.572C>A	c.(571-573)ACT>AAT	p.T191N	TAP2_uc011dqf.1_5'Flank|TAP2_uc003ocb.1_5'Flank|TAP2_uc003ocd.2_5'Flank|PSMB8_uc003ocf.2_Missense_Mutation_p.T187N	NM_148919	NP_683720	P28062	PSB8_HUMAN	proteasome beta 8 subunit isoform E2 proprotein	191					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|type I interferon-mediated signaling pathway|viral reproduction	cytoplasm|nucleus|proteasome core complex	protein binding|threonine-type endopeptidase activity			skin(1)	1																		---	---	---	---
SLC39A7	7922	broad.mit.edu	37	6	33169444	33169444	+	Intron	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33169444A>G	uc003odf.2	+						RXRB_uc003odb.2_5'Flank|RXRB_uc003odc.2_5'Flank|RXRB_uc003odd.2_5'Flank|RXRB_uc011dqr.1_5'Flank|RXRB_uc011dqs.1_5'Flank|RXRB_uc011dqt.1_5'Flank|RXRB_uc011dqu.1_5'Flank|SLC39A7_uc003odg.2_Intron|SLC39A7_uc011dqv.1_Intron|SLC39A7_uc003odh.2_5'Flank|HSD17B8_uc003odi.1_5'Flank	NM_001077516	NP_001070984			solute carrier family 39, member 7							endoplasmic reticulum membrane|integral to membrane|membrane fraction	protein binding|zinc ion transmembrane transporter activity			large_intestine(1)	1																		---	---	---	---
ITPR3	3710	broad.mit.edu	37	6	33638235	33638235	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33638235G>A	uc011drk.1	+	19	2542	c.2323G>A	c.(2323-2325)GCC>ACC	p.A775T		NM_002224	NP_002215	Q14573	ITPR3_HUMAN	inositol 1,4,5-triphosphate receptor, type 3	775	Cytoplasmic (Potential).				activation of phospholipase C activity|calcium ion transport into cytosol|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|nerve growth factor receptor signaling pathway|platelet activation|protein heterooligomerization|protein homooligomerization|regulation of insulin secretion|response to calcium ion	apical part of cell|brush border|endoplasmic reticulum membrane|integral to plasma membrane|myelin sheath|neuronal cell body|nuclear outer membrane|platelet dense tubular network membrane	inositol 1,3,4,5 tetrakisphosphate binding|inositol 1,4,5 trisphosphate binding|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity|inositol hexakisphosphate binding|intracellular ligand-gated calcium channel activity|protein binding			ovary(6)|lung(5)|central_nervous_system(5)|breast(2)|kidney(1)	19																		---	---	---	---
UHRF1BP1	54887	broad.mit.edu	37	6	34826613	34826613	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34826613G>A	uc003oju.3	+	14	2714	c.2480G>A	c.(2479-2481)CGC>CAC	p.R827H	UHRF1BP1_uc010jvm.1_RNA|UHRF1BP1_uc010jvn.2_RNA|UHRF1BP1_uc010jvo.2_RNA	NM_017754	NP_060224	Q6BDS2	URFB1_HUMAN	ICBP90 binding protein 1	827										ovary(3)	3																		---	---	---	---
SCUBE3	222663	broad.mit.edu	37	6	35200656	35200656	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35200656G>A	uc003okf.1	+	5	505	c.499G>A	c.(499-501)GGC>AGC	p.G167S	SCUBE3_uc003okg.1_Missense_Mutation_p.G166S|SCUBE3_uc003okh.1_Missense_Mutation_p.G38S	NM_152753	NP_689966	Q8IX30	SCUB3_HUMAN	signal peptide, CUB domain, EGF-like 3	167	EGF-like 4.				protein heterooligomerization|protein homooligomerization	cell surface|extracellular region	calcium ion binding|protein binding			skin(1)	1																		---	---	---	---
DEF6	50619	broad.mit.edu	37	6	35278224	35278224	+	Intron	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35278224C>T	uc003okk.2	+						DEF6_uc010jvs.2_Intron|DEF6_uc010jvt.2_Intron	NM_022047	NP_071330			differentially expressed in FDCP 6 homolog							cytoplasm|nucleus|plasma membrane					0																		---	---	---	---
FTSJD2	23070	broad.mit.edu	37	6	37427331	37427331	+	Intron	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37427331T>C	uc003ons.2	+						FTSJD2_uc010jwu.2_Intron	NM_015050	NP_055865			FtsJ methyltransferase domain containing 2						mRNA capping	cytoplasm|nucleus	mRNA (nucleoside-2'-O-)-methyltransferase activity|nucleic acid binding			ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	5																		---	---	---	---
DNAH8	1769	broad.mit.edu	37	6	38828371	38828371	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38828371A>G	uc003ooe.1	+	41	6046	c.5446A>G	c.(5446-5448)ACT>GCT	p.T1816A		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																		---	---	---	---
TREML1	340205	broad.mit.edu	37	6	41121543	41121543	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41121543C>T	uc011duc.1	-	2	373	c.329G>A	c.(328-330)AGG>AAG	p.R110K	TREML1_uc003opx.2_Missense_Mutation_p.R110K|TREML1_uc011dud.1_Intron	NM_178174	NP_835468	Q86YW5	TRML1_HUMAN	triggering receptor expressed on myeloid	110	Ig-like V-type.|Extracellular (Potential).				calcium-mediated signaling|innate immune response|platelet activation	cell surface|integral to membrane|plasma membrane|platelet alpha granule	protein binding|receptor activity			breast(1)	1	Ovarian(28;0.0418)|Colorectal(47;0.196)																	---	---	---	---
FOXP4	116113	broad.mit.edu	37	6	41558999	41558999	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41558999A>G	uc003oql.2	+	13	1933	c.1475A>G	c.(1474-1476)GAG>GGG	p.E492G	FOXP4_uc003oqm.2_Missense_Mutation_p.E490G|FOXP4_uc003oqn.2_Missense_Mutation_p.E479G	NM_001012426	NP_001012426	Q8IVH2	FOXP4_HUMAN	forkhead box P4 isoform 1	492	Fork-head.				embryonic foregut morphogenesis|heart development|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding			breast(1)	1	Ovarian(28;0.0327)|Colorectal(47;0.196)																	---	---	---	---
GUCA1A	2978	broad.mit.edu	37	6	42146094	42146094	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42146094G>A	uc003orx.2	+	4	923	c.278G>A	c.(277-279)CGC>CAC	p.R93H	GUCA1A_uc011duo.1_RNA|GUCA1A_uc010jxt.2_Missense_Mutation_p.R93H	NM_000409	NP_000400	P43080	GUC1A_HUMAN	guanylate cyclase activator 1A (retina)	93	EF-hand 3.				signal transduction|visual perception	membrane	calcium ion binding|calcium sensitive guanylate cyclase activator activity				0	Colorectal(47;0.196)		STAD - Stomach adenocarcinoma(11;5.54e-05)|Epithelial(12;0.000167)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)															---	---	---	---
CUL9	23113	broad.mit.edu	37	6	43167106	43167106	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43167106C>T	uc003ouk.2	+	13	3228	c.3153C>T	c.(3151-3153)TCC>TCT	p.S1051S	CUL9_uc003oul.2_Silent_p.S1051S|CUL9_uc010jyk.2_Silent_p.S203S	NM_015089	NP_055904	Q8IWT3	CUL9_HUMAN	p53-associated parkin-like cytoplasmic protein	1051					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																		---	---	---	---
CUL9	23113	broad.mit.edu	37	6	43167827	43167827	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43167827C>T	uc003ouk.2	+	14	3392	c.3317C>T	c.(3316-3318)ACA>ATA	p.T1106I	CUL9_uc003oul.2_Missense_Mutation_p.T1106I|CUL9_uc010jyk.2_Missense_Mutation_p.T258I	NM_015089	NP_055904	Q8IWT3	CUL9_HUMAN	p53-associated parkin-like cytoplasmic protein	1106					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																		---	---	---	---
ZNF318	24149	broad.mit.edu	37	6	43322422	43322422	+	Missense_Mutation	SNP	G	A	A	rs146670568		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43322422G>A	uc003oux.2	-	4	2728	c.2650C>T	c.(2650-2652)CGT>TGT	p.R884C	ZNF318_uc003ouw.2_RNA	NM_014345	NP_055160	Q5VUA4	ZN318_HUMAN	zinc finger protein 318	884	Potential.				meiosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	nucleic acid binding|zinc ion binding			ovary(3)|breast(2)|central_nervous_system(1)|skin(1)	7			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0171)|OV - Ovarian serous cystadenocarcinoma(102;0.0579)															---	---	---	---
CDC5L	988	broad.mit.edu	37	6	44376250	44376250	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44376250G>A	uc003oxl.2	+	8	1232	c.973G>A	c.(973-975)GAG>AAG	p.E325K		NM_001253	NP_001244	Q99459	CDC5L_HUMAN	CDC5-like	325	Interaction with PPP1R8.				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)															---	---	---	---
ICK	22858	broad.mit.edu	37	6	52878542	52878542	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52878542C>A	uc003pbh.2	-	10	1560	c.1070G>T	c.(1069-1071)AGG>ATG	p.R357M	ICK_uc003pbi.2_Missense_Mutation_p.R357M	NM_016513	NP_057597	Q9UPZ9	ICK_HUMAN	intestinal cell kinase	357					intracellular protein kinase cascade|multicellular organismal development	cytosol|nucleus	ATP binding|cyclin-dependent protein kinase activity|magnesium ion binding			ovary(1)|large_intestine(1)|lung(1)|kidney(1)|central_nervous_system(1)	5	Lung NSC(77;0.103)																	---	---	---	---
DST	667	broad.mit.edu	37	6	56382029	56382029	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56382029G>A	uc003pdf.2	-	65	11995	c.11967C>T	c.(11965-11967)ACC>ACT	p.T3989T	DST_uc003pcz.3_Silent_p.T3811T|DST_uc011dxj.1_Silent_p.T3840T|DST_uc011dxk.1_Silent_p.T3851T|DST_uc003pcy.3_Silent_p.T3485T	NM_001144769	NP_001138241	Q03001	DYST_HUMAN	dystonin isoform 2	5897	Spectrin 10.				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)															---	---	---	---
KIAA1586	57691	broad.mit.edu	37	6	56917834	56917834	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56917834T>C	uc003pdj.2	+	4	707	c.537T>C	c.(535-537)CAT>CAC	p.H179H	KIAA1586_uc011dxm.1_Silent_p.H152H	NM_020931	NP_065982	Q9HCI6	K1586_HUMAN	hypothetical protein LOC57691	179							nucleic acid binding				0	Lung NSC(77;0.0969)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)															---	---	---	---
BAI3	577	broad.mit.edu	37	6	70042837	70042837	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70042837T>G	uc003pev.3	+	24	3573	c.3125T>G	c.(3124-3126)TTG>TGG	p.L1042W	BAI3_uc010kak.2_Missense_Mutation_p.L1042W|BAI3_uc011dxx.1_Missense_Mutation_p.L248W|BAI3_uc003pex.1_Missense_Mutation_p.L172W	NM_001704	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	1042	Helical; Name=5; (Potential).				negative regulation of angiogenesis|neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			lung(27)|ovary(8)|skin(6)|pancreas(4)|central_nervous_system(3)|urinary_tract(1)|breast(1)	50		all_lung(197;0.212)																---	---	---	---
OGFRL1	79627	broad.mit.edu	37	6	72011673	72011673	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:72011673A>G	uc003pfx.1	+	7	1440	c.1277A>G	c.(1276-1278)AAC>AGC	p.N426S		NM_024576	NP_078852	Q5TC84	OGRL1_HUMAN	opioid growth factor receptor-like 1	426						membrane	receptor activity				0																		---	---	---	---
KCNQ5	56479	broad.mit.edu	37	6	73787159	73787159	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:73787159G>A	uc003pgk.2	+	4	1078	c.731G>A	c.(730-732)CGC>CAC	p.R244H	KCNQ5_uc003pgj.3_Missense_Mutation_p.R244H|KCNQ5_uc011dyh.1_Missense_Mutation_p.R244H|KCNQ5_uc011dyi.1_Missense_Mutation_p.R244H|KCNQ5_uc010kat.2_Missense_Mutation_p.R244H|KCNQ5_uc011dyj.1_Missense_Mutation_p.R244H|KCNQ5_uc011dyk.1_Missense_Mutation_p.R3H	NM_019842	NP_062816	Q9NR82	KCNQ5_HUMAN	potassium voltage-gated channel, KQT-like	244	Helical; Voltage-sensor; Name=Segment S4; (Potential).		R -> C (in a colorectal cancer sample; somatic mutation).		protein complex assembly|synaptic transmission	voltage-gated potassium channel complex	inward rectifier potassium channel activity	p.R244C(1)		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)														---	---	---	---
FILIP1	27145	broad.mit.edu	37	6	76022149	76022149	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:76022149C>T	uc003pia.2	-	5	3772	c.3399G>A	c.(3397-3399)CCG>CCA	p.P1133P	FILIP1_uc003phy.1_Silent_p.P1133P|FILIP1_uc003phz.2_Silent_p.P1034P|FILIP1_uc010kbe.2_Silent_p.P1136P|FILIP1_uc003pib.1_Silent_p.P885P	NM_015687	NP_056502	Q7Z7B0	FLIP1_HUMAN	filamin A interacting protein 1	1133										skin(3)|ovary(1)	4																		---	---	---	---
KIAA1009	22832	broad.mit.edu	37	6	84872863	84872863	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84872863C>A	uc010kbp.2	-	19	2609	c.2512G>T	c.(2512-2514)GGT>TGT	p.G838C	KIAA1009_uc003pkj.3_Missense_Mutation_p.G762C|KIAA1009_uc003pki.3_Missense_Mutation_p.G224C	NM_014895	NP_055710	Q5TB80	QN1_HUMAN	KIAA1009 protein	838	Potential.				cell division|mitosis	centrosome|nucleus|plasma membrane|spindle	protein binding			ovary(1)	1		all_cancers(76;1.5e-06)|Acute lymphoblastic leukemia(125;2.69e-07)|all_hematologic(105;0.000151)|all_epithelial(107;0.00258)		BRCA - Breast invasive adenocarcinoma(397;0.089)														---	---	---	---
AKIRIN2	55122	broad.mit.edu	37	6	88391397	88391397	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88391397G>A	uc003pmk.2	-	2	903	c.320C>T	c.(319-321)CCG>CTG	p.P107L		NM_018064	NP_060534	Q53H80	AKIR2_HUMAN	akirin 2	107					innate immune response|transcription, DNA-dependent	transcriptional repressor complex					0																		---	---	---	---
CNR1	1268	broad.mit.edu	37	6	88854349	88854349	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88854349G>A	uc011dzq.1	-	2	4208	c.645C>T	c.(643-645)TAC>TAT	p.Y215Y	CNR1_uc010kbz.2_Silent_p.Y215Y|CNR1_uc011dzr.1_Silent_p.Y215Y|CNR1_uc011dzs.1_Silent_p.Y215Y|CNR1_uc003pmq.3_Silent_p.Y215Y|CNR1_uc011dzt.1_Silent_p.Y215Y|CNR1_uc010kca.2_Silent_p.Y182Y	NM_001160260	NP_001153732	P21554	CNR1_HUMAN	cannabinoid receptor 1 isoform a	215	Cytoplasmic (Potential).				G-protein signaling, coupled to cAMP nucleotide second messenger	integral to plasma membrane	cannabinoid receptor activity|protein binding			skin(2)	2		all_cancers(76;8.24e-09)|Acute lymphoblastic leukemia(125;2.15e-10)|Prostate(29;4.11e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;0.00011)		BRCA - Breast invasive adenocarcinoma(108;0.15)	Marinol(DB00470)|Nabilone(DB00486)|Rimonabant(DB06155)													---	---	---	---
BACH2	60468	broad.mit.edu	37	6	90660960	90660960	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90660960T>C	uc011eab.1	-	7	1674	c.865A>G	c.(865-867)ATC>GTC	p.I289V	BACH2_uc003pnw.2_Missense_Mutation_p.I289V|BACH2_uc010kch.2_Missense_Mutation_p.I289V	NM_021813	NP_068585	Q9BYV9	BACH2_HUMAN	BTB and CNC homology 1, basic leucine zipper	289						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)														---	---	---	---
MAP3K7	6885	broad.mit.edu	37	6	91257878	91257878	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:91257878G>A	uc003pnz.1	-	10	1130	c.968C>T	c.(967-969)GCT>GTT	p.A323V	MAP3K7_uc003poa.1_Missense_Mutation_p.A323V|MAP3K7_uc003pob.1_Missense_Mutation_p.A323V|MAP3K7_uc003poc.1_Missense_Mutation_p.A323V	NM_145331	NP_663304	O43318	M3K7_HUMAN	mitogen-activated protein kinase kinase kinase 7	323					activation of MAPK activity|activation of NF-kappaB-inducing kinase activity|histone H3 acetylation|I-kappaB phosphorylation|innate immune response|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-2 production|positive regulation of JUN kinase activity|positive regulation of NF-kappaB transcription factor activity|positive regulation of T cell cytokine production|stress-activated MAPK cascade|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|transforming growth factor beta receptor signaling pathway	Ada2/Gcn5/Ada3 transcription activator complex|cytosol|endosome membrane	ATP binding|magnesium ion binding|MAP kinase kinase kinase activity|protein binding|protein binding			ovary(2)|lung(2)|upper_aerodigestive_tract(1)|stomach(1)	6		all_cancers(76;6.4e-08)|Acute lymphoblastic leukemia(125;1.43e-09)|Prostate(29;9.32e-09)|all_hematologic(105;3.69e-06)|all_epithelial(107;0.000187)|Ovarian(999;0.0164)		OV - Ovarian serous cystadenocarcinoma(136;2.05e-11)|all cancers(137;3.25e-11)|GBM - Glioblastoma multiforme(226;0.0416)|BRCA - Breast invasive adenocarcinoma(108;0.0429)														---	---	---	---
CCNC	892	broad.mit.edu	37	6	99998177	99998177	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:99998177G>T	uc003pqe.2	-	8	734	c.447C>A	c.(445-447)TGC>TGA	p.C149*	uc003pqc.2_Intron|CCNC_uc003pqd.2_Nonsense_Mutation_p.C64*|CCNC_uc010kcr.2_RNA|CCNC_uc010kcs.2_Nonsense_Mutation_p.C149*|CCNC_uc011eah.1_Nonsense_Mutation_p.C64*	NM_005190	NP_005181	P24863	CCNC_HUMAN	cyclin C isoform a	149					regulation of cyclin-dependent protein kinase activity|regulation of transcription, DNA-dependent|transcription, DNA-dependent	DNA-directed RNA polymerase II, holoenzyme	protein kinase binding				0		all_cancers(76;8.46e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0128)|Colorectal(196;0.069)|Lung NSC(302;0.186)		BRCA - Breast invasive adenocarcinoma(108;0.064)														---	---	---	---
PRDM13	59336	broad.mit.edu	37	6	100062101	100062101	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:100062101C>T	uc003pqg.1	+	4	1851	c.1590C>T	c.(1588-1590)TCC>TCT	p.S530S		NM_021620	NP_067633	Q9H4Q3	PRD13_HUMAN	PR domain containing 13	530					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(76;1.64e-05)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0128)|Colorectal(196;0.069)|Lung NSC(302;0.186)		BRCA - Breast invasive adenocarcinoma(108;0.0598)														---	---	---	---
SIM1	6492	broad.mit.edu	37	6	100897523	100897523	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:100897523T>C	uc003pqj.3	-	4	608	c.401A>G	c.(400-402)GAC>GGC	p.D134G	SIM1_uc010kcu.2_Missense_Mutation_p.D134G	NM_005068	NP_005059	P81133	SIM1_HUMAN	single-minded homolog 1	134	PAS 1.				cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			ovary(4)	4		all_cancers(76;9.88e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0248)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0774)														---	---	---	---
ARMC2	84071	broad.mit.edu	37	6	109274297	109274297	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109274297G>A	uc003pss.3	+	13	1832	c.1658G>A	c.(1657-1659)CGT>CAT	p.R553H	ARMC2_uc011eao.1_Missense_Mutation_p.R388H	NM_032131	NP_115507	Q8NEN0	ARMC2_HUMAN	armadillo repeat containing 2	553	ARM 7.						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)														---	---	---	---
DDO	8528	broad.mit.edu	37	6	110736691	110736691	+	Missense_Mutation	SNP	T	C	C	rs151067781	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:110736691T>C	uc003puc.2	-	1	63	c.59A>G	c.(58-60)CAA>CGA	p.Q20R	DDO_uc003pud.2_Missense_Mutation_p.Q20R	NM_003649	NP_003640	Q99489	OXDD_HUMAN	D-aspartate oxidase isoform a	Error:Variant_position_missing_in_Q99489_after_alignment					aspartate catabolic process	peroxisome	binding|D-amino-acid oxidase activity|D-aspartate oxidase activity			ovary(2)|breast(1)	3		all_cancers(87;3.47e-21)|all_epithelial(87;9.03e-20)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_lung(197;2.98e-05)|Lung NSC(302;3.25e-05)|Colorectal(196;3.46e-05)|Ovarian(999;0.00327)		all cancers(137;2.54e-48)|Epithelial(106;3.11e-44)|OV - Ovarian serous cystadenocarcinoma(136;2.08e-24)|BRCA - Breast invasive adenocarcinoma(108;0.000141)|GBM - Glioblastoma multiforme(226;0.00046)														---	---	---	---
TUBE1	51175	broad.mit.edu	37	6	112397615	112397615	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112397615C>A	uc003pvq.2	-	7	660	c.546G>T	c.(544-546)GAG>GAT	p.E182D	TUBE1_uc003pvr.2_Missense_Mutation_p.E107D	NM_016262	NP_057346	Q9UJT0	TBE_HUMAN	tubulin, epsilon 1	182					centrosome cycle|microtubule-based movement|protein polymerization	microtubule|pericentriolar material	GTP binding|GTPase activity|structural constituent of cytoskeleton			ovary(1)	1		all_cancers(87;0.0101)|all_hematologic(75;0.000258)|Colorectal(196;0.0466)|all_epithelial(87;0.1)		all cancers(137;0.0217)|OV - Ovarian serous cystadenocarcinoma(136;0.0613)|Epithelial(106;0.0636)|GBM - Glioblastoma multiforme(226;0.0972)|BRCA - Breast invasive adenocarcinoma(108;0.246)														---	---	---	---
LAMA4	3910	broad.mit.edu	37	6	112430768	112430768	+	Missense_Mutation	SNP	G	A	A	rs145897390	byFrequency	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112430768G>A	uc003pvu.2	-	39	5653	c.5344C>T	c.(5344-5346)CGC>TGC	p.R1782C	LAMA4_uc003pvv.2_Missense_Mutation_p.R1775C|LAMA4_uc003pvt.2_Missense_Mutation_p.R1775C	NM_001105206	NP_001098676	Q16363	LAMA4_HUMAN	laminin, alpha 4 isoform 1 precursor	1782	Laminin G-like 5.				cell adhesion|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	extracellular matrix structural constituent|receptor binding			ovary(4)|breast(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	9		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)														---	---	---	---
RSPH4A	345895	broad.mit.edu	37	6	116938220	116938220	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116938220C>T	uc003pxe.2	+	1	579	c.434C>T	c.(433-435)TCA>TTA	p.S145L	RSPH4A_uc010kee.2_Missense_Mutation_p.S145L	NM_001010892	NP_001010892	Q5TD94	RSH4A_HUMAN	radial spoke head 4 homolog A isoform 1	145					cilium axoneme assembly|cilium movement	cytoplasm|cytoskeleton|radial spoke					0														Kartagener_syndrome				---	---	---	---
CLVS2	134829	broad.mit.edu	37	6	123369846	123369846	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:123369846G>A	uc003pzi.1	+	4	1513	c.644G>A	c.(643-645)CGG>CAG	p.R215Q		NM_001010852	NP_001010852	Q5SYC1	CLVS2_HUMAN	retinaldehyde binding protein 1-like 2	215	CRAL-TRIO.				lysosome organization	clathrin-coated vesicle|early endosome membrane|trans-Golgi network	phosphatidylinositol-3,5-bisphosphate binding|transporter activity			ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	5																		---	---	---	---
PTPRK	5796	broad.mit.edu	37	6	128297831	128297831	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:128297831G>A	uc003qbk.2	-	27	4304	c.3937C>T	c.(3937-3939)CGG>TGG	p.R1313W	PTPRK_uc003qbj.2_Missense_Mutation_p.R1314W|PTPRK_uc010kfc.2_Missense_Mutation_p.R1320W|PTPRK_uc011ebu.1_Missense_Mutation_p.R1336W	NM_002844	NP_002835	Q15262	PTPRK_HUMAN	protein tyrosine phosphatase, receptor type, K	1313	Tyrosine-protein phosphatase 2.|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)														---	---	---	---
PTPRK	5796	broad.mit.edu	37	6	128399951	128399951	+	Intron	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:128399951C>T	uc003qbk.2	-						PTPRK_uc003qbj.2_Intron|PTPRK_uc010kfc.2_Intron|PTPRK_uc011ebu.1_Intron|PTPRK_uc003qbl.1_Intron|PTPRK_uc011ebv.1_Intron	NM_002844	NP_002835			protein tyrosine phosphatase, receptor type, K						cell migration|cellular response to reactive oxygen species|cellular response to UV|focal adhesion assembly|negative regulation of cell cycle|negative regulation of cell migration|negative regulation of keratinocyte proliferation|negative regulation of transcription, DNA-dependent|protein localization at cell surface|transforming growth factor beta receptor signaling pathway	adherens junction|cell surface|cell-cell junction|integral to plasma membrane|leading edge membrane	beta-catenin binding|gamma-catenin binding|protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(3)|skin(2)|pancreas(1)|kidney(1)|central_nervous_system(1)	8				all cancers(137;0.0118)|GBM - Glioblastoma multiforme(226;0.0372)|OV - Ovarian serous cystadenocarcinoma(136;0.24)														---	---	---	---
TMEM200A	114801	broad.mit.edu	37	6	130762848	130762848	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:130762848C>T	uc003qca.2	+	3	2152	c.1281C>T	c.(1279-1281)AGC>AGT	p.S427S	TMEM200A_uc010kfh.2_Silent_p.S427S|TMEM200A_uc010kfi.2_Silent_p.S427S|TMEM200A_uc003qcb.2_Silent_p.S427S	NM_052913	NP_443145	Q86VY9	T200A_HUMAN	transmembrane protein 200A	427	Cytoplasmic (Potential).					integral to membrane				ovary(1)	1				GBM - Glioblastoma multiforme(226;0.0139)|OV - Ovarian serous cystadenocarcinoma(155;0.12)														---	---	---	---
OR2A4	79541	broad.mit.edu	37	6	132021800	132021800	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132021800C>A	uc011ecd.1	-	1	742	c.742G>T	c.(742-744)GGA>TGA	p.G248*	ENPP3_uc003qcu.3_Intron|ENPP3_uc010kfq.2_Intron|ENPP3_uc003qcv.2_Intron	NM_030908	NP_112170	O95047	OR2A4_HUMAN	olfactory receptor, family 2, subfamily A,	248	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.018)|OV - Ovarian serous cystadenocarcinoma(155;0.041)														---	---	---	---
EYA4	2070	broad.mit.edu	37	6	133783564	133783564	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:133783564G>A	uc003qec.3	+	8	987	c.529G>A	c.(529-531)GTC>ATC	p.V177I	EYA4_uc011ecq.1_Missense_Mutation_p.V123I|EYA4_uc011ecr.1_Missense_Mutation_p.V123I|EYA4_uc003qed.3_Missense_Mutation_p.V177I|EYA4_uc003qee.3_Missense_Mutation_p.V154I|EYA4_uc011ecs.1_Missense_Mutation_p.V177I|uc003qef.1_Intron	NM_004100	NP_004091	O95677	EYA4_HUMAN	eyes absent 4 isoform a	177					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)														---	---	---	---
KIAA1244	57221	broad.mit.edu	37	6	138645253	138645253	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138645253G>A	uc003qhu.2	+	31	4963	c.4963G>A	c.(4963-4965)GAG>AAG	p.E1655K		NM_020340	NP_065073	Q5TH69	BIG3_HUMAN	brefeldin A-inhibited guanine	1655					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)														---	---	---	---
HECA	51696	broad.mit.edu	37	6	139488112	139488112	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139488112C>T	uc003qin.2	+	2	1248	c.963C>T	c.(961-963)CAC>CAT	p.H321H		NM_016217	NP_057301	Q9UBI9	HDC_HUMAN	headcase	321					respiratory tube development						0				GBM - Glioblastoma multiforme(68;0.000252)|OV - Ovarian serous cystadenocarcinoma(155;0.000387)														---	---	---	---
TXLNB	167838	broad.mit.edu	37	6	139591652	139591652	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139591652C>T	uc011eds.1	-	4	793	c.628G>A	c.(628-630)GCT>ACT	p.A210T		NM_153235	NP_694967	Q8N3L3	TXLNB_HUMAN	taxilin beta	210	Potential.					cytoplasm				large_intestine(1)|ovary(1)	2				OV - Ovarian serous cystadenocarcinoma(155;0.000185)|GBM - Glioblastoma multiforme(68;0.000235)														---	---	---	---
HIVEP2	3097	broad.mit.edu	37	6	143093401	143093401	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:143093401G>A	uc003qjd.2	-	5	3218	c.2475C>T	c.(2473-2475)TGC>TGT	p.C825C		NM_006734	NP_006725	P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer	825					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)														---	---	---	---
STX11	8676	broad.mit.edu	37	6	144507854	144507854	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144507854C>T	uc003qks.3	+	2	282	c.90C>T	c.(88-90)CAC>CAT	p.H30H		NM_003764	NP_003755	O75558	STX11_HUMAN	syntaxin 11	30					cellular membrane fusion|intracellular protein transport|vesicle-mediated transport	Golgi apparatus|membrane	SNAP receptor activity			ovary(1)|central_nervous_system(1)	2				OV - Ovarian serous cystadenocarcinoma(155;2.17e-06)|GBM - Glioblastoma multiforme(68;0.0492)										Familial_Hemophagocytic_Lymphohistiocytosis				---	---	---	---
FBXO30	84085	broad.mit.edu	37	6	146127423	146127423	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146127423A>G	uc003qla.2	-	2	318	c.119T>C	c.(118-120)GTT>GCT	p.V40A	uc003qky.1_Intron	NM_032145	NP_115521	Q8TB52	FBX30_HUMAN	F-box only protein 30	40							ubiquitin-protein ligase activity|zinc ion binding			ovary(2)|large_intestine(1)	3		Ovarian(120;0.0776)		OV - Ovarian serous cystadenocarcinoma(155;1.95e-07)|GBM - Glioblastoma multiforme(68;0.0149)														---	---	---	---
SHPRH	257218	broad.mit.edu	37	6	146247425	146247425	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146247425T>C	uc003qlf.2	-	16	3608	c.3209A>G	c.(3208-3210)CAT>CGT	p.H1070R	SHPRH_uc003qld.2_Missense_Mutation_p.H1079R|SHPRH_uc003qle.2_Missense_Mutation_p.H1079R|SHPRH_uc003qlg.1_Missense_Mutation_p.H626R|SHPRH_uc003qlh.2_5'UTR|SHPRH_uc003qli.1_5'UTR	NM_001042683	NP_001036148	Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase isoform a	1070					DNA repair|nucleosome assembly	nucleosome|nucleus	ATP binding|DNA binding|helicase activity|ligase activity|zinc ion binding			ovary(1)|kidney(1)|central_nervous_system(1)	3		Ovarian(120;0.0365)		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)														---	---	---	---
SHPRH	257218	broad.mit.edu	37	6	146269406	146269406	+	Splice_Site	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146269406A>G	uc003qlf.2	-	5	1460	c.1061_splice	c.e5+1	p.C354_splice	SHPRH_uc003qld.2_Splice_Site_p.C354_splice|SHPRH_uc003qle.2_Splice_Site_p.C354_splice|SHPRH_uc003qlg.1_Splice_Site|SHPRH_uc003qlj.1_Splice_Site_p.C243_splice|SHPRH_uc003qlk.1_Splice_Site_p.C354_splice	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	146720261	146720261	+	Silent	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146720261C>A	uc010khw.1	+	8	2556	c.2086C>A	c.(2086-2088)CGG>AGG	p.R696R	GRM1_uc010khv.1_Silent_p.R696R|GRM1_uc003qll.2_Silent_p.R696R|GRM1_uc011edz.1_Silent_p.R696R|GRM1_uc011eea.1_Silent_p.R696R	NM_000838	NP_000829	Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1 isoform alpha	696	Cytoplasmic (Potential).		R -> W (in a colorectal cancer sample; somatic mutation).		synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity	p.R696W(1)		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)													---	---	---	---
STXBP5	134957	broad.mit.edu	37	6	147704088	147704088	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:147704088C>T	uc003qlz.2	+	27	3529	c.3368C>T	c.(3367-3369)GCG>GTG	p.A1123V	STXBP5_uc010khz.1_Missense_Mutation_p.A1087V|STXBP5_uc003qlx.2_RNA|STXBP5_uc003qly.2_Missense_Mutation_p.A778V	NM_001127715	NP_001121187	Q5T5C0	STXB5_HUMAN	syntaxin binding protein 5 (tomosyn) isoform b	1123	v-SNARE coiled-coil homology.				exocytosis|positive regulation of exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|nicotinic acetylcholine-gated receptor-channel complex|synaptic vesicle	syntaxin-1 binding				0		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;1.77e-09)|GBM - Glioblastoma multiforme(68;0.0694)														---	---	---	---
PLEKHG1	57480	broad.mit.edu	37	6	151161754	151161754	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151161754C>T	uc003qny.1	+	17	4192	c.3880C>T	c.(3880-3882)CTA>TTA	p.L1294L	PLEKHG1_uc011eem.1_Silent_p.L1353L	NM_001029884	NP_001025055	Q9ULL1	PKHG1_HUMAN	pleckstrin homology domain containing, family G	1294					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	151334921	151334921	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151334921G>A	uc003qob.2	+	22	2540	c.2272G>A	c.(2272-2274)GCT>ACT	p.A758T	MTHFD1L_uc011een.1_RNA|MTHFD1L_uc011eeo.1_Missense_Mutation_p.A759T|MTHFD1L_uc003qoc.2_Missense_Mutation_p.A706T	NM_015440	NP_056255	Q6UB35	C1TM_HUMAN	methylenetetrahydrofolate dehydrogenase (NADP+	758	Formyltetrahydrofolate synthetase.				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)														---	---	---	---
SYNE1	23345	broad.mit.edu	37	6	152637972	152637972	+	Intron	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152637972T>C	uc010kiw.2	-						SYNE1_uc010kiv.2_Intron|SYNE1_uc003qos.3_Intron|SYNE1_uc003qot.3_Intron|SYNE1_uc003qou.3_Intron|SYNE1_uc010kiz.2_Silent_p.G1329G	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)			---	---	---	---
ARID1B	57492	broad.mit.edu	37	6	157405929	157405929	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:157405929C>T	uc003qqn.2	+	5	2110	c.1958C>T	c.(1957-1959)GCG>GTG	p.A653V	ARID1B_uc003qqo.2_Missense_Mutation_p.A666V|ARID1B_uc003qqp.2_Missense_Mutation_p.A653V|ARID1B_uc003qqq.1_Missense_Mutation_p.A95V	NM_017519	NP_059989	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	711	Ser-rich.				chromatin-mediated maintenance of transcription|nervous system development|transcription, DNA-dependent	SWI/SNF complex	DNA binding|protein binding|transcription coactivator activity			ovary(1)|breast(1)	2		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)														---	---	---	---
SYNJ2	8871	broad.mit.edu	37	6	158490659	158490659	+	Missense_Mutation	SNP	G	A	A	rs144180367	byFrequency	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158490659G>A	uc003qqx.1	+	14	1969	c.1894G>A	c.(1894-1896)GTC>ATC	p.V632I	SYNJ2_uc003qqw.1_Missense_Mutation_p.V632I|SYNJ2_uc003qqy.1_Missense_Mutation_p.V345I|SYNJ2_uc003qqz.1_Missense_Mutation_p.V249I|SYNJ2_uc003qra.1_5'Flank	NM_003898	NP_003889	O15056	SYNJ2_HUMAN	synaptojanin 2	632	Catalytic (By similarity).						nucleotide binding|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity|RNA binding			skin(1)	1				OV - Ovarian serous cystadenocarcinoma(65;4.42e-18)|BRCA - Breast invasive adenocarcinoma(81;4.23e-05)														---	---	---	---
TULP4	56995	broad.mit.edu	37	6	158834180	158834180	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158834180C>T	uc003qrf.2	+	2	1693	c.336C>T	c.(334-336)TAC>TAT	p.Y112Y	TULP4_uc011efo.1_Silent_p.Y112Y|TULP4_uc003qrg.2_Silent_p.Y112Y	NM_020245	NP_064630	Q9NRJ4	TULP4_HUMAN	tubby like protein 4 isoform 1	112	WD 1.				intracellular signal transduction|response to nutrient	cytoplasm	protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Breast(66;0.000781)|Ovarian(120;0.0308)|Lung SC(201;0.164)|Prostate(117;0.171)		OV - Ovarian serous cystadenocarcinoma(65;1.64e-18)|BRCA - Breast invasive adenocarcinoma(81;2.67e-05)														---	---	---	---
TULP4	56995	broad.mit.edu	37	6	158923412	158923412	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158923412G>A	uc003qrf.2	+	13	4074	c.2717G>A	c.(2716-2718)CGG>CAG	p.R906Q	TULP4_uc003qrg.2_Intron	NM_020245	NP_064630	Q9NRJ4	TULP4_HUMAN	tubby like protein 4 isoform 1	906					intracellular signal transduction|response to nutrient	cytoplasm	protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Breast(66;0.000781)|Ovarian(120;0.0308)|Lung SC(201;0.164)|Prostate(117;0.171)		OV - Ovarian serous cystadenocarcinoma(65;1.64e-18)|BRCA - Breast invasive adenocarcinoma(81;2.67e-05)														---	---	---	---
PNLDC1	154197	broad.mit.edu	37	6	160227084	160227084	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160227084A>G	uc003qsx.1	+	7	669	c.498A>G	c.(496-498)GAA>GAG	p.E166E	PNLDC1_uc003qsy.1_Silent_p.E177E	NM_173516	NP_775787	Q8NA58	PNDC1_HUMAN	poly(A)-specific ribonuclease (PARN)-like domain	166	Cytoplasmic (Potential).					integral to membrane|nucleus	nucleic acid binding				0		Breast(66;0.00519)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;1.55e-18)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)														---	---	---	---
PNLDC1	154197	broad.mit.edu	37	6	160237639	160237639	+	Intron	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160237639C>T	uc003qsx.1	+						PNLDC1_uc003qsy.1_Intron	NM_173516	NP_775787			poly(A)-specific ribonuclease (PARN)-like domain							integral to membrane|nucleus	nucleic acid binding				0		Breast(66;0.00519)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;1.55e-18)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)														---	---	---	---
AGPAT4	56895	broad.mit.edu	37	6	161560485	161560485	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161560485C>T	uc003qtr.1	-	8	1238	c.1011G>A	c.(1009-1011)ACG>ACA	p.T337T	AGPAT4_uc003qts.1_Silent_p.T197T|AGPAT4_uc011egb.1_Silent_p.T175T	NM_020133	NP_064518	Q9NRZ5	PLCD_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 4	337					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	161587387	161587387	+	Missense_Mutation	SNP	C	T	T	rs115923077	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161587387C>T	uc003qtr.1	-	3	468	c.241G>A	c.(241-243)GCC>ACC	p.A81T	AGPAT4_uc003qts.1_Intron|AGPAT4_uc011egb.1_Intron|AGPAT4_uc003qtt.1_RNA|AGPAT4_uc011egc.1_Missense_Mutation_p.A81T|AGPAT4_uc011egd.1_Missense_Mutation_p.A19T|AGPAT4_uc011ege.1_Intron	NM_020133	NP_064518	Q9NRZ5	PLCD_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 4	81					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)														---	---	---	---
UNC93A	54346	broad.mit.edu	37	6	167721271	167721271	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167721271G>A	uc003qvq.2	+	7	1156	c.981G>A	c.(979-981)GCG>GCA	p.A327A	UNC93A_uc003qvr.2_Silent_p.A285A	NM_018974	NP_061847	Q86WB7	UN93A_HUMAN	unc-93 homolog A isoform 1	327	Helical; (Potential).					integral to membrane|plasma membrane					0		Breast(66;7.62e-05)|Ovarian(120;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)														---	---	---	---
MLLT4	4301	broad.mit.edu	37	6	168315892	168315892	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168315892C>T	uc003qwd.2	+	18	2462	c.2320C>T	c.(2320-2322)CGC>TGC	p.R774C	MLLT4_uc003qwb.1_Missense_Mutation_p.R759C|MLLT4_uc003qwc.1_Missense_Mutation_p.R775C|MLLT4_uc003qwg.1_Missense_Mutation_p.R84C	NM_001040001	NP_001035090	P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia	775	Dilute.				adherens junction organization|cell adhesion|cell junction assembly|cell-cell signaling|signal transduction	adherens junction|cell-cell junction|cytosol|nucleus	protein C-terminus binding			ovary(2)|lung(1)|kidney(1)|central_nervous_system(1)	5		Breast(66;1.07e-05)|Ovarian(120;0.024)		Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117)				T	MLL	AL								---	---	---	---
THBS2	7058	broad.mit.edu	37	6	169648753	169648753	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169648753G>A	uc003qwt.2	-	4	616	c.368C>T	c.(367-369)ACG>ATG	p.T123M		NM_003247	NP_003238	P35442	TSP2_HUMAN	thrombospondin 2 precursor	123	TSP N-terminal.|Heparin-binding (Potential).				cell adhesion	extracellular region	calcium ion binding|heparin binding|protein binding|structural molecule activity			ovary(5)	5		Breast(66;1.78e-05)|Ovarian(120;0.0728)|Esophageal squamous(34;0.247)		OV - Ovarian serous cystadenocarcinoma(33;1.85e-21)|BRCA - Breast invasive adenocarcinoma(81;1.43e-06)|GBM - Glioblastoma multiforme(31;0.000379)														---	---	---	---
ADAP1	11033	broad.mit.edu	37	7	939112	939112	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:939112G>A	uc003sjo.3	-	9	987	c.811C>T	c.(811-813)CGG>TGG	p.R271W	ADAP1_uc003sjm.3_Missense_Mutation_p.R97W|ADAP1_uc011jvs.1_Missense_Mutation_p.R176W|ADAP1_uc003sjn.3_Missense_Mutation_p.R199W|ADAP1_uc010ksc.2_Missense_Mutation_p.R199W	NM_006869	NP_006860	O75689	ADAP1_HUMAN	centaurin, alpha 1	271	PH 2.				cell surface receptor linked signaling pathway|regulation of ARF GTPase activity	cytoplasm|nucleus|plasma membrane	ARF GTPase activator activity|inositol 1,3,4,5 tetrakisphosphate binding|protein binding|zinc ion binding			upper_aerodigestive_tract(1)	1																		---	---	---	---
INTS1	26173	broad.mit.edu	37	7	1538916	1538916	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1538916C>A	uc003skn.2	-	7	1026	c.925G>T	c.(925-927)GAG>TAG	p.E309*	INTS1_uc003skq.2_Nonsense_Mutation_p.E309*	NM_001080453	NP_001073922	Q8N201	INT1_HUMAN	integrator complex subunit 1	309					snRNA processing	integral to membrane|integrator complex|nuclear membrane					0		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)														---	---	---	---
SDK1	221935	broad.mit.edu	37	7	4172065	4172065	+	Intron	SNP	C	T	T	rs113375564		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4172065C>T	uc003smx.2	+						SDK1_uc010kso.2_Intron|SDK1_uc003smy.2_Intron	NM_152744	NP_689957			sidekick 1 precursor						cell adhesion	integral to membrane				large_intestine(3)|ovary(2)|skin(1)	6		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)														---	---	---	---
ZDHHC4	55146	broad.mit.edu	37	7	6620233	6620233	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6620233T>C	uc003sqi.2	+	4	399	c.41T>C	c.(40-42)GTG>GCG	p.V14A	ZDHHC4_uc003sqg.2_Missense_Mutation_p.V14A|ZDHHC4_uc003sql.2_Missense_Mutation_p.V14A|ZDHHC4_uc003sqh.2_Missense_Mutation_p.V14A|ZDHHC4_uc003sqj.2_Missense_Mutation_p.V14A|ZDHHC4_uc003sqk.2_Missense_Mutation_p.V14A|ZDHHC4_uc003sqm.2_Missense_Mutation_p.V14A	NM_001134388	NP_001127860	Q9NPG8	ZDHC4_HUMAN	zinc finger, DHHC-type containing 4	14	Helical; (Potential).					integral to membrane	acyltransferase activity|zinc ion binding			breast(1)|pancreas(1)	2		Ovarian(82;0.232)		UCEC - Uterine corpus endometrioid carcinoma (126;0.1)														---	---	---	---
ZNF12	7559	broad.mit.edu	37	7	6731401	6731401	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6731401G>A	uc003sqt.1	-	5	1726	c.1172C>T	c.(1171-1173)TCG>TTG	p.S391L	ZNF12_uc011jxa.1_Missense_Mutation_p.S229L|ZNF12_uc003sqs.1_Missense_Mutation_p.S353L	NM_016265	NP_057349	P17014	ZNF12_HUMAN	zinc finger protein 12 isoform a	391	C2H2-type 5.				negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Ovarian(82;0.0776)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0231)														---	---	---	---
THSD7A	221981	broad.mit.edu	37	7	11485803	11485803	+	Silent	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11485803C>A	uc003ssf.3	-	13	3201	c.2949G>T	c.(2947-2949)CTG>CTT	p.L983L		NM_015204	NP_056019	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	983	TSP type-1 10.|Extracellular (Potential).					integral to membrane				ovary(3)	3				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)											HNSCC(18;0.044)			---	---	---	---
TMEM195	392636	broad.mit.edu	37	7	15458233	15458233	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:15458233C>T	uc003stb.1	-	5	729	c.559G>A	c.(559-561)GCT>ACT	p.A187T		NM_001004320	NP_001004320	Q6ZNB7	ALKMO_HUMAN	transmembrane protein 195	187					ether lipid metabolic process|fatty acid biosynthetic process|membrane lipid metabolic process	endoplasmic reticulum membrane|integral to membrane	glyceryl-ether monooxygenase activity|iron ion binding				0																		---	---	---	---
MPP6	51678	broad.mit.edu	37	7	24681374	24681374	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:24681374A>G	uc003swx.2	+	4	456	c.157A>G	c.(157-159)AGT>GGT	p.S53G	MPP6_uc003swy.2_Missense_Mutation_p.S53G	NM_016447	NP_057531	Q9NZW5	MPP6_HUMAN	membrane protein, palmitoylated 6	53	L27 2.				protein complex assembly		protein binding				0																		---	---	---	---
CCDC129	223075	broad.mit.edu	37	7	31592688	31592688	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31592688A>G	uc003tcj.1	+	2	1043	c.50A>G	c.(49-51)GAA>GGA	p.E17G	CCDC129_uc011kad.1_Missense_Mutation_p.E27G|CCDC129_uc003tci.1_Missense_Mutation_p.E16G|CCDC129_uc011kae.1_Missense_Mutation_p.E43G|CCDC129_uc003tck.1_5'Flank	NM_194300	NP_919276	Q6ZRS4	CC129_HUMAN	coiled-coil domain containing 129	17											0																		---	---	---	---
PDE1C	5137	broad.mit.edu	37	7	32109997	32109997	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:32109997C>T	uc003tcm.1	-	1	478	c.9G>A	c.(7-9)TCG>TCA	p.S3S	PDE1C_uc003tcn.1_Silent_p.S3S|PDE1C_uc003tco.1_Intron|PDE1C_uc003tcr.2_Silent_p.S3S|PDE1C_uc003tcs.2_Silent_p.S3S	NM_005020	NP_005011	Q14123	PDE1C_HUMAN	phosphodiesterase 1C	3					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)															---	---	---	---
BBS9	27241	broad.mit.edu	37	7	33427709	33427709	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33427709G>A	uc003tdn.1	+	19	2581	c.2068G>A	c.(2068-2070)GCC>ACC	p.A690T	BBS9_uc003tdo.1_Missense_Mutation_p.A655T|BBS9_uc003tdp.1_Missense_Mutation_p.A685T|BBS9_uc003tdq.1_Missense_Mutation_p.A650T|BBS9_uc010kwn.1_RNA|BBS9_uc003tdr.1_Missense_Mutation_p.A214T|BBS9_uc003tds.1_Missense_Mutation_p.A113T|BBS9_uc003tdt.2_RNA	NM_198428	NP_940820	Q3SYG4	PTHB1_HUMAN	parathyroid hormone-responsive B1 isoform 2	690					fat cell differentiation|response to stimulus|visual perception	BBSome|cilium membrane|microtubule organizing center|nucleus	protein binding			ovary(3)|upper_aerodigestive_tract(1)|skin(1)	5			GBM - Glioblastoma multiforme(11;0.0894)											Bardet-Biedl_syndrome				---	---	---	---
ANLN	54443	broad.mit.edu	37	7	36450724	36450724	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36450724G>T	uc003tff.2	+	7	1548	c.1344G>T	c.(1342-1344)TGG>TGT	p.W448C	ANLN_uc011kaz.1_Missense_Mutation_p.W360C|ANLN_uc003tfg.2_Missense_Mutation_p.W448C|ANLN_uc010kxe.2_Missense_Mutation_p.W448C	NM_018685	NP_061155	Q9NQW6	ANLN_HUMAN	anillin, actin binding protein	448	Interaction with F-actin.				cytokinesis|mitosis|regulation of exit from mitosis|septin ring assembly	actomyosin contractile ring|nucleus	actin binding			ovary(2)|skin(1)	3																		---	---	---	---
ELMO1	9844	broad.mit.edu	37	7	37052934	37052934	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37052934T>C	uc003tfk.1	-	16	1714	c.1407A>G	c.(1405-1407)GAA>GAG	p.E469E	ELMO1_uc011kbc.1_Silent_p.E373E|ELMO1_uc010kxg.1_Silent_p.E469E	NM_014800	NP_055615	Q92556	ELMO1_HUMAN	engulfment and cell motility 1 isoform 1	469	ELMO.				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																		---	---	---	---
SFRP4	6424	broad.mit.edu	37	7	37949294	37949294	+	Intron	SNP	T	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37949294T>A	uc003tfo.3	-							NM_003014	NP_003005			secreted frizzled-related  protein 4 precursor						brain development|cell differentiation|decidualization|embryo development|epithelium development|gonad development|mammary gland involution|menstrual cycle phase|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cell proliferation|negative regulation of JNK cascade|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of sodium-dependent phosphate transport|phosphate ion homeostasis|positive regulation of apoptosis|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of epidermal cell differentiation|positive regulation of gene expression|positive regulation of receptor internalization|vasculature development|Wnt receptor signaling pathway	cell surface|cytoplasm|extracellular space|nucleus	PDZ domain binding|Wnt receptor activity|Wnt-protein binding			lung(1)	1																		---	---	---	---
CDK13	8621	broad.mit.edu	37	7	40132832	40132832	+	Silent	SNP	G	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:40132832G>C	uc003thh.3	+	13	3966	c.3684G>C	c.(3682-3684)GTG>GTC	p.V1228V	CDK13_uc003thi.3_Silent_p.V1168V|CDK13_uc003thj.2_Silent_p.V279V|CDK13_uc003thk.2_Silent_p.V161V	NM_003718	NP_003709	Q14004	CDK13_HUMAN	cell division cycle 2-like 5 isoform 1	1228					alternative nuclear mRNA splicing, via spliceosome|hemopoiesis|interspecies interaction between organisms|phosphorylation of RNA polymerase II C-terminal domain|positive regulation of cell proliferation|regulation of mitosis	nuclear cyclin-dependent protein kinase holoenzyme complex|nuclear speck	ATP binding|cyclin-dependent protein kinase activity|protein binding|RNA polymerase II carboxy-terminal domain kinase activity			lung(2)|skin(2)|ovary(1)	5																		---	---	---	---
GLI3	2737	broad.mit.edu	37	7	42005251	42005251	+	Silent	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:42005251G>T	uc011kbh.1	-	15	3511	c.3420C>A	c.(3418-3420)GGC>GGA	p.G1140G	GLI3_uc011kbg.1_Silent_p.G1081G	NM_000168	NP_000159	P10071	GLI3_HUMAN	GLI-Kruppel family member GLI3	1140					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				---	---	---	---
NUDCD3	23386	broad.mit.edu	37	7	44507818	44507818	+	Intron	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44507818G>A	uc003tkz.2	-						NUDCD3_uc010kye.2_Intron	NM_015332	NP_056147			NudC domain containing 3												0																		---	---	---	---
DDX56	54606	broad.mit.edu	37	7	44612618	44612618	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44612618C>T	uc003tlg.2	-	3	897	c.254G>A	c.(253-255)GGC>GAC	p.G85D	DDX56_uc003tle.2_RNA|DDX56_uc003tlf.2_Missense_Mutation_p.G21D|DDX56_uc003tlh.2_RNA|DDX56_uc010kyg.2_Missense_Mutation_p.G85D|DDX56_uc010kyh.1_Intron	NM_019082	NP_061955	Q9NY93	DDX56_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 56	85	Helicase ATP-binding.				rRNA processing	nucleolus	ATP binding|ATP-dependent RNA helicase activity|identical protein binding|RNA binding			upper_aerodigestive_tract(1)	1																		---	---	---	---
OGDH	4967	broad.mit.edu	37	7	44713473	44713473	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44713473C>T	uc003tln.2	+	6	830	c.721C>T	c.(721-723)CCT>TCT	p.P241S	OGDH_uc003tlm.2_Missense_Mutation_p.P241S|OGDH_uc011kbx.1_Missense_Mutation_p.P237S|OGDH_uc011kby.1_Intron|OGDH_uc003tlp.2_Missense_Mutation_p.P252S|OGDH_uc011kbz.1_Intron|OGDH_uc003tlo.1_Missense_Mutation_p.P74S	NM_002541	NP_002532	Q02218	ODO1_HUMAN	oxoglutarate dehydrogenase isoform 1 precursor	241					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)													---	---	---	---
IKZF1	10320	broad.mit.edu	37	7	50467674	50467674	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:50467674C>T	uc003tow.3	+	9	1077	c.909C>T	c.(907-909)AAC>AAT	p.N303N	IKZF1_uc003tox.3_Silent_p.N261N|IKZF1_uc003toy.3_Silent_p.N261N|IKZF1_uc011kck.1_Silent_p.N216N|IKZF1_uc003toz.3_Silent_p.N273N|IKZF1_uc010kyx.2_Silent_p.N43N|IKZF1_uc003tpa.3_Silent_p.N45N	NM_006060	NP_006051	Q13422	IKZF1_HUMAN	zinc finger protein, subfamily 1A, 1 (Ikaros)	303					cell cycle|chromatin modification|mesoderm development	cytoplasm|nucleus	zinc ion binding			haematopoietic_and_lymphoid_tissue(147)|lung(1)	148	Glioma(55;0.08)|all_neural(89;0.245)	Acute lymphoblastic leukemia(4;7.29e-10)|all_hematologic(4;4.8e-07)						D		ALL								---	---	---	---
COBL	23242	broad.mit.edu	37	7	51096609	51096609	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:51096609G>A	uc003tpr.3	-	10	2369	c.2184C>T	c.(2182-2184)ACC>ACT	p.T728T	COBL_uc003tps.2_Silent_p.T785T|COBL_uc011kcl.1_Silent_p.T728T|COBL_uc003tpp.3_Silent_p.T514T|COBL_uc003tpq.3_Silent_p.T669T|COBL_uc003tpo.3_Silent_p.T270T	NM_015198	NP_056013	O75128	COBL_HUMAN	cordon-bleu homolog	728										skin(3)|ovary(2)	5	Glioma(55;0.08)																	---	---	---	---
ZNF680	340252	broad.mit.edu	37	7	63981628	63981628	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:63981628A>T	uc003tta.2	-	4	1677	c.1504T>A	c.(1504-1506)TCC>ACC	p.S502T	ZNF680_uc010kzr.2_Missense_Mutation_p.S429T	NM_178558	NP_848653	Q8NEM1	ZN680_HUMAN	zinc finger protein 680 isoform 1	502	C2H2-type 12.				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)																---	---	---	---
VKORC1L1	154807	broad.mit.edu	37	7	65419074	65419074	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65419074C>T	uc003tul.2	+	3	420	c.318C>T	c.(316-318)AGC>AGT	p.S106S	VKORC1L1_uc011kds.1_Missense_Mutation_p.R70C|VKORC1L1_uc003tum.1_5'Flank	NM_173517	NP_775788	Q8N0U8	VKORL_HUMAN	vitamin K epoxide reductase complex, subunit	106	Helical; (Potential).					integral to membrane					0		Lung NSC(55;0.197)			Menadione(DB00170)|Warfarin(DB00682)													---	---	---	---
TBL2	26608	broad.mit.edu	37	7	72988315	72988315	+	Silent	SNP	G	A	A	rs147754612		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72988315G>A	uc003tyh.2	-	3	533	c.399C>T	c.(397-399)AAC>AAT	p.N133N	TBL2_uc011kex.1_Silent_p.N97N|TBL2_uc010lbg.2_Silent_p.N38N|TBL2_uc003tyi.2_Translation_Start_Site|TBL2_uc011key.1_Silent_p.N4N|TBL2_uc010lbh.2_Silent_p.N38N	NM_012453	NP_036585	Q9Y4P3	TBL2_HUMAN	transducin (beta)-like 2	133											0		Lung NSC(55;0.0659)|all_lung(88;0.152)																---	---	---	---
CLDN4	1364	broad.mit.edu	37	7	73246173	73246173	+	3'UTR	SNP	T	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73246173T>A	uc003tzi.3	+	1					RFC2_uc011kfa.1_Intron|CLDN4_uc003tzh.1_RNA	NM_001305	NP_001296			claudin 4						calcium-independent cell-cell adhesion	integral to plasma membrane|tight junction	identical protein binding|structural molecule activity|transmembrane receptor activity				0		Lung NSC(55;0.159)																---	---	---	---
CLIP2	7461	broad.mit.edu	37	7	73778608	73778608	+	Missense_Mutation	SNP	G	A	A	rs140333329		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73778608G>A	uc003uam.2	+	8	1670	c.1343G>A	c.(1342-1344)CGC>CAC	p.R448H	CLIP2_uc003uan.2_Missense_Mutation_p.R448H	NM_003388	NP_003379	Q9UDT6	CLIP2_HUMAN	CAP-GLY domain containing linker protein 2	448	Potential.					microtubule associated complex				skin(3)	3																		---	---	---	---
POM121C	100101267	broad.mit.edu	37	7	75053846	75053846	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75053846T>C	uc003udk.3	-	11	1719	c.834A>G	c.(832-834)TCA>TCG	p.S278S		NM_001099415	NP_001092885	A8CG34	P121C_HUMAN	POM121 membrane glycoprotein (rat)-like	520	Pore side (Potential).				mRNA transport|protein transport|transmembrane transport	endoplasmic reticulum membrane|nuclear membrane|nuclear pore	protein binding				0																		---	---	---	---
YWHAG	7532	broad.mit.edu	37	7	75959484	75959484	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75959484C>T	uc011kgj.1	-	2	371	c.154G>A	c.(154-156)GTT>ATT	p.V52I		NM_012479	NP_036611	P61981	1433G_HUMAN	tyrosine 3-monooxygenase/tryptophan	52					G2/M transition of mitotic cell cycle|regulation of neuron differentiation|regulation of signal transduction|regulation of synaptic plasticity	cytosol	insulin-like growth factor receptor binding|protein kinase C binding|protein kinase C inhibitor activity			ovary(1)|lung(1)	2																		---	---	---	---
ZP3	7784	broad.mit.edu	37	7	76062907	76062907	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76062907C>T	uc003ufd.3	+	4	666	c.656C>T	c.(655-657)GCC>GTC	p.A219V	ZP3_uc003ufc.3_Missense_Mutation_p.A168V|ZP3_uc003ufe.2_Missense_Mutation_p.A127V	NM_001110354	NP_001103824	P21754	ZP3_HUMAN	zona pellucida glycoprotein 3 isoform 1	219	Extracellular (Potential).|ZP.				binding of sperm to zona pellucida|blastocyst formation|egg coat formation|humoral immune response mediated by circulating immunoglobulin|intracellular protein transport|negative regulation of binding of sperm to zona pellucida|negative regulation of transcription, DNA-dependent|oocyte development|phosphatidylinositol-mediated signaling|positive regulation of acrosomal vesicle exocytosis|positive regulation of acrosome reaction|positive regulation of antral ovarian follicle growth|positive regulation of calcium ion import|positive regulation of calcium ion transport via store-operated calcium channel activity|positive regulation of humoral immune response|positive regulation of interferon-gamma production|positive regulation of interleukin-4 production|positive regulation of leukocyte migration|positive regulation of ovarian follicle development|positive regulation of phosphatidylinositol biosynthetic process|positive regulation of protein kinase activity|positive regulation of protein kinase B signaling cascade|positive regulation of T cell proliferation|positive regulation of transcription, DNA-dependent|positive regulation of type IV hypersensitivity|protein kinase C signaling cascade	endoplasmic reticulum|extracellular space|Golgi apparatus|integral to membrane|multivesicular body|outer acrosomal membrane|perinuclear region of cytoplasm|plasma membrane|proteinaceous extracellular matrix	acrosin binding|manganese ion transmembrane transporter activity|receptor activity|sugar binding				0																		---	---	---	---
CCDC146	57639	broad.mit.edu	37	7	76891552	76891552	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76891552G>T	uc003uga.2	+	9	1228	c.1101G>T	c.(1099-1101)ATG>ATT	p.M367I	CCDC146_uc010ldp.2_Missense_Mutation_p.M113I	NM_020879	NP_065930	Q8IYE0	CC146_HUMAN	coiled-coil domain containing 146	367										ovary(1)|central_nervous_system(1)	2		all_cancers(73;0.128)|all_lung(88;0.0986)|all_epithelial(88;0.163)|Myeloproliferative disorder(862;0.205)																---	---	---	---
GNAI1	2770	broad.mit.edu	37	7	79818534	79818534	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:79818534A>G	uc003uhb.1	+	3	627	c.290A>G	c.(289-291)GAC>GGC	p.D97G	GNAI1_uc011kgt.1_Missense_Mutation_p.D45G	NM_002069	NP_002060	P63096	GNAI1_HUMAN	guanine nucleotide binding protein (G protein),	97					cell cycle|cell division|inhibition of adenylate cyclase activity by G-protein signaling pathway|platelet activation|synaptic transmission	centrosome|heterotrimeric G-protein complex|midbody|nucleus	G-protein beta/gamma-subunit complex binding|GTP binding|metabotropic serotonin receptor binding|signal transducer activity			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
PCLO	27445	broad.mit.edu	37	7	82579728	82579728	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82579728G>A	uc003uhx.2	-	6	10465	c.10176C>T	c.(10174-10176)AGC>AGT	p.S3392S	PCLO_uc003uhv.2_Silent_p.S3392S|PCLO_uc010lec.2_Silent_p.S357S	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	3323					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	82584025	82584025	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82584025G>T	uc003uhx.2	-	5	6533	c.6244C>A	c.(6244-6246)CCA>ACA	p.P2082T	PCLO_uc003uhv.2_Missense_Mutation_p.P2082T	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	2013					cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity			ovary(7)	7																		---	---	---	---
SEMA3A	10371	broad.mit.edu	37	7	83764138	83764138	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:83764138T>A	uc003uhz.2	-	2	557	c.242A>T	c.(241-243)GAC>GTC	p.D81V		NM_006080	NP_006071	Q14563	SEM3A_HUMAN	semaphorin 3A precursor	81	Sema.				axon guidance	extracellular region|membrane	receptor activity			ovary(2)|breast(1)|kidney(1)	4																		---	---	---	---
ABCB1	5243	broad.mit.edu	37	7	87196110	87196110	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87196110C>T	uc003uiz.1	-	7	939	c.521G>A	c.(520-522)CGA>CAA	p.R174Q	ABCB1_uc011khc.1_Intron	NM_000927	NP_000918	P08183	MDR1_HUMAN	ATP-binding cassette, subfamily B, member 1	174	ABC transmembrane type-1 1.				G2/M transition of mitotic cell cycle|stem cell proliferation	apical plasma membrane|cell surface|Golgi membrane|integral to membrane|intercellular canaliculus|membrane fraction	ATP binding|protein binding|xenobiotic-transporting ATPase activity			ovary(4)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	7	Esophageal squamous(14;0.00164)				Adenosine triphosphate(DB00171)|Alfentanil(DB00802)|Arsenic trioxide(DB01169)|Atazanavir(DB01072)|Carvedilol(DB01136)|Colchicine(DB01394)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dipyridamole(DB00975)|Estramustine(DB01196)|Flupenthixol(DB00875)|Imatinib(DB00619)|Itraconazole(DB01167)|Nicardipine(DB00622)|Propafenone(DB01182)|Quinacrine(DB01103)|Quinidine(DB00908)|Ranolazine(DB00243)|Rifampin(DB01045)|Roxithromycin(DB00778)|Saquinavir(DB01232)|Tamoxifen(DB00675)|Vinblastine(DB00570)													---	---	---	---
ZNF804B	219578	broad.mit.edu	37	7	88964957	88964957	+	Silent	SNP	G	A	A	rs138375583	byFrequency	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:88964957G>A	uc011khi.1	+	4	3199	c.2661G>A	c.(2659-2661)AGG>AGA	p.R887R		NM_181646	NP_857597	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	887						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)			---	---	---	---
STEAP1	26872	broad.mit.edu	37	7	89790129	89790129	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:89790129C>T	uc003ujx.2	+	3	295	c.95C>T	c.(94-96)ACG>ATG	p.T32M	STEAP1_uc010lem.2_Missense_Mutation_p.T32M	NM_012449	NP_036581	Q9UHE8	STEA1_HUMAN	six transmembrane epithelial antigen of the	32					electron transport chain|ion transport|iron ion homeostasis	cell-cell junction|endosome membrane|integral to plasma membrane	channel activity|electron carrier activity|flavin adenine dinucleotide binding|iron ion binding|oxidoreductase activity				0	all_hematologic(106;0.112)																	---	---	---	---
PEX1	5189	broad.mit.edu	37	7	92146932	92146932	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92146932G>A	uc003uly.2	-	5	993	c.897C>T	c.(895-897)AAC>AAT	p.N299N	PEX1_uc011khr.1_Silent_p.N91N|PEX1_uc010ley.2_Silent_p.N299N|PEX1_uc011khs.1_Intron|PEX1_uc011kht.1_RNA	NM_000466	NP_000457	O43933	PEX1_HUMAN	peroxin1	299					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	92163897	92163897	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92163897T>C	uc003ulz.2	+	4	671	c.630T>C	c.(628-630)TGT>TGC	p.C210C	C7orf64_uc011khu.1_3'UTR|C7orf64_uc003uma.2_Silent_p.C210C	NM_032120	NP_115496	Q5RL73	CG064_HUMAN	hypothetical protein LOC84060	210							nucleotide binding			ovary(2)	2																		---	---	---	---
HEPACAM2	253012	broad.mit.edu	37	7	92848540	92848540	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92848540G>A	uc003umm.2	-	2	327	c.304C>T	c.(304-306)CCA>TCA	p.P102S	HEPACAM2_uc003uml.2_Missense_Mutation_p.P90S|HEPACAM2_uc010lff.2_Missense_Mutation_p.P90S|HEPACAM2_uc011khy.1_Missense_Mutation_p.P125S	NM_001039372	NP_001034461	A8MVW5	HECA2_HUMAN	HEPACAM family member 2 isoform 1	102	Extracellular (Potential).					integral to membrane		p.F102L(1)		ovary(3)|breast(1)|kidney(1)	5																		---	---	---	---
CCDC132	55610	broad.mit.edu	37	7	92882054	92882054	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92882054T>C	uc003umo.2	+	3	319	c.191T>C	c.(190-192)GTG>GCG	p.V64A	CCDC132_uc003umq.2_RNA|CCDC132_uc003ump.2_Missense_Mutation_p.V34A|CCDC132_uc003umr.2_Intron|CCDC132_uc011khz.1_Intron|CCDC132_uc003umn.2_Missense_Mutation_p.V64A	NM_017667	NP_060137	Q96JG6	CC132_HUMAN	coiled-coil domain containing 132 isoform a	64											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)															---	---	---	---
CASD1	64921	broad.mit.edu	37	7	94184921	94184921	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94184921G>A	uc003uni.3	+	18	2472	c.2245G>A	c.(2245-2247)GCA>ACA	p.A749T	CASD1_uc003unj.3_Missense_Mutation_p.A749T	NM_022900	NP_075051	Q96PB1	CASD1_HUMAN	CAS1 domain containing 1 precursor	749						integral to membrane				ovary(2)	2	all_cancers(62;6.71e-10)|all_epithelial(64;5e-09)|Lung NSC(181;0.188)|all_lung(186;0.215)		STAD - Stomach adenocarcinoma(171;0.0031)															---	---	---	---
SGCE	8910	broad.mit.edu	37	7	94252690	94252690	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94252690C>T	uc003unl.2	-	4	521	c.410G>A	c.(409-411)CGC>CAC	p.R137H	SGCE_uc003unm.2_Missense_Mutation_p.R137H|SGCE_uc003unn.2_Missense_Mutation_p.R137H|SGCE_uc011kic.1_Missense_Mutation_p.R96H|SGCE_uc011kid.1_Missense_Mutation_p.R173H	NM_003919	NP_003910	O43556	SGCE_HUMAN	sarcoglycan, epsilon isoform 2	137	Extracellular (Potential).				cell-matrix adhesion|muscle organ development	cytoplasm|cytoskeleton|integral to plasma membrane|sarcoglycan complex|sarcolemma	calcium ion binding			ovary(1)	1	all_cancers(62;8.26e-10)|all_epithelial(64;5.59e-09)|Lung NSC(181;0.188)|all_lung(186;0.215)		STAD - Stomach adenocarcinoma(171;0.0031)															---	---	---	---
PPP1R9A	55607	broad.mit.edu	37	7	94915646	94915646	+	Intron	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94915646A>G	uc003unp.2	+						PPP1R9A_uc010lfj.2_Intron|PPP1R9A_uc011kif.1_Intron|PPP1R9A_uc003unq.2_Intron|PPP1R9A_uc011kig.1_Intron|PPP1R9A_uc003unr.2_Intron	NM_017650	NP_060120			protein phosphatase 1, regulatory (inhibitor)							cell junction|synapse|synaptosome	actin binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	4	all_cancers(62;9.12e-11)|all_epithelial(64;4.34e-09)		STAD - Stomach adenocarcinoma(171;0.0031)												HNSCC(28;0.073)			---	---	---	---
LMTK2	22853	broad.mit.edu	37	7	97823050	97823050	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97823050G>A	uc003upd.1	+	11	3566	c.3273G>A	c.(3271-3273)ACG>ACA	p.T1091T		NM_014916	NP_055731	Q8IWU2	LMTK2_HUMAN	lemur tyrosine kinase 2 precursor	1091					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	97872868	97872868	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97872868G>A	uc003upg.2	-	6	773	c.568C>T	c.(568-570)CCC>TCC	p.P190S	TECPR1_uc003uph.1_Missense_Mutation_p.P111S	NM_015395	NP_056210	Q7Z6L1	TCPR1_HUMAN	tectonin beta-propeller repeat containing 1	190						integral to membrane	protein binding			pancreas(1)	1																		---	---	---	---
AGFG2	3268	broad.mit.edu	37	7	100151089	100151089	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100151089C>T	uc003uvf.2	+	4	687	c.551C>T	c.(550-552)CCG>CTG	p.P184L	AGFG2_uc003uvg.1_Intron|AGFG2_uc010lgy.2_Missense_Mutation_p.R46C	NM_006076	NP_006067	O95081	AGFG2_HUMAN	ArfGAP with FG repeats 2	184					regulation of ARF GTPase activity		ARF GTPase activator activity|zinc ion binding			central_nervous_system(1)	1																		---	---	---	---
ACTL6B	51412	broad.mit.edu	37	7	100247736	100247736	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100247736T>A	uc003uvy.2	-	5	499	c.392A>T	c.(391-393)GAG>GTG	p.E131V	ACTL6B_uc003uvx.1_5'Flank|ACTL6B_uc003uvz.2_RNA	NM_016188	NP_057272	O94805	ACL6B_HUMAN	actin-like 6B	131					chromatin modification|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nBAF complex|SWI/SNF complex	ATP binding|protein binding|structural constituent of cytoskeleton			ovary(1)	1	Lung NSC(181;0.035)|all_lung(186;0.0509)|Esophageal squamous(72;0.0817)																	---	---	---	---
GIGYF1	64599	broad.mit.edu	37	7	100282135	100282135	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100282135C>T	uc003uwg.1	-	13	2576	c.1567G>A	c.(1567-1569)GAG>AAG	p.E523K		NM_022574	NP_072096	O75420	PERQ1_HUMAN	PERQ amino acid rich, with GYF domain 1	523										large_intestine(1)|central_nervous_system(1)	2	Lung NSC(181;0.035)|all_lung(186;0.0509)|Esophageal squamous(72;0.0817)																	---	---	---	---
TRIP6	7205	broad.mit.edu	37	7	100469244	100469244	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100469244C>A	uc003uww.2	+	7	1249	c.1079C>A	c.(1078-1080)CCT>CAT	p.P360H		NM_003302	NP_003293	Q15654	TRIP6_HUMAN	thyroid receptor-interacting protein 6	360	LIM zinc-binding 2.				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)																	---	---	---	---
MUC17	140453	broad.mit.edu	37	7	100677874	100677874	+	Silent	SNP	G	A	A	rs147962629	byFrequency	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100677874G>A	uc003uxp.1	+	3	3230	c.3177G>A	c.(3175-3177)ACG>ACA	p.T1059T	MUC17_uc010lho.1_RNA	NM_001040105	NP_001035194	Q685J3	MUC17_HUMAN	mucin 17 precursor	1059	Extracellular (Potential).|Ser-rich.|59 X approximate tandem repeats.|15.					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)																	---	---	---	---
SERPINE1	5054	broad.mit.edu	37	7	100773872	100773872	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100773872G>A	uc003uxt.2	+	3	590	c.442G>A	c.(442-444)GAC>AAC	p.D148N	SERPINE1_uc011kkj.1_Missense_Mutation_p.D133N|SERPINE1_uc003uxu.1_5'Flank	NM_000602	NP_000593	P05121	PAI1_HUMAN	plasminogen activator inhibitor-1 isoform 1	148					angiogenesis|cellular response to chemical stimulus|cellular response to lipopolysaccharide|chronological cell aging|defense response to Gram-negative bacterium|fibrinolysis|negative regulation of apoptosis|negative regulation of cell adhesion mediated by integrin|negative regulation of fibrinolysis|negative regulation of plasminogen activation|negative regulation of smooth muscle cell migration|negative regulation of smooth muscle cell-matrix adhesion|negative regulation of vascular wound healing|platelet activation|platelet degranulation|positive regulation of angiogenesis|positive regulation of interleukin-8 production|positive regulation of leukotriene production involved in inflammatory response|positive regulation of monocyte chemotaxis|positive regulation of receptor-mediated endocytosis|regulation of receptor activity	extracellular matrix|extracellular space|plasma membrane|platelet alpha granule lumen	protease binding|serine-type endopeptidase inhibitor activity			ovary(1)|lung(1)|central_nervous_system(1)	3	Lung NSC(181;0.136)|all_lung(186;0.182)				Atorvastatin(DB01076)|Dimethyl sulfoxide(DB01093)|Drotrecogin alfa(DB00055)|Simvastatin(DB00641)|Tenecteplase(DB00031)|Troglitazone(DB00197)|Urokinase(DB00013)													---	---	---	---
CUX1	1523	broad.mit.edu	37	7	101459368	101459368	+	5'Flank	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101459368C>T	uc003uyx.3	+						CUX1_uc003uys.3_Silent_p.L20L|CUX1_uc003uyt.2_Silent_p.L20L|CUX1_uc011kkn.1_Silent_p.L20L|CUX1_uc003uyw.2_Silent_p.L20L|CUX1_uc003uyv.2_Silent_p.L20L|CUX1_uc003uyu.2_Silent_p.L20L	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																		---	---	---	---
ORAI2	80228	broad.mit.edu	37	7	102086989	102086989	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102086989G>A	uc010lhz.1	+	4	490	c.255G>A	c.(253-255)ACG>ACA	p.T85T	ORAI2_uc003uzj.2_Silent_p.T85T|ORAI2_uc003uzk.2_Silent_p.T85T|ORAI2_uc011kks.1_Silent_p.T8T	NM_001126340	NP_001119812	Q96SN7	ORAI2_HUMAN	ORAI calcium release-activated calcium modulator	85						integral to membrane	protein binding			ovary(1)|kidney(1)	2																		---	---	---	---
PSMC2	5701	broad.mit.edu	37	7	103002424	103002424	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103002424C>T	uc003vbs.2	+	5	381	c.311C>T	c.(310-312)GCT>GTT	p.A104V	SLC26A5_uc003vbt.1_Intron|SLC26A5_uc003vbu.1_Intron|SLC26A5_uc003vbv.1_Intron|PSMC2_uc011kln.1_Missense_Mutation_p.A104V|PSMC2_uc011klo.1_5'UTR	NM_002803	NP_002794	P35998	PRS7_HUMAN	proteasome 26S ATPase subunit 2	104					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|interspecies interaction between organisms|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	mitochondrion|nucleus|proteasome complex	ATP binding|ATPase activity|protein binding				0																		---	---	---	---
RELN	5649	broad.mit.edu	37	7	103138557	103138557	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103138557G>A	uc003vca.2	-	54	8970	c.8810C>T	c.(8809-8811)GCG>GTG	p.A2937V	RELN_uc010liz.2_Missense_Mutation_p.A2937V	NM_005045	NP_005036	P78509	RELN_HUMAN	reelin isoform a	2937					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	103474007	103474007	+	Silent	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103474007C>A	uc003vca.2	-	3	610	c.450G>T	c.(448-450)GCG>GCT	p.A150A	RELN_uc010liz.2_Silent_p.A150A	NM_005045	NP_005036	P78509	RELN_HUMAN	reelin isoform a	150	Reelin.				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)														---	---	---	---
COG5	10466	broad.mit.edu	37	7	106851578	106851578	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:106851578G>A	uc003ved.2	-	19	2816	c.2291C>T	c.(2290-2292)ACG>ATG	p.T764M	COG5_uc003vec.2_Missense_Mutation_p.T785M|COG5_uc003vee.2_Missense_Mutation_p.T785M	NM_181733	NP_859422	Q9UP83	COG5_HUMAN	component of oligomeric golgi complex 5 isoform	764					intra-Golgi vesicle-mediated transport|protein transport	cytosol|Golgi membrane|Golgi transport complex|nucleus	protein binding			central_nervous_system(2)|skin(2)	4																		---	---	---	---
FOXP2	93986	broad.mit.edu	37	7	114270000	114270000	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:114270000G>A	uc003vhb.2	+	5	911	c.537G>A	c.(535-537)CAG>CAA	p.Q179Q	FOXP2_uc003vgu.2_RNA|FOXP2_uc003vgz.2_Silent_p.Q204Q|FOXP2_uc003vha.2_Silent_p.Q87Q|FOXP2_uc011kmu.1_Silent_p.Q196Q|FOXP2_uc011kmv.1_Silent_p.Q179Q|FOXP2_uc010ljz.1_Silent_p.Q87Q|FOXP2_uc003vgt.1_RNA|FOXP2_uc003vgv.1_Silent_p.Q179Q|FOXP2_uc003vgx.2_Silent_p.Q179Q|FOXP2_uc003vhd.2_Silent_p.Q179Q|FOXP2_uc003vhc.2_Silent_p.Q204Q	NM_014491	NP_055306	O15409	FOXP2_HUMAN	forkhead box P2 isoform I	179	Gln-rich.				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																		---	---	---	---
CFTR	1080	broad.mit.edu	37	7	117232480	117232480	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117232480C>T	uc003vjd.2	+	14	2391	c.2259C>T	c.(2257-2259)AGC>AGT	p.S753S	CFTR_uc011knq.1_Silent_p.S159S	NM_000492	NP_000483	P13569	CFTR_HUMAN	cystic fibrosis transmembrane conductance	753	Cytoplasmic (Potential).				respiratory gaseous exchange	apical plasma membrane|basolateral plasma membrane|chloride channel complex|early endosome membrane	ATP binding|ATP-binding and phosphorylation-dependent chloride channel activity|channel-conductance-controlling ATPase activity|chloride channel regulator activity|enzyme binding|PDZ domain binding			central_nervous_system(2)|skin(2)|ovary(1)	5	Lung NSC(10;0.00148)|all_lung(10;0.00171)		STAD - Stomach adenocarcinoma(10;0.000534)		Bumetanide(DB00887)|Glibenclamide(DB01016)									Cystic_Fibrosis				---	---	---	---
CTTNBP2	83992	broad.mit.edu	37	7	117407207	117407207	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117407207C>T	uc003vjf.2	-	9	2894	c.2802G>A	c.(2800-2802)AGG>AGA	p.R934R		NM_033427	NP_219499	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	934	ANK 6.									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)														---	---	---	---
C7orf58	79974	broad.mit.edu	37	7	120629693	120629693	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:120629693G>A	uc003vjq.3	+	2	465	c.18G>A	c.(16-18)GTG>GTA	p.V6V	C7orf58_uc003vjr.1_Silent_p.V6V|C7orf58_uc003vjs.3_Silent_p.V6V	NM_024913	NP_079189	A4D0V7	CG058_HUMAN	hypothetical protein LOC79974 isoform 1	6						endoplasmic reticulum				ovary(4)|large_intestine(2)|skin(2)|pancreas(1)	9	all_neural(327;0.117)																	---	---	---	---
RNF133	168433	broad.mit.edu	37	7	122337836	122337836	+	3'UTR	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122337836A>G	uc003vkj.1	-	1					CADPS2_uc010lkp.2_Intron|CADPS2_uc010lkq.2_Intron	NM_139175	NP_631914			ring finger protein 133							endoplasmic reticulum membrane|integral to membrane	ligase activity|zinc ion binding			skin(1)	1																		---	---	---	---
ASB15	142685	broad.mit.edu	37	7	123267253	123267253	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123267253C>T	uc003vku.1	+	9	1079	c.787C>T	c.(787-789)CTG>TTG	p.L263L	ASB15_uc003vkv.1_Silent_p.L263L|ASB15_uc003vkw.1_Silent_p.L263L	NM_080928	NP_563616	Q8WXK1	ASB15_HUMAN	ankyrin repeat and SOCS box-containing 15	263	ANK 5.				intracellular signal transduction					skin(2)|lung(1)	3																		---	---	---	---
FLNC	2318	broad.mit.edu	37	7	128484899	128484899	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128484899G>A	uc003vnz.3	+	21	3589	c.3380G>A	c.(3379-3381)GGC>GAC	p.G1127D	FLNC_uc003voa.3_Missense_Mutation_p.G1127D	NM_001458	NP_001449	Q14315	FLNC_HUMAN	gamma filamin isoform a	1127	Filamin 9.				cell junction assembly	cytoskeleton|cytosol|plasma membrane|sarcomere	actin binding			breast(5)|large_intestine(3)|ovary(2)|central_nervous_system(1)|skin(1)	12																		---	---	---	---
FLNC	2318	broad.mit.edu	37	7	128486107	128486107	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128486107G>A	uc003vnz.3	+	22	4063	c.3854G>A	c.(3853-3855)GGC>GAC	p.G1285D	FLNC_uc003voa.3_Missense_Mutation_p.G1285D	NM_001458	NP_001449	Q14315	FLNC_HUMAN	gamma filamin isoform a	1285	Filamin 11.				cell junction assembly	cytoskeleton|cytosol|plasma membrane|sarcomere	actin binding			breast(5)|large_intestine(3)|ovary(2)|central_nervous_system(1)|skin(1)	12																		---	---	---	---
AHCYL2	23382	broad.mit.edu	37	7	129019487	129019487	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129019487G>C	uc011kov.1	+	2	426	c.372G>C	c.(370-372)CAG>CAC	p.Q124H	AHCYL2_uc003vot.2_Missense_Mutation_p.Q123H|AHCYL2_uc003vov.2_Missense_Mutation_p.Q21H|AHCYL2_uc011kow.1_Missense_Mutation_p.Q22H|AHCYL2_uc011kox.1_Missense_Mutation_p.Q21H	NM_015328	NP_056143	Q96HN2	SAHH3_HUMAN	S-adenosylhomocysteine hydrolase-like 2 isoform	124					one-carbon metabolic process		adenosylhomocysteinase activity			ovary(2)	2																		---	---	---	---
FAM40B	57464	broad.mit.edu	37	7	129096401	129096401	+	Missense_Mutation	SNP	C	T	T	rs150058386		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129096401C>T	uc011koy.1	+	9	996	c.956C>T	c.(955-957)CCG>CTG	p.P319L	FAM40B_uc003vow.2_Missense_Mutation_p.P319L|FAM40B_uc011koz.1_5'Flank	NM_020704	NP_065755	Q9ULQ0	FA40B_HUMAN	hypothetical protein LOC57464 isoform a	319											0																		---	---	---	---
TSGA13	114960	broad.mit.edu	37	7	130364019	130364019	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130364019A>G	uc003vqi.2	-	5	818	c.361T>C	c.(361-363)TCC>CCC	p.S121P	TSGA13_uc003vqj.2_Missense_Mutation_p.S121P	NM_052933	NP_443165	Q96PP4	TSG13_HUMAN	testis specific, 13	121										ovary(2)	2	Melanoma(18;0.0435)																	---	---	---	---
PLXNA4	91584	broad.mit.edu	37	7	131866287	131866287	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131866287G>A	uc003vra.3	-	18	3574	c.3345C>T	c.(3343-3345)CCC>CCT	p.P1115P		NM_020911	NP_065962	Q9HCM2	PLXA4_HUMAN	plexin A4 isoform 1	1115	Extracellular (Potential).|IPT/TIG 3.					integral to membrane|intracellular|plasma membrane				ovary(1)	1																		---	---	---	---
LRGUK	136332	broad.mit.edu	37	7	133906546	133906546	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:133906546A>G	uc003vrm.1	+	16	1875	c.1859A>G	c.(1858-1860)CAC>CGC	p.H620R		NM_144648	NP_653249	Q96M69	LRGUK_HUMAN	leucine-rich repeats and guanylate kinase domain	620							ATP binding|kinase activity			lung(2)|skin(2)|kidney(1)	5																		---	---	---	---
AKR1B1	231	broad.mit.edu	37	7	134135578	134135578	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134135578T>C	uc003vrp.1	-	3	385	c.311A>G	c.(310-312)TAC>TGC	p.Y104C	AKR1B1_uc003vrq.1_RNA	NM_001628	NP_001619	P15121	ALDR_HUMAN	aldo-keto reductase family 1, member B1	104					C21-steroid hormone biosynthetic process|carbohydrate metabolic process|response to stress	cytosol|extracellular space|nucleus	alditol:NADP+ 1-oxidoreductase activity|electron carrier activity|protein binding			ovary(3)	3					NADH(DB00157)|Sulindac(DB00605)													---	---	---	---
DGKI	9162	broad.mit.edu	37	7	137172408	137172408	+	Missense_Mutation	SNP	C	T	T	rs148779791		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:137172408C>T	uc003vtt.2	-	23	2331	c.2330G>A	c.(2329-2331)CGT>CAT	p.R777H	DGKI_uc003vtu.2_Missense_Mutation_p.R477H	NM_004717	NP_004708	O75912	DGKI_HUMAN	diacylglycerol kinase, iota	777					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																		---	---	---	---
ATP6V0A4	50617	broad.mit.edu	37	7	138418958	138418958	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138418958C>T	uc003vuf.2	-	15	1852	c.1614G>A	c.(1612-1614)TCG>TCA	p.S538S	ATP6V0A4_uc003vug.2_Silent_p.S538S|ATP6V0A4_uc003vuh.2_Silent_p.S538S	NM_130841	NP_570856	Q9HBG4	VPP4_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit	538	Cytoplasmic (Potential).				cellular iron ion homeostasis|excretion|insulin receptor signaling pathway|ossification|regulation of pH|sensory perception of sound|transferrin transport	apical plasma membrane|brush border membrane|endosome membrane|integral to membrane|proton-transporting two-sector ATPase complex, proton-transporting domain	ATPase binding|hydrogen ion transmembrane transporter activity			pancreas(1)	1																		---	---	---	---
TTC26	79989	broad.mit.edu	37	7	138865925	138865925	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138865925T>A	uc003vus.2	+	16	1514	c.1400T>A	c.(1399-1401)ATT>AAT	p.I467N	TTC26_uc011kqn.1_Missense_Mutation_p.I467N|TTC26_uc011kqo.1_Missense_Mutation_p.I436N|TTC26_uc011kqp.1_Missense_Mutation_p.I362N|TTC26_uc003vut.2_Missense_Mutation_p.I327N|TTC26_uc011kqq.1_Missense_Mutation_p.I336N	NM_024926	NP_079202	A0AVF1	TTC26_HUMAN	tetratricopeptide repeat domain 26 isoform 1	467							binding			ovary(1)	1																		---	---	---	---
BRAF	673	broad.mit.edu	37	7	140453128	140453128	+	Nonsense_Mutation	SNP	G	A	A	rs104886015		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140453128G>A	uc003vwc.3	-	15	1868	c.1807C>T	c.(1807-1809)CGA>TGA	p.R603*		NM_004333	NP_004324	P15056	BRAF_HUMAN	B-Raf	603	Protein kinase.				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	p.R603*(4)|p.T599_R603>I(2)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.V600_W604del(1)	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				---	---	---	---
OR9A2	135924	broad.mit.edu	37	7	142723873	142723873	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142723873A>G	uc003wcc.1	-	1	347	c.347T>C	c.(346-348)GTG>GCG	p.V116A		NM_001001658	NP_001001658	Q8NGT5	OR9A2_HUMAN	olfactory receptor, family 9, subfamily A,	116					sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1	Melanoma(164;0.059)																	---	---	---	---
TPK1	27010	broad.mit.edu	37	7	144320278	144320278	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:144320278A>G	uc003weq.2	-	6	438	c.335T>C	c.(334-336)ATA>ACA	p.I112T	TPK1_uc003weo.2_Missense_Mutation_p.I107T|TPK1_uc003wep.2_RNA|TPK1_uc003wer.2_Missense_Mutation_p.I112T|TPK1_uc003wes.2_RNA	NM_022445	NP_071890	Q9H3S4	TPK1_HUMAN	thiamin pyrophosphokinase 1 isoform a	112					thiamine diphosphate biosynthetic process	cytosol	ATP binding|kinase activity|thiamine diphosphokinase activity			ovary(2)	2					Thiamine(DB00152)													---	---	---	---
ZNF398	57541	broad.mit.edu	37	7	148876693	148876693	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148876693C>T	uc003wfl.2	+	6	2004	c.1729C>T	c.(1729-1731)CGC>TGC	p.R577C	ZNF398_uc011kul.1_Missense_Mutation_p.R406C|ZNF398_uc011kum.1_Missense_Mutation_p.R582C	NM_170686	NP_733787	Q8TD17	ZN398_HUMAN	zinc finger 398 isoform a	577	C2H2-type 9.				positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00143)															---	---	---	---
ZNF777	27153	broad.mit.edu	37	7	149129387	149129387	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149129387G>A	uc003wfv.2	-	6	2139	c.1976C>T	c.(1975-1977)ACG>ATG	p.T659M		NM_015694	NP_056509	Q9ULD5	ZN777_HUMAN	zinc finger protein 777	659					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1	Melanoma(164;0.165)		OV - Ovarian serous cystadenocarcinoma(82;0.00358)															---	---	---	---
ZNF777	27153	broad.mit.edu	37	7	149133705	149133705	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149133705C>T	uc003wfv.2	-	5	1463	c.1300G>A	c.(1300-1302)GAA>AAA	p.E434K		NM_015694	NP_056509	Q9ULD5	ZN777_HUMAN	zinc finger protein 777	434	Glu-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1	Melanoma(164;0.165)		OV - Ovarian serous cystadenocarcinoma(82;0.00358)															---	---	---	---
SSPO	23145	broad.mit.edu	37	7	149485990	149485990	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149485990C>T	uc010lpk.2	+	29	4209	c.4209C>T	c.(4207-4209)GGC>GGT	p.G1403G		NM_198455	NP_940857	A2VEC9	SSPO_HUMAN	SCO-spondin precursor	1403	LDL-receptor class A 1.				cell adhesion	extracellular space	peptidase inhibitor activity				0	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)															---	---	---	---
SSPO	23145	broad.mit.edu	37	7	149508064	149508064	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149508064C>T	uc010lpk.2	+	67	9458	c.9458C>T	c.(9457-9459)CCG>CTG	p.P3153L		NM_198455	NP_940857	A2VEC9	SSPO_HUMAN	SCO-spondin precursor	3153					cell adhesion	extracellular space	peptidase inhibitor activity				0	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)															---	---	---	---
ZNF862	643641	broad.mit.edu	37	7	149547397	149547397	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149547397C>T	uc010lpn.2	+	5	1279	c.1087C>T	c.(1087-1089)CGG>TGG	p.R363W	ZNF862_uc003wgm.2_RNA	NM_001099220	NP_001092690	O60290	ZN862_HUMAN	zinc finger protein 862	363	KRAB 2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|nucleic acid binding|protein dimerization activity			skin(1)	1																		---	---	---	---
SLC4A2	6522	broad.mit.edu	37	7	150761604	150761604	+	Intron	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150761604T>C	uc003wit.3	+						SLC4A2_uc011kve.1_Intron|SLC4A2_uc003wiu.3_Intron	NM_003040	NP_003031			solute carrier family 4, anion exchanger, member						bicarbonate transport	integral to membrane|membrane fraction	inorganic anion exchanger activity				0			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)														---	---	---	---
CHPF2	54480	broad.mit.edu	37	7	150935265	150935265	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150935265G>A	uc003wjr.1	+	4	3330	c.1817G>A	c.(1816-1818)CGC>CAC	p.R606H	CHPF2_uc003wjq.1_Missense_Mutation_p.R598H|MIR671_hsa-mir-671|MI0003760_5'Flank	NM_019015	NP_061888	Q9P2E5	CHPF2_HUMAN	chondroitin polymerizing factor 2	606	Lumenal (Potential).					Golgi cisterna membrane|integral to membrane	N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	152142770	152142770	+	IGR	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152142770C>T								FABP5L3 (2672 upstream) : LOC100128822 (18439 downstream)																																			---	---	---	---
HTR5A	3361	broad.mit.edu	37	7	154862889	154862889	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154862889A>G	uc003wlu.1	+	1	344	c.280A>G	c.(280-282)ATG>GTG	p.M94V	uc011kvt.1_Missense_Mutation_p.M42T|uc003wlt.2_Missense_Mutation_p.M42T	NM_024012	NP_076917	P47898	5HT5A_HUMAN	5-hydroxytryptamine receptor 5A	94	Helical; Name=2; (By similarity).					integral to plasma membrane	serotonin receptor activity			ovary(2)|large_intestine(1)	3	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.0238)	UCEC - Uterine corpus endometrioid carcinoma (81;0.171)														---	---	---	---
PTPRN2	5799	broad.mit.edu	37	7	157959878	157959878	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157959878G>A	uc003wno.2	-	6	776	c.655C>T	c.(655-657)CGG>TGG	p.R219W	PTPRN2_uc003wnp.2_Missense_Mutation_p.R202W|PTPRN2_uc003wnq.2_Missense_Mutation_p.R219W|PTPRN2_uc003wnr.2_Missense_Mutation_p.R181W|PTPRN2_uc011kwa.1_Missense_Mutation_p.R242W	NM_002847	NP_002838	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N	219	Extracellular (Potential).					integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)|skin(1)	7	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)														---	---	---	---
WDR60	55112	broad.mit.edu	37	7	158734693	158734693	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158734693G>A	uc003woe.3	+	24	3014	c.2856G>A	c.(2854-2856)ACG>ACA	p.T952T	WDR60_uc010lqv.2_RNA|WDR60_uc010lqw.2_Silent_p.T584T	NM_018051	NP_060521	Q8WVS4	WDR60_HUMAN	WD repeat domain 60	952	WD 4.									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)														---	---	---	---
CSMD1	64478	broad.mit.edu	37	8	3008925	3008925	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3008925C>T	uc011kwk.1	-	40	6418	c.6028G>A	c.(6028-6030)GGC>AGC	p.G2010S	CSMD1_uc011kwj.1_Missense_Mutation_p.G1402S|CSMD1_uc003wqe.2_Missense_Mutation_p.G1166S|CSMD1_uc010lrg.2_Missense_Mutation_p.G78S	NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor	2010	Extracellular (Potential).|CUB 12.					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)														---	---	---	---
MCPH1	79648	broad.mit.edu	37	8	6302423	6302423	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6302423C>T	uc003wqi.2	+	8	1248	c.1180C>T	c.(1180-1182)CTG>TTG	p.L394L	MCPH1_uc003wqh.2_Silent_p.L394L|MCPH1_uc011kwl.1_Silent_p.L346L	NM_024596	NP_078872	Q8NEM0	MCPH1_HUMAN	microcephalin	394						microtubule organizing center				central_nervous_system(1)|skin(1)	2		Hepatocellular(245;0.0663)		Colorectal(4;0.0505)														---	---	---	---
SOX7	83595	broad.mit.edu	37	8	10692279	10692279	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10692279C>T	uc011kwz.1	-	2	59	c.26G>A	c.(25-27)CGG>CAG	p.R9Q	PINX1_uc003wth.2_Missense_Mutation_p.R9Q|PINX1_uc003wti.2_Missense_Mutation_p.R9Q	NM_031439	NP_113627	Q9BT81	SOX7_HUMAN	SRY-box 7	Error:Variant_position_missing_in_Q9BT81_after_alignment					endoderm formation|negative regulation of cell proliferation|negative regulation of transcription, DNA-dependent|positive regulation of caspase activity|regulation of canonical Wnt receptor signaling pathway	cytoplasm|nucleus	transcription regulatory region DNA binding			breast(1)	1				COAD - Colon adenocarcinoma(149;0.0732)														---	---	---	---
DLC1	10395	broad.mit.edu	37	8	12947986	12947986	+	Intron	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12947986G>A	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	12957788	12957788	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12957788C>T	uc003wwm.2	-	9	2502	c.2058G>A	c.(2056-2058)GCG>GCA	p.A686A	DLC1_uc003wwk.1_Silent_p.A249A|DLC1_uc003wwl.1_Silent_p.A283A|DLC1_uc011kxx.1_Silent_p.A175A	NM_182643	NP_872584	Q96QB1	RHG07_HUMAN	deleted in liver cancer 1 isoform 1	686					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																		---	---	---	---
MTUS1	57509	broad.mit.edu	37	8	17611860	17611860	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17611860G>C	uc003wxv.2	-	2	1931	c.1457C>G	c.(1456-1458)ACG>AGG	p.T486R	MTUS1_uc010lsy.2_RNA|MTUS1_uc003wxw.2_Missense_Mutation_p.T486R|MTUS1_uc010lsz.2_Missense_Mutation_p.T486R	NM_001001924	NP_001001924	Q9ULD2	MTUS1_HUMAN	mitochondrial tumor suppressor 1 isoform 1	486						Golgi apparatus|microtubule|microtubule organizing center|mitochondrion|nucleus|plasma membrane|spindle				ovary(1)|skin(1)	2				Colorectal(111;0.0778)														---	---	---	---
XPO7	23039	broad.mit.edu	37	8	21848376	21848376	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21848376C>T	uc003xaa.3	+	18	2089	c.1987C>T	c.(1987-1989)CGG>TGG	p.R663W	XPO7_uc010lti.2_Missense_Mutation_p.R672W|XPO7_uc010ltk.2_Missense_Mutation_p.R664W	NM_015024	NP_055839	Q9UIA9	XPO7_HUMAN	exportin 7 isoform b	663					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	21857142	21857142	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21857142C>T	uc003xaa.3	+	24	2841	c.2739C>T	c.(2737-2739)ATC>ATT	p.I913I	XPO7_uc010lti.2_Silent_p.I922I|XPO7_uc010ltk.2_Silent_p.I914I	NM_015024	NP_055839	Q9UIA9	XPO7_HUMAN	exportin 7 isoform b	913					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)														---	---	---	---
REEP4	80346	broad.mit.edu	37	8	21996976	21996976	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21996976G>A	uc003xau.1	-	5	823	c.370C>T	c.(370-372)CGG>TGG	p.R124W	REEP4_uc010ltt.1_Missense_Mutation_p.R124W|REEP4_uc011kyz.1_Missense_Mutation_p.R124W	NM_025232	NP_079508	Q9H6H4	REEP4_HUMAN	receptor accessory protein 4	124						integral to membrane				skin(1)	1				Colorectal(74;0.00187)|COAD - Colon adenocarcinoma(73;0.061)|READ - Rectum adenocarcinoma(644;0.0993)														---	---	---	---
PIWIL2	55124	broad.mit.edu	37	8	22147407	22147407	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22147407A>G	uc003xbn.2	+	9	1182	c.1034A>G	c.(1033-1035)GAC>GGC	p.D345G	PIWIL2_uc011kzf.1_Missense_Mutation_p.D345G|PIWIL2_uc010ltv.2_Missense_Mutation_p.D345G	NM_018068	NP_060538	Q8TC59	PIWL2_HUMAN	piwi-like 2	345					DNA methylation involved in gamete generation|gene silencing by RNA|germ-line stem cell maintenance|multicellular organismal development|oogenesis|piRNA metabolic process|positive regulation of translation|RNA 5'-end processing|spermatogenesis	chromatoid body|pi-body	piRNA binding			skin(1)	1				Colorectal(74;0.018)|COAD - Colon adenocarcinoma(73;0.0707)														---	---	---	---
PIWIL2	55124	broad.mit.edu	37	8	22210726	22210726	+	Splice_Site	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22210726G>A	uc003xbn.2	+	21	2805	c.2657_splice	c.e21+1	p.W886_splice	PIWIL2_uc011kzf.1_Splice_Site_p.W886_splice|PIWIL2_uc010ltv.2_Splice_Site_p.W886_splice|PIWIL2_uc003xbo.2_Splice_Site_p.W40_splice	NM_018068	NP_060538			piwi-like 2						DNA methylation involved in gamete generation|gene silencing by RNA|germ-line stem cell maintenance|multicellular organismal development|oogenesis|piRNA metabolic process|positive regulation of translation|RNA 5'-end processing|spermatogenesis	chromatoid body|pi-body	piRNA binding			skin(1)	1				Colorectal(74;0.018)|COAD - Colon adenocarcinoma(73;0.0707)														---	---	---	---
KIAA1967	57805	broad.mit.edu	37	8	22463333	22463333	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22463333G>A	uc003xch.2	+	2	184	c.47G>A	c.(46-48)CGC>CAC	p.R16H	KIAA1967_uc003xci.2_Missense_Mutation_p.R16H|KIAA1967_uc003xcj.1_5'Flank	NM_199205	NP_954675	Q8N163	K1967_HUMAN	p30 DBC protein	16					apoptosis|positive regulation of apoptosis	mitochondrial matrix|nucleus	enzyme binding|enzyme inhibitor activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Prostate(55;0.0421)|Breast(100;0.102)|all_epithelial(46;0.142)		BRCA - Breast invasive adenocarcinoma(99;0.00593)|Colorectal(74;0.0157)|COAD - Colon adenocarcinoma(73;0.064)														---	---	---	---
RHOBTB2	23221	broad.mit.edu	37	8	22864897	22864897	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22864897C>T	uc003xcq.2	+	5	1676	c.1139C>T	c.(1138-1140)CCG>CTG	p.P380L	RHOBTB2_uc003xcp.2_Missense_Mutation_p.P402L|RHOBTB2_uc011kzp.1_Missense_Mutation_p.P387L|uc003xcr.2_RNA	NM_015178	NP_055993	Q9BYZ6	RHBT2_HUMAN	Rho-related BTB domain containing 2 isoform 3	380	BTB 1.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|plasma membrane	GTP binding			ovary(1)|lung(1)	2		Prostate(55;0.0513)|Breast(100;0.214)		Colorectal(74;0.0157)|COAD - Colon adenocarcinoma(73;0.064)														---	---	---	---
NEFL	4747	broad.mit.edu	37	8	24813156	24813156	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24813156C>T	uc003xee.2	-	1	976	c.874G>A	c.(874-876)GCC>ACC	p.A292T		NM_006158	NP_006149	P07196	NFL_HUMAN	neurofilament, light polypeptide 68kDa	292	Rod.|Coil 2B.				anterograde axon cargo transport|axon transport of mitochondrion|neurofilament bundle assembly|retrograde axon cargo transport|synaptic transmission	cytosol|neurofilament	identical protein binding|protein C-terminus binding|structural constituent of cytoskeleton			ovary(1)|central_nervous_system(1)	2		Ovarian(32;0.00965)|Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0197)|Epithelial(17;2.44e-10)|Colorectal(74;0.0108)|COAD - Colon adenocarcinoma(73;0.0375)														---	---	---	---
DPYSL2	1808	broad.mit.edu	37	8	26501484	26501484	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26501484G>A	uc003xfb.1	+	10	1337	c.987G>A	c.(985-987)ACG>ACA	p.T329T	DPYSL2_uc003xfa.2_Silent_p.T434T|DPYSL2_uc010luk.1_RNA|DPYSL2_uc011lah.1_Silent_p.T293T	NM_001386	NP_001377	Q16555	DPYL2_HUMAN	dihydropyrimidinase-like 2	329					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	26501587	26501587	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26501587G>A	uc003xfb.1	+	10	1440	c.1090G>A	c.(1090-1092)GTC>ATC	p.V364I	DPYSL2_uc003xfa.2_Missense_Mutation_p.V469I|DPYSL2_uc010luk.1_RNA|DPYSL2_uc011lah.1_Missense_Mutation_p.V328I	NM_001386	NP_001377	Q16555	DPYL2_HUMAN	dihydropyrimidinase-like 2	364					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)														---	---	---	---
PTK2B	2185	broad.mit.edu	37	8	27303434	27303434	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27303434C>T	uc003xfn.1	+	29	3146	c.2338C>T	c.(2338-2340)CGG>TGG	p.R780W	PTK2B_uc003xfo.1_Missense_Mutation_p.R780W|PTK2B_uc003xfp.1_Missense_Mutation_p.R780W|PTK2B_uc003xfq.1_Intron	NM_173174	NP_775266	Q14289	FAK2_HUMAN	PTK2B protein tyrosine kinase 2 beta isoform a	780				R -> G (in Ref. 2; AAB47217).	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)														---	---	---	---
ESCO2	157570	broad.mit.edu	37	8	27641506	27641506	+	Intron	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27641506T>C	uc003xgg.2	+						ESCO2_uc010luy.1_Intron	NM_001017420	NP_001017420			establishment of cohesion 1 homolog 2						cell cycle|post-translational protein acetylation|regulation of DNA replication	chromatin|nucleus	acyltransferase activity|metal ion binding			central_nervous_system(1)	1		Ovarian(32;0.000953)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0204)|KIRC - Kidney renal clear cell carcinoma(542;0.0955)|Kidney(114;0.115)|Colorectal(74;0.132)										SC_Phocomelia_syndrome				---	---	---	---
KIF13B	23303	broad.mit.edu	37	8	29005050	29005050	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29005050C>T	uc003xhh.3	-	17	1942	c.1883G>A	c.(1882-1884)CGC>CAC	p.R628H	KIF13B_uc003xhj.2_Missense_Mutation_p.R525H	NM_015254	NP_056069	Q9NQT8	KI13B_HUMAN	kinesin family member 13B	628	Potential.				microtubule-based movement|protein targeting|signal transduction|T cell activation	cytoplasm|microtubule	ATP binding|microtubule motor activity|protein kinase binding				0		Ovarian(32;0.000536)		KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)														---	---	---	---
TACC1	6867	broad.mit.edu	37	8	38677242	38677242	+	Silent	SNP	G	T	T	rs16887780	byFrequency;by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38677242G>T	uc010lwp.2	+	3	859	c.480G>T	c.(478-480)ACG>ACT	p.T160T	TACC1_uc011lby.1_5'UTR|TACC1_uc003xma.2_Intron|TACC1_uc003xlz.2_5'UTR|TACC1_uc003xmc.3_5'UTR|TACC1_uc011lbz.1_Silent_p.T176T|TACC1_uc003xmb.3_Silent_p.T115T|TACC1_uc003xme.1_Intron|TACC1_uc003xmd.1_Intron|TACC1_uc010lwo.1_Intron|TACC1_uc003xmf.3_Intron|TACC1_uc011lca.1_Silent_p.T160T|TACC1_uc011lcb.1_5'UTR|TACC1_uc011lcc.1_5'UTR|TACC1_uc011lcd.1_RNA|TACC1_uc003xmh.3_5'UTR|TACC1_uc010lwq.2_5'UTR	NM_006283	NP_006274	O75410	TACC1_HUMAN	transforming, acidic coiled-coil containing	160	Interaction with TDRD7.				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)															---	---	---	---
ADAM32	203102	broad.mit.edu	37	8	39068795	39068795	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39068795C>T	uc003xmt.3	+	12	1430	c.1185C>T	c.(1183-1185)GGC>GGT	p.G395G	ADAM32_uc011lch.1_Intron|ADAM32_uc003xmu.3_Intron	NM_145004	NP_659441	Q8TC27	ADA32_HUMAN	a disintegrin and metalloprotease domain 32	395	Disintegrin.|Extracellular (Potential).				proteolysis	integral to membrane	metalloendopeptidase activity|zinc ion binding			ovary(1)|lung(1)|kidney(1)	3		all_cancers(7;3e-05)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00771)|Breast(189;0.0503)	LUSC - Lung squamous cell carcinoma(45;6.2e-07)|Colorectal(1;0.00699)|READ - Rectum adenocarcinoma(1;0.146)															---	---	---	---
ADAM18	8749	broad.mit.edu	37	8	39495209	39495209	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39495209G>T	uc003xni.2	+	9	814	c.814G>T	c.(814-816)GCA>TCA	p.A272S	ADAM18_uc010lww.2_RNA|ADAM18_uc010lwx.2_Missense_Mutation_p.A248S	NM_014237	NP_055052	Q9Y3Q7	ADA18_HUMAN	a disintegrin and metalloprotease domain 18	272	Peptidase M12B.|Extracellular (Potential).				cell differentiation|multicellular organismal development|proteolysis|spermatogenesis	integral to membrane|membrane fraction	metalloendopeptidase activity|zinc ion binding			central_nervous_system(2)|upper_aerodigestive_tract(1)|ovary(1)|kidney(1)|skin(1)	6		all_cancers(7;1.32e-05)|all_epithelial(6;3.08e-10)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00769)|Breast(189;0.0112)	LUSC - Lung squamous cell carcinoma(45;0.000199)															---	---	---	---
ANK1	286	broad.mit.edu	37	8	41550195	41550195	+	Missense_Mutation	SNP	C	T	T	rs148942046	byFrequency	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41550195C>T	uc003xok.2	-	31	3913	c.3829G>A	c.(3829-3831)GTG>ATG	p.V1277M	NKX6-3_uc010lxa.1_Intron|ANK1_uc003xoh.2_Missense_Mutation_p.V593M|ANK1_uc003xoi.2_Missense_Mutation_p.V1277M|ANK1_uc003xoj.2_Missense_Mutation_p.V1277M|ANK1_uc003xol.2_Missense_Mutation_p.V1277M|ANK1_uc003xom.2_Missense_Mutation_p.V1318M	NM_020476	NP_065209	P16157	ANK1_HUMAN	ankyrin 1 isoform 1	1277					axon guidance|cytoskeleton organization|exocytosis|maintenance of epithelial cell apical/basal polarity|signal transduction	basolateral plasma membrane|cytosol|sarcomere|sarcoplasmic reticulum|spectrin-associated cytoskeleton	cytoskeletal adaptor activity|enzyme binding|protein binding|spectrin binding|structural constituent of cytoskeleton			ovary(3)|central_nervous_system(3)|lung(2)|breast(1)	9	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)															---	---	---	---
AP3M2	10947	broad.mit.edu	37	8	42023047	42023047	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42023047C>T	uc003xop.2	+	7	1063	c.772C>T	c.(772-774)CGC>TGC	p.R258C	AP3M2_uc003xoo.2_Missense_Mutation_p.R258C|AP3M2_uc010lxe.2_RNA|AP3M2_uc003xoq.1_Missense_Mutation_p.R143C|AP3M2_uc003xor.1_Missense_Mutation_p.R258C	NM_001134296	NP_001127768	P53677	AP3M2_HUMAN	adaptor-related protein complex 3, mu 2 subunit	258	MHD.				intracellular protein transport|vesicle-mediated transport	clathrin adaptor complex|Golgi apparatus					0	all_cancers(6;8.14e-25)|all_epithelial(6;2.41e-27)|all_lung(13;5.09e-13)|Lung NSC(13;8.38e-12)|Ovarian(28;0.00438)|Prostate(17;0.0119)|Colorectal(14;0.0221)|Lung SC(25;0.211)	all_lung(54;0.000434)|Lung NSC(58;0.00161)|Hepatocellular(245;0.0524)|Esophageal squamous(32;0.0954)|Renal(179;0.0983)	BRCA - Breast invasive adenocarcinoma(8;5.23e-10)|Colorectal(10;0.00165)|OV - Ovarian serous cystadenocarcinoma(14;0.00346)|Lung(22;0.00467)|COAD - Colon adenocarcinoma(11;0.0171)|LUSC - Lung squamous cell carcinoma(45;0.024)															---	---	---	---
PRKDC	5591	broad.mit.edu	37	8	48690324	48690324	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48690324G>A	uc003xqi.2	-	85	12022	c.11965C>T	c.(11965-11967)CGG>TGG	p.R3989W	PRKDC_uc003xqj.2_Missense_Mutation_p.R3958W|PRKDC_uc011ldh.1_Intron	NM_006904	NP_008835	P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic	3989	PI3K/PI4K.				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					---	---	---	---
EFCAB1	79645	broad.mit.edu	37	8	49647682	49647682	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49647682G>A	uc003xqo.2	-	1	189	c.29C>T	c.(28-30)ACG>ATG	p.T10M	EFCAB1_uc003xqn.3_RNA|EFCAB1_uc011ldj.1_Missense_Mutation_p.T10M|EFCAB1_uc010lxx.2_RNA|EFCAB1_uc011ldk.1_RNA	NM_024593	NP_078869	Q9HAE3	EFCB1_HUMAN	EF-hand calcium binding domain 1 isoform a	10							calcium ion binding				0		all_epithelial(80;0.0134)|Lung NSC(129;0.0207)|all_lung(136;0.0464)																---	---	---	---
PXDNL	137902	broad.mit.edu	37	8	52321554	52321554	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52321554G>A	uc003xqu.3	-	17	2731	c.2630C>T	c.(2629-2631)ACG>ATG	p.T877M	PXDNL_uc003xqt.3_RNA	NM_144651	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog-like precursor	877					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	52321594	52321594	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52321594G>A	uc003xqu.3	-	17	2691	c.2590C>T	c.(2590-2592)CGC>TGC	p.R864C	PXDNL_uc003xqt.3_RNA	NM_144651	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog-like precursor	864					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)																---	---	---	---
NPBWR1	2831	broad.mit.edu	37	8	53853442	53853442	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53853442C>T	uc011ldu.1	+	1	975	c.975C>T	c.(973-975)CGC>CGT	p.R325R		NM_005285	NP_005276	P48145	NPBW1_HUMAN	G protein-coupled receptor 7	325	Cytoplasmic (Potential).				synaptic transmission	plasma membrane	opioid receptor activity|protein binding			ovary(2)|breast(1)	3		Lung NSC(129;0.0222)|all_epithelial(80;0.0301)|all_lung(136;0.0431)																---	---	---	---
RP1	6101	broad.mit.edu	37	8	55533986	55533986	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55533986C>T	uc003xsd.1	+	2	608	c.460C>T	c.(460-462)CGG>TGG	p.R154W	RP1_uc011ldy.1_Missense_Mutation_p.R154W	NM_006269	NP_006260	P56715	RP1_HUMAN	retinitis pigmentosa RP1 protein	154	Doublecortin 2.				axoneme assembly|intracellular signal transduction|photoreceptor cell maintenance|photoreceptor cell outer segment organization|phototransduction, visible light|retinal cone cell development|retinal rod cell development	cilium axoneme|cytoplasm|microtubule|microtubule associated complex|photoreceptor connecting cilium|photoreceptor inner segment|photoreceptor outer segment	microtubule binding			skin(7)|ovary(4)|pancreas(1)	12		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)															---	---	---	---
CHD7	55636	broad.mit.edu	37	8	61765392	61765392	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61765392G>A	uc003xue.2	+	31	6585	c.6108G>A	c.(6106-6108)CCG>CCA	p.P2036P		NM_017780	NP_060250	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	2036					central nervous system development|chromatin modification|cognition|cranial nerve development|face development|heart morphogenesis|in utero embryonic development|inner ear morphogenesis|nose development|palate development|regulation of growth hormone secretion|regulation of transcription, DNA-dependent|retina development in camera-type eye|skeletal system development|T cell differentiation|transcription, DNA-dependent	nucleus	ATP binding|chromatin binding|DNA binding|helicase activity			ovary(4)|large_intestine(1)|central_nervous_system(1)|lung(1)|breast(1)|pancreas(1)	9		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)															---	---	---	---
CYP7B1	9420	broad.mit.edu	37	8	65528376	65528376	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65528376A>G	uc003xvj.2	-	3	926	c.722T>C	c.(721-723)ATT>ACT	p.I241T		NM_004820	NP_004811	O75881	CP7B1_HUMAN	cytochrome P450, family 7, subfamily B,	241					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)																---	---	---	---
ADHFE1	137872	broad.mit.edu	37	8	67369347	67369347	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67369347A>G	uc003xwb.3	+	12	1142	c.1108A>G	c.(1108-1110)ACT>GCT	p.T370A	ADHFE1_uc003xwd.3_RNA|ADHFE1_uc003xwc.3_Missense_Mutation_p.T322A|ADHFE1_uc003xwe.3_RNA|ADHFE1_uc003xwf.3_RNA|ADHFE1_uc011les.1_Missense_Mutation_p.T300A	NM_144650	NP_653251	Q8IWW8	HOT_HUMAN	alcohol dehydrogenase, iron containing, 1	370					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)															---	---	---	---
C8orf45	157777	broad.mit.edu	37	8	67789611	67789611	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67789611T>G	uc003xwz.3	+	5	484	c.313T>G	c.(313-315)TTA>GTA	p.L105V	C8orf45_uc003xwv.2_Missense_Mutation_p.L105V|C8orf45_uc011lev.1_Missense_Mutation_p.L105V|C8orf45_uc011lew.1_Missense_Mutation_p.L36V|C8orf45_uc011lex.1_Intron|C8orf45_uc003xwy.3_Missense_Mutation_p.L105V	NM_173518	NP_775789	Q4G0Z9	CH045_HUMAN	minichromosome maintenance complex	105					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)															---	---	---	---
NCOA2	10499	broad.mit.edu	37	8	71068296	71068296	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:71068296T>C	uc003xyn.1	-	11	2466	c.2304A>G	c.(2302-2304)AGA>AGG	p.R768R		NM_006540	NP_006531	Q15596	NCOA2_HUMAN	nuclear receptor coactivator 2	768					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	71068364	71068364	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:71068364G>A	uc003xyn.1	-	11	2398	c.2236C>T	c.(2236-2238)CGC>TGC	p.R746C		NM_006540	NP_006531	Q15596	NCOA2_HUMAN	nuclear receptor coactivator 2	746	LXXLL motif 3.				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								---	---	---	---
TRPA1	8989	broad.mit.edu	37	8	72946564	72946564	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72946564T>C	uc003xza.2	-	22	2779	c.2604A>G	c.(2602-2604)AAA>AAG	p.K868K	uc011lff.1_Intron|uc003xyy.2_Intron	NM_007332	NP_015628	O75762	TRPA1_HUMAN	ankyrin-like protein 1	868	Cytoplasmic (Potential).					integral to plasma membrane				ovary(4)|lung(1)|kidney(1)	6			Epithelial(68;0.223)		Menthol(DB00825)													---	---	---	---
JPH1	56704	broad.mit.edu	37	8	75171672	75171672	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75171672G>A	uc003yae.2	-	3	1246	c.1206C>T	c.(1204-1206)TGC>TGT	p.C402C	JPH1_uc003yaf.2_Silent_p.C402C|JPH1_uc003yag.1_Silent_p.C266C	NM_020647	NP_065698	Q9HDC5	JPH1_HUMAN	junctophilin 1	402	Ala-rich.|Cytoplasmic (Potential).				calcium ion transport into cytosol|regulation of ryanodine-sensitive calcium-release channel activity	integral to membrane|junctional membrane complex|junctional sarcoplasmic reticulum membrane|plasma membrane				ovary(1)	1	Breast(64;0.00576)		BRCA - Breast invasive adenocarcinoma(89;0.0499)|Epithelial(68;0.0728)|all cancers(69;0.176)															---	---	---	---
ZFHX4	79776	broad.mit.edu	37	8	77768354	77768354	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77768354G>A	uc003yav.2	+	10	9449	c.9062G>A	c.(9061-9063)CGT>CAT	p.R3021H	ZFHX4_uc003yau.1_Missense_Mutation_p.R3066H|ZFHX4_uc003yaw.1_Missense_Mutation_p.R3021H	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	3021						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|large_intestine(4)|breast(2)|lung(1)	15			BRCA - Breast invasive adenocarcinoma(89;0.0895)												HNSCC(33;0.089)			---	---	---	---
PSKH2	85481	broad.mit.edu	37	8	87060712	87060712	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87060712C>T	uc011lfy.1	-	3	1137	c.1137G>A	c.(1135-1137)TCG>TCA	p.S379S		NM_033126	NP_149117	Q96QS6	KPSH2_HUMAN	protein serine kinase H2	379							ATP binding|protein serine/threonine kinase activity			stomach(2)|lung(2)|ovary(1)	5			STAD - Stomach adenocarcinoma(118;0.129)															---	---	---	---
MMP16	4325	broad.mit.edu	37	8	89053678	89053678	+	3'UTR	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:89053678A>G	uc003yeb.3	-	10						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																		---	---	---	---
RUNX1T1	862	broad.mit.edu	37	8	93026963	93026963	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93026963A>G	uc003yfd.2	-	3	396	c.312T>C	c.(310-312)TCT>TCC	p.S104S	RUNX1T1_uc003yfc.1_Silent_p.S77S|RUNX1T1_uc003yfe.1_Silent_p.S67S|RUNX1T1_uc010mao.2_Silent_p.S77S|RUNX1T1_uc011lgi.1_Silent_p.S115S|RUNX1T1_uc003yfh.1_Silent_p.S67S|RUNX1T1_uc003yfb.1_Silent_p.S67S|RUNX1T1_uc003yff.1_Silent_p.S67S|RUNX1T1_uc003yfg.1_Silent_p.S67S	NM_175634	NP_783552	Q06455	MTG8_HUMAN	acute myelogenous leukemia 1 translocation 1	104	Poly-Ser.				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)															---	---	---	---
GEM	2669	broad.mit.edu	37	8	95272569	95272569	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95272569G>A	uc003ygj.2	-	2	412	c.163C>T	c.(163-165)CGC>TGC	p.R55C	GEM_uc003ygi.2_Missense_Mutation_p.R55C	NM_005261	NP_005252	P55040	GEM_HUMAN	GTP-binding mitogen-induced T-cell protein	55					cell surface receptor linked signaling pathway|immune response|small GTPase mediated signal transduction	internal side of plasma membrane	calmodulin binding|GDP binding|GTP binding|GTPase activity|magnesium ion binding			lung(1)	1	Breast(36;4.65e-06)	Myeloproliferative disorder(644;0.204)	BRCA - Breast invasive adenocarcinoma(8;0.00691)															---	---	---	---
CCNE2	9134	broad.mit.edu	37	8	95900288	95900288	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95900288T>C	uc003yhc.2	-	7	576	c.467A>G	c.(466-468)TAC>TGC	p.Y156C	CCNE2_uc003yhd.2_Missense_Mutation_p.Y156C	NM_057749	NP_477097	O96020	CCNE2_HUMAN	cyclin E2	156					cell cycle checkpoint|cell division|G1/S transition of mitotic cell cycle|regulation of cyclin-dependent protein kinase activity	cytosol|nucleoplasm	protein kinase binding				0	Breast(36;8.75e-07)																	---	---	---	---
C8orf38	137682	broad.mit.edu	37	8	96059246	96059246	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96059246A>G	uc003yhj.2	+	6	621	c.605A>G	c.(604-606)CAT>CGT	p.H202R	C8orf38_uc003yhe.1_RNA|C8orf38_uc003yhf.2_Missense_Mutation_p.H110R|C8orf38_uc011lgs.1_RNA|C8orf38_uc003yhi.2_Missense_Mutation_p.H150R|C8orf38_uc003yhk.2_RNA|C8orf38_uc003yhl.2_Missense_Mutation_p.H110R	NM_152416	NP_689629	Q330K2	CH038_HUMAN	hypothetical protein LOC137682 precursor	202					biosynthetic process	mitochondrion	transferase activity				0	Breast(36;3.32e-06)																	---	---	---	---
VPS13B	157680	broad.mit.edu	37	8	100568810	100568810	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100568810C>T	uc003yiv.2	+	31	5064	c.4953C>T	c.(4951-4953)GTC>GTT	p.V1651V	VPS13B_uc003yiw.2_Silent_p.V1626V	NM_017890	NP_060360	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13B isoform 5	1651					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	100654376	100654376	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100654376C>A	uc003yiv.2	+	34	5744	c.5633C>A	c.(5632-5634)CCA>CAA	p.P1878Q	VPS13B_uc003yiw.2_Missense_Mutation_p.P1853Q	NM_017890	NP_060360	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13B isoform 5	1878					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)															---	---	---	---
RNF19A	25897	broad.mit.edu	37	8	101300355	101300355	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101300355C>T	uc003yjj.1	-	3	365	c.48G>A	c.(46-48)CTG>CTA	p.L16L	RNF19A_uc003yjk.1_Silent_p.L16L|RNF19A_uc003yjl.1_Silent_p.L16L	NM_015435	NP_056250	Q9NV58	RN19A_HUMAN	ring finger protein 19	16					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)															---	---	---	---
UBR5	51366	broad.mit.edu	37	8	103358524	103358524	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103358524G>A	uc003ykr.1	-	7	709	c.676C>T	c.(676-678)CGG>TGG	p.R226W	UBR5_uc003yks.1_Missense_Mutation_p.R226W	NM_015902	NP_056986	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin	226					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)															---	---	---	---
DPYS	1807	broad.mit.edu	37	8	105393553	105393553	+	Intron	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105393553A>G	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)															---	---	---	---
OXR1	55074	broad.mit.edu	37	8	107718844	107718844	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:107718844G>A	uc011lht.1	+	8	1197	c.1098G>A	c.(1096-1098)GCG>GCA	p.A366A	OXR1_uc003ymf.2_Silent_p.A365A|OXR1_uc011lhu.1_Silent_p.A358A|OXR1_uc010mcg.2_Intron|OXR1_uc010mch.2_Silent_p.A63A|OXR1_uc003ymg.1_Silent_p.A298A|OXR1_uc003ymi.1_Silent_p.A277A	NM_018002	NP_060472	Q8N573	OXR1_HUMAN	oxidation resistance 1 isoform 1	366					cell wall macromolecule catabolic process|response to oxidative stress	mitochondrion					0			OV - Ovarian serous cystadenocarcinoma(57;1.81e-09)															---	---	---	---
EIF3E	3646	broad.mit.edu	37	8	109248393	109248393	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109248393A>G	uc003ymu.2	-	4	391	c.363T>C	c.(361-363)CAT>CAC	p.H121H	EIF3E_uc003ymt.2_Silent_p.H72H|EIF3E_uc003ymv.2_Silent_p.H28H|EIF3E_uc010mci.1_Silent_p.H121H|EIF3E_uc010mcj.1_Silent_p.H121H	NM_001568	NP_001559	P60228	EIF3E_HUMAN	eukaryotic translation initiation factor 3,	121	Sufficient for interaction with TRIM27.|Sufficient for interaction with EPAS1.				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)															---	---	---	---
PKHD1L1	93035	broad.mit.edu	37	8	110510979	110510979	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110510979A>G	uc003yne.2	+	67	10911	c.10807A>G	c.(10807-10809)AGT>GGT	p.S3603G		NM_177531	NP_803875	Q86WI1	PKHL1_HUMAN	fibrocystin L precursor	3603	Extracellular (Potential).				immune response	cytosol|extracellular space|integral to membrane	receptor activity			ovary(9)|central_nervous_system(2)|large_intestine(1)|breast(1)|pancreas(1)	14			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)												HNSCC(38;0.096)			---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	113841970	113841970	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113841970T>C	uc003ynu.2	-	12	1963	c.1804A>G	c.(1804-1806)ACC>GCC	p.T602A	CSMD3_uc003ynt.2_Missense_Mutation_p.T562A|CSMD3_uc011lhx.1_Missense_Mutation_p.T498A	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	602	Extracellular (Potential).|CUB 3.					integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63															HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			---	---	---	---
TRPS1	7227	broad.mit.edu	37	8	116427198	116427198	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116427198G>A	uc003ynz.2	-	6	3358	c.2899C>T	c.(2899-2901)CAG>TAG	p.Q967*	TRPS1_uc011lhy.1_Nonsense_Mutation_p.Q971*|TRPS1_uc003yny.2_Nonsense_Mutation_p.Q980*|TRPS1_uc010mcy.2_Nonsense_Mutation_p.Q967*	NM_014112	NP_054831	Q9UHF7	TRPS1_HUMAN	zinc finger transcription factor TRPS1	967					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	116599384	116599384	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116599384G>A	uc003ynz.2	-	4	2964	c.2505C>T	c.(2503-2505)GCC>GCT	p.A835A	TRPS1_uc011lhy.1_Silent_p.A839A|TRPS1_uc003yny.2_Silent_p.A848A|TRPS1_uc010mcy.2_Silent_p.A835A	NM_014112	NP_054831	Q9UHF7	TRPS1_HUMAN	zinc finger transcription factor TRPS1	835					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				---	---	---	---
EIF3H	8667	broad.mit.edu	37	8	117658816	117658816	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117658816A>G	uc003yoa.2	-	7	881	c.855T>C	c.(853-855)AAT>AAC	p.N285N	EIF3H_uc003yob.2_Silent_p.N299N	NM_003756	NP_003747	O15372	EIF3H_HUMAN	eukaryotic translation initiation factor 3,	285					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)																	---	---	---	---
SLC30A8	169026	broad.mit.edu	37	8	118170036	118170036	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118170036G>A	uc003yoh.2	+	4	755	c.525G>A	c.(523-525)GCG>GCA	p.A175A	SLC30A8_uc010mcz.2_Silent_p.A126A|SLC30A8_uc011lia.1_Silent_p.A126A|SLC30A8_uc003yog.2_Silent_p.A126A	NM_173851	NP_776250	Q8IWU4	ZNT8_HUMAN	solute carrier family 30 member 8	175	Extracellular (Potential).				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	118184853	118184853	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118184853C>T	uc003yoh.2	+	8	1273	c.1043C>T	c.(1042-1044)ACC>ATC	p.T348I	SLC30A8_uc010mcz.2_Missense_Mutation_p.T299I|SLC30A8_uc011lia.1_Missense_Mutation_p.T299I|SLC30A8_uc003yog.2_Missense_Mutation_p.T299I	NM_173851	NP_776250	Q8IWU4	ZNT8_HUMAN	solute carrier family 30 member 8	348	Cytoplasmic (Potential).				insulin secretion|positive regulation of insulin secretion|regulation of sequestering of zinc ion|regulation of vesicle-mediated transport|response to glucose stimulus|sequestering of zinc ion	integral to membrane|plasma membrane|secretory granule membrane|transport vesicle membrane	protein homodimerization activity|zinc ion transmembrane transporter activity			ovary(2)|skin(2)	4	all_cancers(13;2.11e-22)|Lung NSC(37;6.08e-05)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.203)															---	---	---	---
EXT1	2131	broad.mit.edu	37	8	118817060	118817060	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118817060A>G	uc003yok.1	-	10	2729	c.1956T>C	c.(1954-1956)TGT>TGC	p.C652C		NM_000127	NP_000118	Q16394	EXT1_HUMAN	exostosin 1	652	Lumenal (Potential).				glycosaminoglycan biosynthetic process|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|ossification|signal transduction|skeletal system development	Golgi membrane|integral to endoplasmic reticulum membrane	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|heparan sulfate N-acetylglucosaminyltransferase activity|N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity|protein heterodimerization activity|protein homodimerization activity			ovary(2)|lung(2)	4	all_cancers(13;2.36e-26)|Lung NSC(37;5.02e-07)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.012)					Mis|N|F|S			exostoses|osteosarcoma			Hereditary_Multiple_Exostoses|Langer-Giedion_syndrome				---	---	---	---
DEPDC6	64798	broad.mit.edu	37	8	120886177	120886177	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120886177G>A	uc003yow.3	+	1	278	c.91G>A	c.(91-93)GCT>ACT	p.A31T	DEPDC6_uc011lid.1_Missense_Mutation_p.A31T	NM_022783	NP_073620	Q8TB45	DPTOR_HUMAN	DEP domain containing 6	31					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	121256225	121256225	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121256225C>T	uc003yox.2	+	20	2722	c.2457C>T	c.(2455-2457)AGC>AGT	p.S819S	COL14A1_uc003yoy.2_Silent_p.S497S	NM_021110	NP_066933	Q05707	COEA1_HUMAN	collagen, type XIV, alpha 1 precursor	819	Fibronectin type-III 6.				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)															---	---	---	---
HAS2	3037	broad.mit.edu	37	8	122627011	122627011	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122627011G>A	uc003yph.2	-	4	1535	c.997C>T	c.(997-999)CGA>TGA	p.R333*		NM_005328	NP_005319	Q92819	HAS2_HUMAN	hyaluronan synthase 2	333	Cytoplasmic (Potential).					integral to plasma membrane	hyaluronan synthase activity		HAS2/PLAG1(10)	soft_tissue(10)|ovary(5)	15	Lung NSC(37;3.12e-08)|Ovarian(258;0.0254)|Hepatocellular(40;0.0997)|all_neural(195;0.142)		STAD - Stomach adenocarcinoma(47;0.00503)															---	---	---	---
KLHL38	340359	broad.mit.edu	37	8	124663889	124663889	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124663889G>A	uc003yqs.1	-	1	1302	c.1278C>T	c.(1276-1278)GTC>GTT	p.V426V		NM_001081675	NP_001075144	Q2WGJ6	KLH38_HUMAN	kelch-like 38	426	Kelch 3.										0																		---	---	---	---
FAM91A1	157769	broad.mit.edu	37	8	124824810	124824810	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124824810C>A	uc003yqv.2	+	24	2444	c.2383C>A	c.(2383-2385)CTT>ATT	p.L795I	FAM91A1_uc011lil.1_Missense_Mutation_p.L553I	NM_144963	NP_659400	Q658Y4	F91A1_HUMAN	hypothetical protein LOC157769	795										ovary(1)|central_nervous_system(1)	2	Lung NSC(37;8.76e-13)|Ovarian(258;0.00744)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00192)															---	---	---	---
FER1L6	654463	broad.mit.edu	37	8	125074138	125074138	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125074138G>A	uc003yqw.2	+	25	3399	c.3193G>A	c.(3193-3195)GTG>ATG	p.V1065M	uc003yqy.1_Intron	NM_001039112	NP_001034201	Q2WGJ9	FR1L6_HUMAN	fer-1-like 6	1065	Cytoplasmic (Potential).|C2 4.					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)															---	---	---	---
TG	7038	broad.mit.edu	37	8	133899619	133899619	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133899619C>T	uc003ytw.2	+	9	2043	c.2002C>T	c.(2002-2004)CGC>TGC	p.R668C		NM_003235	NP_003226	P01266	THYG_HUMAN	thyroglobulin precursor	668	Thyroglobulin type-1 6.				hormone biosynthetic process|signal transduction|thyroid gland development|thyroid hormone generation	extracellular space	hormone activity			ovary(8)|breast(4)|pancreas(1)|central_nervous_system(1)|skin(1)	15	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)														---	---	---	---
ZFAT	57623	broad.mit.edu	37	8	135649947	135649947	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135649947C>T	uc003yup.2	-	3	380	c.205G>A	c.(205-207)GTC>ATC	p.V69I	ZFAT_uc003yun.2_Missense_Mutation_p.V57I|ZFAT_uc003yuo.2_Missense_Mutation_p.V57I|ZFAT_uc010meh.2_Missense_Mutation_p.V57I|ZFAT_uc010mei.2_RNA|ZFAT_uc003yuq.2_Missense_Mutation_p.V57I|ZFAT_uc010mej.2_Missense_Mutation_p.V69I|ZFAT_uc003yur.2_Missense_Mutation_p.V57I	NM_020863	NP_065914	Q9P243	ZFAT_HUMAN	zinc finger protein 406 isoform ZFAT-1	69					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)															---	---	---	---
KHDRBS3	10656	broad.mit.edu	37	8	136594174	136594174	+	Missense_Mutation	SNP	C	T	T	rs150971318		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136594174C>T	uc003yuv.2	+	6	1059	c.665C>T	c.(664-666)ACG>ATG	p.T222M	KHDRBS3_uc003yuw.2_Missense_Mutation_p.T222M|KHDRBS3_uc010mek.2_RNA	NM_006558	NP_006549	O75525	KHDR3_HUMAN	KH domain containing, RNA binding, signal	222	Interaction with SIAH1.			Missing: Complete loss of SIAH1-mediated degradation.	regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	nucleus	SH3 domain binding			ovary(2)	2	all_epithelial(106;2.85e-16)|all_neural(2;2.72e-06)|Lung NSC(106;3.95e-06)|all_lung(105;1.11e-05)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.247)															---	---	---	---
FAM135B	51059	broad.mit.edu	37	8	139158294	139158294	+	Splice_Site	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139158294C>A	uc003yuy.2	-	15	3620	c.3449_splice	c.e15-1	p.G1150_splice	FAM135B_uc003yux.2_Splice_Site_p.G1051_splice|FAM135B_uc003yuz.2_Splice_Site|FAM135B_uc003yva.2_Splice_Site_p.G712_splice|FAM135B_uc003yvb.2_Splice_Site_p.W677_splice	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)			---	---	---	---
EIF2C2	27161	broad.mit.edu	37	8	141561392	141561392	+	Intron	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141561392G>T	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	141567204	141567204	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141567204G>C	uc003yvn.2	-	8	1050	c.1010C>G	c.(1009-1011)ACC>AGC	p.T337S	EIF2C2_uc010men.2_Missense_Mutation_p.T260S|EIF2C2_uc010meo.2_Missense_Mutation_p.T337S	NM_012154	NP_036286	Q9UKV8	AGO2_HUMAN	argonaute 2 isoform 1	337	PAZ.				mRNA cleavage involved in gene silencing by miRNA|negative regulation of translation involved in gene silencing by miRNA|negative regulation of translational initiation|pre-miRNA processing|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol|micro-ribonucleoprotein complex|mRNA cap binding complex|nucleus|polysome|RNA-induced silencing complex	endoribonuclease activity, cleaving siRNA-paired mRNA|metal ion binding|protein binding|RNA 7-methylguanosine cap binding|siRNA binding|translation initiation factor activity				0	all_cancers(97;2.54e-14)|all_epithelial(106;5.99e-13)|Lung NSC(106;1.45e-05)|all_lung(105;2.07e-05)|Ovarian(258;0.0154)|Acute lymphoblastic leukemia(118;0.155)	Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.158)															---	---	---	---
DENND3	22898	broad.mit.edu	37	8	142186732	142186732	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142186732C>T	uc003yvy.2	+	15	2616	c.2338C>T	c.(2338-2340)CCC>TCC	p.P780S	DENND3_uc010mep.2_Missense_Mutation_p.P741S	NM_014957	NP_055772	A2RUS2	DEND3_HUMAN	DENN/MADD domain containing 3	780										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)															---	---	---	---
EPPK1	83481	broad.mit.edu	37	8	144942358	144942358	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144942358G>A	uc003zaa.1	-	1	5077	c.5064C>T	c.(5062-5064)GGC>GGT	p.G1688G		NM_031308	NP_112598	P58107	EPIPL_HUMAN	epiplakin 1	1688	Plectin 29.					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)															---	---	---	---
KIFC2	90990	broad.mit.edu	37	8	145697317	145697317	+	Intron	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145697317T>C	uc003zcz.2	+						KIFC2_uc003zda.2_5'Flank	NM_145754	NP_665697			kinesin family member C2						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity|protein binding			ovary(2)|central_nervous_system(1)	3	all_cancers(97;4.61e-11)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;8.67e-41)|all cancers(56;1.1e-35)|BRCA - Breast invasive adenocarcinoma(115;0.035)|Colorectal(110;0.055)															---	---	---	---
LRRC14	9684	broad.mit.edu	37	8	145745377	145745377	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145745377C>A	uc003zdk.1	+	2	414	c.268C>A	c.(268-270)CTG>ATG	p.L90M	RECQL4_uc003zdj.2_5'Flank|LRRC14_uc003zdl.1_Missense_Mutation_p.L90M|LRRC14_uc003zdo.2_5'Flank	NM_014665	NP_055480	Q15048	LRC14_HUMAN	leucine rich repeat containing 14	90											0	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)															---	---	---	---
ARHGAP39	80728	broad.mit.edu	37	8	145771022	145771022	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145771022C>T	uc003zdt.1	-	7	2687	c.2132G>A	c.(2131-2133)CGG>CAG	p.R711Q	ARHGAP39_uc011llk.1_Missense_Mutation_p.R711Q|ARHGAP39_uc003zds.1_Missense_Mutation_p.R711Q	NM_025251	NP_079527	Q9C0H5	RHG39_HUMAN	KIAA1688 protein	711					axon guidance|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytoskeleton|cytosol|nucleus	GTPase activator activity				0																		---	---	---	---
FOXD4	2298	broad.mit.edu	37	9	117619	117619	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117619G>A	uc003zfz.2	-	1	799	c.501C>T	c.(499-501)CGC>CGT	p.R167R		NM_207305	NP_997188	Q12950	FOXD4_HUMAN	forkhead box D4	167	Fork-head.				axon extension involved in axon guidance|cartilage development|dichotomous subdivision of terminal units involved in ureteric bud branching|embryo development|enteric nervous system development|iridophore differentiation|lateral line nerve glial cell development|melanocyte differentiation|neural crest cell migration|pattern specification process|peripheral nervous system development|positive regulation of BMP signaling pathway|positive regulation of kidney development|positive regulation of transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity|sympathetic nervous system development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			skin(1)	1	all_lung(41;0.218)	all_cancers(5;0.0395)|Acute lymphoblastic leukemia(5;1.91e-07)|all_hematologic(5;1.95e-06)	Kidney(42;0.112)|KIRC - Kidney renal clear cell carcinoma(5;0.157)	all cancers(5;0.000704)|Lung(218;0.00755)|GBM - Glioblastoma multiforme(5;0.0149)|Epithelial(6;0.0154)														---	---	---	---
KANK1	23189	broad.mit.edu	37	9	711849	711849	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:711849G>A	uc003zgl.1	+	7	1732	c.1083G>A	c.(1081-1083)ACG>ACA	p.T361T	KANK1_uc003zgm.2_Silent_p.T361T|KANK1_uc003zgn.1_Silent_p.T361T|KANK1_uc003zgo.1_Silent_p.T361T|KANK1_uc003zgp.1_Silent_p.T361T|KANK1_uc003zgq.2_Silent_p.T203T|KANK1_uc003zgr.1_Silent_p.T203T|KANK1_uc003zgs.1_Silent_p.T203T	NM_015158	NP_055973	Q14678	KANK1_HUMAN	KN motif and ankyrin repeat domains 1 isoform a	361	Potential.				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)														---	---	---	---
DMRT3	58524	broad.mit.edu	37	9	990216	990216	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:990216C>T	uc003zgw.1	+	2	668	c.630C>T	c.(628-630)AAC>AAT	p.N210N		NM_021240	NP_067063	Q9NQL9	DMRT3_HUMAN	doublesex and mab-3 related transcription factor	210					cell differentiation|multicellular organismal development|sex differentiation	nucleus	DNA binding|metal ion binding|sequence-specific DNA binding transcription factor activity			ovary(2)|central_nervous_system(1)	3		all_lung(10;1.39e-08)|Lung NSC(10;1.42e-08)		Lung(218;0.0196)														---	---	---	---
PTPRD	5789	broad.mit.edu	37	9	8518269	8518269	+	Silent	SNP	C	T	T	rs137892356		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:8518269C>T	uc003zkk.2	-	20	1833	c.1122G>A	c.(1120-1122)GCG>GCA	p.A374A	PTPRD_uc003zkp.2_Silent_p.A374A|PTPRD_uc003zkq.2_Silent_p.A374A|PTPRD_uc003zkr.2_Silent_p.A368A|PTPRD_uc003zks.2_Silent_p.A364A|PTPRD_uc003zkl.2_Silent_p.A374A|PTPRD_uc003zkm.2_Silent_p.A361A|PTPRD_uc003zkn.2_Silent_p.A374A|PTPRD_uc003zko.2_Silent_p.A371A	NM_002839	NP_002830	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	374	Fibronectin type-III 1.|Extracellular (Potential).				transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(14)|large_intestine(3)|ovary(2)|breast(2)|urinary_tract(1)	22		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)											TSP Lung(15;0.13)			---	---	---	---
CNTLN	54875	broad.mit.edu	37	9	17394855	17394855	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:17394855A>G	uc003zmz.2	+	15	2429	c.2403A>G	c.(2401-2403)TCA>TCG	p.S801S	CNTLN_uc003zmy.2_Silent_p.S801S|CNTLN_uc010mio.2_Silent_p.S480S	NM_017738	NP_060208	Q9NXG0	CNTLN_HUMAN	centlein isoform 1	801						centriole|membrane	two-component sensor activity			pancreas(1)	1				GBM - Glioblastoma multiforme(50;6.14e-10)														---	---	---	---
ACO1	48	broad.mit.edu	37	9	32431791	32431791	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32431791C>T	uc003zqw.3	+	15	1956	c.1801C>T	c.(1801-1803)CGT>TGT	p.R601C	ACO1_uc010mjh.1_Missense_Mutation_p.R435C|ACO1_uc003zqx.3_Missense_Mutation_p.R601C|ACO1_uc003zqy.3_RNA	NM_002197	NP_002188	P21399	ACOC_HUMAN	aconitase 1	601					citrate metabolic process|response to iron(II) ion|tricarboxylic acid cycle	cytosol|endoplasmic reticulum|Golgi apparatus	4 iron, 4 sulfur cluster binding|aconitate hydratase activity|citrate hydro-lyase (cis-aconitate-forming) activity|iron-responsive element binding|isocitrate hydro-lyase (cis-aconitate-forming) activity|metal ion binding|protein binding				0			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;3.94e-06)												OREG0019130	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
DDX58	23586	broad.mit.edu	37	9	32500949	32500949	+	Intron	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32500949A>G	uc003zra.2	-						DDX58_uc010mjj.2_Intron|DDX58_uc010mjk.1_Intron|DDX58_uc011lnr.1_Intron|DDX58_uc010mji.2_Intron	NM_014314	NP_055129			DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide						detection of virus|innate immune response|negative regulation of type I interferon production|positive regulation of defense response to virus by host|positive regulation of interferon-alpha production|positive regulation of interferon-beta production|positive regulation of transcription factor import into nucleus|positive regulation of transcription from RNA polymerase II promoter	cytosol	ATP binding|ATP-dependent helicase activity|double-stranded RNA binding|protein binding|zinc ion binding			ovary(2)|liver(1)|pancreas(1)	4			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;0.00056)														---	---	---	---
UBAP2	55833	broad.mit.edu	37	9	33927811	33927811	+	Silent	SNP	C	T	T	rs144703983	byFrequency;by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33927811C>T	uc003ztq.1	-	20	2468	c.2355G>A	c.(2353-2355)GCG>GCA	p.A785A	UBAP2_uc011loc.1_Silent_p.A694A|UBAP2_uc011lod.1_Silent_p.A518A|UBAP2_uc011loe.1_Silent_p.A540A|UBAP2_uc011lof.1_Silent_p.A710A|UBAP2_uc011log.1_3'UTR|UBAP2_uc003ztn.1_Silent_p.A24A|UBAP2_uc003zto.1_Silent_p.A24A|UBAP2_uc003ztp.1_Silent_p.A24A	NM_018449	NP_060919	Q5T6F2	UBAP2_HUMAN	ubiquitin associated protein 2	785										ovary(3)	3			LUSC - Lung squamous cell carcinoma(29;0.00575)	GBM - Glioblastoma multiforme(74;0.168)														---	---	---	---
C9orf25	203259	broad.mit.edu	37	9	34402759	34402759	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34402759G>A	uc011lok.1	-	3	514	c.207C>T	c.(205-207)AGC>AGT	p.S69S	C9orf25_uc003zuj.2_Silent_p.S52S|C9orf25_uc003zuk.2_Silent_p.S41S|C9orf25_uc011lol.1_Silent_p.S58S|C9orf25_uc003zul.2_Silent_p.S41S	NM_147202	NP_671735	Q8IW50	CI025_HUMAN	hypothetical protein LOC203259	69											0	all_epithelial(49;0.244)		LUSC - Lung squamous cell carcinoma(29;0.0107)	GBM - Glioblastoma multiforme(74;0.0858)														---	---	---	---
PIGO	84720	broad.mit.edu	37	9	35089116	35089116	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35089116C>T	uc003zwd.2	-	11	3639	c.3243G>A	c.(3241-3243)AGG>AGA	p.R1081R	PIGO_uc003zwc.1_3'UTR|PIGO_uc003zwe.2_Silent_p.R664R|PIGO_uc003zwf.2_Silent_p.R664R|PIGO_uc003zwg.1_3'UTR	NM_032634	NP_116023	Q8TEQ8	PIGO_HUMAN	phosphatidylinositol glycan anchor biosynthesis,	1081					C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	transferase activity			large_intestine(1)|ovary(1)|skin(1)	3			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)															---	---	---	---
PIGO	84720	broad.mit.edu	37	9	35095095	35095095	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35095095G>A	uc003zwd.2	-	2	864	c.468C>T	c.(466-468)CAC>CAT	p.H156H	PIGO_uc003zwc.1_Silent_p.H156H|PIGO_uc003zwe.2_Silent_p.H156H|PIGO_uc003zwf.2_Silent_p.H156H|PIGO_uc003zwg.1_Translation_Start_Site	NM_032634	NP_116023	Q8TEQ8	PIGO_HUMAN	phosphatidylinositol glycan anchor biosynthesis,	156					C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	transferase activity			large_intestine(1)|ovary(1)|skin(1)	3			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)															---	---	---	---
TPM2	7169	broad.mit.edu	37	9	35685419	35685419	+	Intron	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35685419C>T	uc003zxq.2	-						TPM2_uc003zxr.2_Intron|TPM2_uc003zxs.2_Intron|TPM2_uc010mkz.2_Intron|TPM2_uc011lpa.1_Intron	NM_213674	NP_998839			tropomyosin 2 (beta) isoform 2						muscle filament sliding|regulation of ATPase activity	cytosol|muscle thin filament tropomyosin	actin binding|structural constituent of muscle			ovary(1)	1	all_epithelial(49;0.121)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)															---	---	---	---
TLN1	7094	broad.mit.edu	37	9	35720426	35720426	+	Intron	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35720426G>A	uc003zxt.2	-							NM_006289	NP_006280			talin 1						axon guidance|cell adhesion|cell-cell junction assembly|cellular component movement|cytoskeletal anchoring at plasma membrane|muscle contraction|platelet activation|platelet degranulation	actin cytoskeleton|centrosome|cytosol|extracellular region|focal adhesion|intracellular membrane-bounded organelle|ruffle membrane	actin binding|insulin receptor binding|LIM domain binding|structural constituent of cytoskeleton|vinculin binding			lung(7)|breast(3)|ovary(2)|central_nervous_system(1)	13	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)															---	---	---	---
TMEM8B	51754	broad.mit.edu	37	9	35842713	35842713	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35842713C>T	uc003zym.2	+	7	1293	c.278C>T	c.(277-279)GCG>GTG	p.A93V	TMEM8B_uc003zyk.2_Missense_Mutation_p.A93V|TMEM8B_uc003zyl.2_Missense_Mutation_p.A260V|TMEM8B_uc003zyn.2_Intron|TMEM8B_uc003zyo.2_Missense_Mutation_p.A93V	NM_001042589	NP_001036054	A6NDV4	TMM8B_HUMAN	transmembrane protein 8B isoform a	93	Extracellular (Potential).				cell-matrix adhesion|regulation of growth|regulation of mitotic cell cycle	cell surface|endoplasmic reticulum|integral to membrane|mitochondrion|nucleus|plasma membrane	protein binding			ovary(1)	1																		---	---	---	---
FBXO10	26267	broad.mit.edu	37	9	37537214	37537214	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37537214G>A	uc004aab.2	-	3	1361	c.1312C>T	c.(1312-1314)CGG>TGG	p.R438W	FBXO10_uc004aac.2_Missense_Mutation_p.R454W|FBXO10_uc004aad.2_Intron	NM_012166	NP_036298	Q9UK96	FBX10_HUMAN	F-box protein 10	438	PbH1 3.					ubiquitin ligase complex	ubiquitin-protein ligase activity			lung(5)	5				GBM - Glioblastoma multiforme(29;0.0107)														---	---	---	---
PGM5	5239	broad.mit.edu	37	9	70993145	70993145	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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																		---	---	---	---
TMEM2	23670	broad.mit.edu	37	9	74309467	74309467	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74309467A>G	uc011lsa.1	-	21	4194	c.3654T>C	c.(3652-3654)CCT>CCC	p.P1218P	TMEM2_uc011lrz.1_Silent_p.P211P|TMEM2_uc010mos.2_Silent_p.P1155P|TMEM2_uc011lsb.1_RNA|TMEM2_uc004aik.2_Silent_p.P52P	NM_013390	NP_037522	Q9UHN6	TMEM2_HUMAN	transmembrane protein 2 isoform a	1218						integral to membrane				ovary(2)	2		all_epithelial(88;4.56e-14)|Myeloproliferative disorder(762;0.0255)		GBM - Glioblastoma multiforme(74;7.45e-21)|OV - Ovarian serous cystadenocarcinoma(323;1.02e-16)														---	---	---	---
C9orf79	286234	broad.mit.edu	37	9	90502650	90502650	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90502650T>C	uc004app.3	+	4	3283	c.3248T>C	c.(3247-3249)GTT>GCT	p.V1083A		NM_178828	NP_849150	Q6ZUB1	CI079_HUMAN	chromosome 9 open reading frame 79	1083						integral to membrane				ovary(3)	3																		---	---	---	---
S1PR3	1903	broad.mit.edu	37	9	91616512	91616512	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91616512G>A	uc004aqe.2	+	2	793	c.397G>A	c.(397-399)GCC>ACC	p.A133T		NM_005226	NP_005217	Q99500	S1PR3_HUMAN	sphingosine-1-phosphate receptor 3	133	Helical; Name=3; (By similarity).				anatomical structure morphogenesis|elevation of cytosolic calcium ion concentration|inflammatory response|positive regulation of cell proliferation	integral to plasma membrane	lipid binding|lysosphingolipid and lysophosphatidic acid receptor activity			ovary(2)|lung(1)|central_nervous_system(1)|skin(1)	5																OREG0019291	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
C9orf129	445577	broad.mit.edu	37	9	96097723	96097723	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96097723C>T	uc010mre.2	-	3	662	c.298G>A	c.(298-300)GCC>ACC	p.A100T		NM_001098808	NP_001092278	Q5T035	CI129_HUMAN	hypothetical protein LOC445577	100										ovary(1)	1																		---	---	---	---
FANCC	2176	broad.mit.edu	37	9	97869413	97869413	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97869413G>A	uc004avh.2	-	14	1730	c.1468C>T	c.(1468-1470)CTT>TTT	p.L490F		NM_000136	NP_000127	Q00597	FANCC_HUMAN	Fanconi anemia, complementation group C	490					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				---	---	---	---
ZNF782	158431	broad.mit.edu	37	9	99581109	99581109	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99581109C>T	uc004awp.1	-	6	1477	c.1196G>A	c.(1195-1197)TGC>TAC	p.C399Y	ZNF782_uc011lup.1_Missense_Mutation_p.C267Y	NM_001001662	NP_001001662	Q6ZMW2	ZN782_HUMAN	zinc finger protein 782	399	C2H2-type 5.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Acute lymphoblastic leukemia(62;0.0527)																---	---	---	---
TRIM14	9830	broad.mit.edu	37	9	100854204	100854204	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100854204C>T	uc004ayd.2	-	5	798	c.780G>A	c.(778-780)TCG>TCA	p.S260S	TRIM14_uc004ayf.1_Silent_p.S167S|TRIM14_uc011luz.1_Silent_p.S38S|TRIM14_uc011lva.1_Silent_p.S41S|TRIM14_uc004ayg.1_Silent_p.S260S|TRIM14_uc004ayh.1_Silent_p.S260S|TRIM14_uc004ayi.1_Intron|TRIM14_uc004ayj.1_Silent_p.S167S	NM_033220	NP_150089	Q14142	TRI14_HUMAN	tripartite motif protein TRIM14 isoform alpha	260	B30.2/SPRY.					cytoplasm|intracellular	zinc ion binding			central_nervous_system(1)	1		Acute lymphoblastic leukemia(62;0.0559)																---	---	---	---
CORO2A	7464	broad.mit.edu	37	9	100887136	100887136	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100887136G>A	uc004ayl.2	-	12	1764	c.1498C>T	c.(1498-1500)CTG>TTG	p.L500L	CORO2A_uc004aym.2_Silent_p.L500L|CORO2A_uc004ayk.2_Silent_p.L147L	NM_003389	NP_003380	Q92828	COR2A_HUMAN	coronin, actin binding protein, 2A	500	Potential.				actin cytoskeleton organization|intracellular signal transduction	actin cytoskeleton|transcriptional repressor complex	actin filament binding			skin(2)|ovary(1)|pancreas(1)	4		Acute lymphoblastic leukemia(62;0.0559)																---	---	---	---
INVS	27130	broad.mit.edu	37	9	103035322	103035322	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:103035322T>C	uc004bap.1	+	12	1960	c.1748T>C	c.(1747-1749)ATG>ACG	p.M583T	INVS_uc010mta.1_Missense_Mutation_p.M487T|INVS_uc011lve.1_Missense_Mutation_p.M487T|INVS_uc004bao.1_Missense_Mutation_p.M583T|INVS_uc004baq.1_Missense_Mutation_p.M487T|INVS_uc004bar.1_Missense_Mutation_p.M487T|INVS_uc010mtb.1_Missense_Mutation_p.M257T	NM_014425	NP_055240	Q9Y283	INVS_HUMAN	inversin isoform a	583	IQ 1.				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)																---	---	---	---
RNF20	56254	broad.mit.edu	37	9	104312994	104312994	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104312994C>T	uc004bbn.2	+	10	1289	c.1199C>T	c.(1198-1200)GCA>GTA	p.A400V		NM_019592	NP_062538	Q5VTR2	BRE1A_HUMAN	ring finger protein 20	400					histone H2B ubiquitination|histone monoubiquitination|negative regulation of cell migration|positive regulation of transcription, DNA-dependent|protein polyubiquitination|ubiquitin-dependent protein catabolic process	nucleolus|ubiquitin ligase complex	histone binding|p53 binding|transcription coactivator activity|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(1)|breast(1)|kidney(1)|skin(1)	8		all_hematologic(171;8.99e-06)|Acute lymphoblastic leukemia(62;0.000365)|Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;2.88e-19)|STAD - Stomach adenocarcinoma(157;0.00311)														---	---	---	---
CYLC2	1539	broad.mit.edu	37	9	105767799	105767799	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:105767799G>A	uc004bbs.2	+	5	956	c.886G>A	c.(886-888)GCC>ACC	p.A296T		NM_001340	NP_001331	Q14093	CYLC2_HUMAN	cylicin 2	296	31 X 3 AA repeats of K-K-X.				cell differentiation|multicellular organismal development|spermatogenesis	cytoskeletal calyx	structural constituent of cytoskeleton			skin(1)	1		all_hematologic(171;0.125)																---	---	---	---
ABCA1	19	broad.mit.edu	37	9	107645350	107645350	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107645350T>A	uc004bcl.2	-	5	704	c.391A>T	c.(391-393)ACA>TCA	p.T131S	ABCA1_uc004bcm.2_Missense_Mutation_p.T71S	NM_005502	NP_005493	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A member 1	131	Extracellular.				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)													---	---	---	---
CTNNAL1	8727	broad.mit.edu	37	9	111741587	111741587	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111741587G>A	uc004bdo.1	-	7	1117	c.1075C>T	c.(1075-1077)CAG>TAG	p.Q359*	CTNNAL1_uc010mts.1_Nonsense_Mutation_p.Q95*|CTNNAL1_uc010mtt.1_Nonsense_Mutation_p.Q359*|CTNNAL1_uc004bdp.1_Nonsense_Mutation_p.Q359*	NM_003798	NP_003789	Q9UBT7	CTNL1_HUMAN	catenin, alpha-like 1	359					cell adhesion|Rho protein signal transduction	actin cytoskeleton|cytosol|plasma membrane	cadherin binding|structural molecule activity			ovary(1)	1				STAD - Stomach adenocarcinoma(157;0.0768)														---	---	---	---
WDR31	114987	broad.mit.edu	37	9	116079127	116079127	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116079127C>T	uc004bhe.2	-	11	1258	c.1006G>A	c.(1006-1008)GCC>ACC	p.A336T	uc004bhb.2_5'Flank|WDR31_uc004bhc.2_Missense_Mutation_p.A335T|WDR31_uc004bhd.2_Missense_Mutation_p.A211T|WDR31_uc004bhf.2_RNA	NM_001012361	NP_001012361	Q8NA23	WDR31_HUMAN	WD repeat domain 31 isoform 1	336											0																		---	---	---	---
RGS3	5998	broad.mit.edu	37	9	116241776	116241776	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116241776C>A	uc004bhq.2	+	5	630	c.421C>A	c.(421-423)CTG>ATG	p.L141M	RGS3_uc004bhr.2_Missense_Mutation_p.L29M|RGS3_uc004bhs.2_Translation_Start_Site	NM_144488	NP_652759	P49796	RGS3_HUMAN	regulator of G-protein signalling 3 isoform 6	141	C2.				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																		---	---	---	---
TNC	3371	broad.mit.edu	37	9	117848173	117848173	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117848173C>T	uc004bjj.3	-	3	2199	c.1837G>A	c.(1837-1839)GAG>AAG	p.E613K	TNC_uc010mvf.2_Missense_Mutation_p.E613K	NM_002160	NP_002151	P24821	TENA_HUMAN	tenascin C precursor	613	EGF-like 15.				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																		---	---	---	---
DAB2IP	153090	broad.mit.edu	37	9	124528811	124528811	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124528811G>T	uc004bln.2	+	9	1484	c.1415G>T	c.(1414-1416)TGG>TTG	p.W472L	DAB2IP_uc004blo.2_Missense_Mutation_p.W376L|DAB2IP_uc004blp.2_5'Flank	NM_032552	NP_115941	Q5VWQ8	DAB2P_HUMAN	disabled homolog 2 interacting protein isoform	500	Ras-GAP.				activation of JUN kinase activity|apoptosis in response to endoplasmic reticulum stress|cellular response to epidermal growth factor stimulus|cellular response to tumor necrosis factor|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of catenin import into nucleus|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of epithelial cell migration|negative regulation of epithelial cell proliferation|negative regulation of epithelial to mesenchymal transition|negative regulation of fibroblast proliferation|negative regulation of I-kappaB kinase/NF-kappaB cascade|negative regulation of MAP kinase activity|negative regulation of NF-kappaB transcription factor activity|negative regulation of Ras GTPase activity|negative regulation of transcription from RNA polymerase II promoter|positive regulation of apoptosis|positive regulation of transcription from RNA polymerase II promoter	cytoplasm|intrinsic to internal side of plasma membrane	14-3-3 protein binding|death receptor binding|mitogen-activated protein kinase kinase kinase binding|protein homodimerization activity|protein phosphatase 2A binding|Ras GTPase activator activity|signaling adaptor activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
PTGS1	5742	broad.mit.edu	37	9	125140783	125140783	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125140783G>A	uc004bmg.1	+	4	418	c.283G>A	c.(283-285)GGG>AGG	p.G95R	PTGS1_uc011lys.1_Missense_Mutation_p.G70R|PTGS1_uc010mwb.1_5'UTR|PTGS1_uc004bmf.1_Missense_Mutation_p.G95R|PTGS1_uc004bmh.1_5'UTR|PTGS1_uc011lyt.1_5'UTR	NM_000962	NP_000953	P23219	PGH1_HUMAN	prostaglandin-endoperoxide synthase 1 isoform 1	95					cyclooxygenase pathway|hormone biosynthetic process|regulation of blood pressure|response to oxidative stress|xenobiotic metabolic process	endoplasmic reticulum membrane|Golgi apparatus|microsome|plasma membrane	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)|skin(1)	2					Acetaminophen(DB00316)|Aspirin(DB00945)|Balsalazide(DB01014)|Bromfenac(DB00963)|Ciclopirox(DB01188)|Diclofenac(DB00586)|Diflunisal(DB00861)|Dipyrone(DB04817)|Etodolac(DB00749)|Fenoprofen(DB00573)|Flurbiprofen(DB00712)|gamma-Homolinolenic acid(DB00154)|Ibuprofen(DB01050)|Icosapent(DB00159)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Ketorolac(DB00465)|Lumiracoxib(DB01283)|Meclofenamic acid(DB00939)|Mefenamic acid(DB00784)|Mesalazine(DB00244)|Minoxidil(DB00350)|Nabumetone(DB00461)|Naproxen(DB00788)|Phenacetin(DB03783)|Piroxicam(DB00554)|Rofecoxib(DB00533)|Salicyclic acid(DB00936)|Salsalate(DB01399)|Sulindac(DB00605)|Suprofen(DB00870)|Tenoxicam(DB00469)|Tolmetin(DB00500)													---	---	---	---
ZBTB26	57684	broad.mit.edu	37	9	125681367	125681367	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125681367G>A	uc004bnj.2	-	2	1059	c.847C>T	c.(847-849)CGT>TGT	p.R283C	ZBTB26_uc004bnk.2_Missense_Mutation_p.R283C	NM_020924	NP_065975	Q9HCK0	ZBT26_HUMAN	zinc finger and BTB domain containing 26	283	C2H2-type 1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
LHX2	9355	broad.mit.edu	37	9	126777589	126777589	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126777589C>T	uc004boe.1	+	3	1251	c.512C>T	c.(511-513)GCG>GTG	p.A171V	LHX2_uc010mwi.1_Missense_Mutation_p.A179V	NM_004789	NP_004780	P50458	LHX2_HUMAN	LIM homeobox protein 2	171						nucleus	sequence-specific DNA binding transcription factor activity|zinc ion binding				0																		---	---	---	---
NR6A1	2649	broad.mit.edu	37	9	127455987	127455987	+	Intron	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127455987C>T	uc004bor.1	-						NR6A1_uc004boq.1_Intron|NR6A1_uc010mwq.1_Intron|uc004bou.2_5'Flank|MIR181B2_hsa-mir-181b-2|MI0000683_5'Flank	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																		---	---	---	---
ARPC5L	81873	broad.mit.edu	37	9	127637424	127637424	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127637424C>T	uc004bpa.3	+	3	479	c.393C>T	c.(391-393)CAC>CAT	p.H131H	ARPC5L_uc011lzq.1_Silent_p.H79H	NM_030978	NP_112240	Q9BPX5	ARP5L_HUMAN	actin related protein 2/3 complex, subunit	131					regulation of actin filament polymerization	cytoplasm|cytoskeleton	actin binding				0																		---	---	---	---
FAM125B	89853	broad.mit.edu	37	9	129154437	129154437	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129154437C>T	uc004bqh.1	+	5	583	c.502C>T	c.(502-504)CGG>TGG	p.R168W	FAM125B_uc004bqg.1_Missense_Mutation_p.R168W|FAM125B_uc011lzy.1_Missense_Mutation_p.R153W|FAM125B_uc010mxd.2_Missense_Mutation_p.R161W|FAM125B_uc011lzz.1_Missense_Mutation_p.R161W	NM_033446	NP_258257	Q9H7P6	F125B_HUMAN	hypothetical protein LOC89853 isoform 1	168	MABP.				protein transport	late endosome membrane					0																		---	---	---	---
ZBTB34	403341	broad.mit.edu	37	9	129642791	129642791	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129642791G>A	uc004bqm.3	+	2	1198	c.1101G>A	c.(1099-1101)CCG>CCA	p.P367P		NM_001099270	NP_001092740	Q8NCN2	ZBT34_HUMAN	zinc finger and BTB domain containing 34	367					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
FAM129B	64855	broad.mit.edu	37	9	130271277	130271277	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130271277C>T	uc004brh.2	-	10	1497	c.1295G>A	c.(1294-1296)CGA>CAA	p.R432Q	FAM129B_uc004bri.2_Missense_Mutation_p.R419Q|FAM129B_uc004brj.3_Missense_Mutation_p.R432Q	NM_022833	NP_073744	Q96TA1	NIBL1_HUMAN	hypothetical protein LOC64855 isoform 1	432							protein binding				0																		---	---	---	---
PTGES2	80142	broad.mit.edu	37	9	130886796	130886796	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130886796C>T	uc004bti.2	-	3	989	c.511G>A	c.(511-513)GCC>ACC	p.A171T	PTGES2_uc004btj.2_RNA|PTGES2_uc004btk.2_5'UTR|PTGES2_uc004btl.2_5'UTR|PTGES2_uc004btm.2_RNA	NM_025072	NP_079348	Q9H7Z7	PGES2_HUMAN	prostaglandin E synthase 2	171	Glutaredoxin.|Cytoplasmic (Potential).				cell redox homeostasis|prostaglandin biosynthetic process	Golgi membrane|integral to membrane|mitochondrion|perinuclear region of cytoplasm	electron carrier activity|prostaglandin-E synthase activity|protein binding|protein disulfide oxidoreductase activity				0																		---	---	---	---
ODF2	4957	broad.mit.edu	37	9	131221920	131221920	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131221920C>A	uc011mbd.1	+	3	418	c.107C>A	c.(106-108)CCC>CAC	p.P36H	ODF2_uc011maz.1_Missense_Mutation_p.P36H|ODF2_uc011mba.1_5'UTR|ODF2_uc010myb.2_5'UTR|ODF2_uc011mbb.1_5'UTR|ODF2_uc011mbc.1_5'UTR|ODF2_uc004bva.2_5'UTR|ODF2_uc004bvb.2_5'UTR|ODF2_uc011mbe.1_5'UTR|ODF2_uc004bvc.2_5'UTR|ODF2_uc010myc.2_Missense_Mutation_p.P36H|ODF2_uc011mbf.1_Missense_Mutation_p.P36H|ODF2_uc004bvd.3_Missense_Mutation_p.P36H|ODF2_uc004bve.2_Missense_Mutation_p.P36H	NM_002540	NP_002531	Q5BJF6	ODFP2_HUMAN	outer dense fiber of sperm tails 2 isoform 1	36					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																		---	---	---	---
WDR34	89891	broad.mit.edu	37	9	131396155	131396155	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131396155C>T	uc004bvq.1	-	9	1603	c.1479G>A	c.(1477-1479)CAG>CAA	p.Q493Q	WDR34_uc004bvs.1_Silent_p.Q484Q|WDR34_uc004bvr.1_Silent_p.Q465Q	NM_052844	NP_443076	Q96EX3	WDR34_HUMAN	WD repeat domain 34	493	WD 5.					cytoplasm				central_nervous_system(2)|skin(1)	3																		---	---	---	---
DOLK	22845	broad.mit.edu	37	9	131708027	131708027	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131708027T>C	uc004bwr.2	-	1	1986	c.1556A>G	c.(1555-1557)TAC>TGC	p.Y519C	NUP188_uc004bws.1_5'Flank|NUP188_uc004bwq.1_Intron	NM_014908	NP_055723	Q9UPQ8	DOLK_HUMAN	dolichol kinase	519	Cytoplasmic (Potential).				dolichyl diphosphate biosynthetic process|dolichyl monophosphate biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	integral to endoplasmic reticulum membrane|membrane fraction	dolichol kinase activity				0																		---	---	---	---
SH3GLB2	56904	broad.mit.edu	37	9	131777085	131777085	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131777085G>A	uc004bwv.2	-	4	579	c.433C>T	c.(433-435)CGC>TGC	p.R145C	SH3GLB2_uc004bww.2_Missense_Mutation_p.R145C|SH3GLB2_uc004bwx.1_Missense_Mutation_p.R145C|SH3GLB2_uc011mbm.1_Missense_Mutation_p.R145C	NM_020145	NP_064530	Q9NR46	SHLB2_HUMAN	SH3-domain GRB2-like endophilin B2	145	BAR.				filopodium assembly|signal transduction	cytoplasm|nucleus	cytoskeletal adaptor activity|SH3 domain binding				0																		---	---	---	---
CRAT	1384	broad.mit.edu	37	9	131870275	131870275	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131870275G>A	uc004bxh.2	-	2	391	c.109C>T	c.(109-111)CGG>TGG	p.R37W	CRAT_uc004bxg.2_Missense_Mutation_p.R16W|CRAT_uc004bxk.3_Missense_Mutation_p.R16W|CRAT_uc004bxj.2_Missense_Mutation_p.R38W|PPP2R4_uc004bxl.1_5'Flank	NM_000755	NP_000746	P43155	CACP_HUMAN	carnitine acetyltransferase precursor	37					energy derivation by oxidation of organic compounds|fatty acid beta-oxidation using acyl-CoA oxidase|transport	endoplasmic reticulum|mitochondrial inner membrane|peroxisomal matrix	carnitine O-acetyltransferase activity			central_nervous_system(1)	1				UCEC - Uterine corpus endometrioid carcinoma (4;0.0178)	L-Carnitine(DB00583)													---	---	---	---
USP20	10868	broad.mit.edu	37	9	132630629	132630629	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132630629G>A	uc004bys.2	+	11	1247	c.1036G>A	c.(1036-1038)GAG>AAG	p.E346K	USP20_uc004byr.2_Missense_Mutation_p.E346K|USP20_uc004byt.1_Missense_Mutation_p.E346K	NM_001110303	NP_001103773	Q9Y2K6	UBP20_HUMAN	ubiquitin specific protease 20	346					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)																---	---	---	---
GPR107	57720	broad.mit.edu	37	9	132838709	132838709	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132838709C>A	uc004bze.2	+	3	501	c.274C>A	c.(274-276)CGT>AGT	p.R92S	GPR107_uc004bzb.2_5'UTR|GPR107_uc004bzc.3_RNA|GPR107_uc011mbx.1_Missense_Mutation_p.R92S|GPR107_uc004bzd.2_Missense_Mutation_p.R92S	NM_001136557	NP_001130029	Q5VW38	GP107_HUMAN	G protein-coupled receptor 107 isoform 1	92						integral to membrane				upper_aerodigestive_tract(1)	1		Ovarian(14;0.000531)																---	---	---	---
FUBP3	8939	broad.mit.edu	37	9	133506010	133506010	+	Intron	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133506010C>T	uc004bzr.1	+						FUBP3_uc004bzs.1_Intron	NM_003934	NP_003925			far upstream element (FUSE) binding protein 3						positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|RNA binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(145;0.000279)														---	---	---	---
LAMC3	10319	broad.mit.edu	37	9	133951290	133951290	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133951290G>A	uc004caa.1	+	21	3665	c.3567G>A	c.(3565-3567)GCG>GCA	p.A1189A		NM_006059	NP_006050	Q9Y6N6	LAMC3_HUMAN	laminin, gamma 3 precursor	1189	Domain II and I.				cell adhesion	basement membrane|membrane	structural molecule activity			ovary(2)|pancreas(1)	3	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.06e-05)|Epithelial(140;0.000551)														---	---	---	---
NUP214	8021	broad.mit.edu	37	9	134074323	134074323	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134074323G>A	uc004cag.2	+	29	5553	c.5442G>A	c.(5440-5442)CAG>CAA	p.Q1814Q	NUP214_uc004cah.2_Silent_p.Q1804Q|NUP214_uc004cai.2_Silent_p.Q1244Q|NUP214_uc010mzg.2_RNA|NUP214_uc011mcg.1_Silent_p.Q640Q|NUP214_uc011mcf.1_Silent_p.Q591Q|NUP214_uc010mzh.1_Silent_p.Q328Q|NUP214_uc010mzi.1_Silent_p.Q328Q	NM_005085	NP_005076	P35658	NU214_HUMAN	nucleoporin 214kDa	1814	Pro/Ser/Thr-rich.|11 X 3 AA approximate repeats.|11 X 5 AA approximate repeats.|18 X 4 AA approximate repeats.				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								---	---	---	---
RAPGEF1	2889	broad.mit.edu	37	9	134459910	134459910	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134459910T>C	uc004cbc.2	-	20	2879	c.2749A>G	c.(2749-2751)ATG>GTG	p.M917V	RAPGEF1_uc004cbb.2_Missense_Mutation_p.M935V	NM_005312	NP_005303	Q13905	RPGF1_HUMAN	guanine nucleotide-releasing factor 2 isoform a	917	Ras-GEF.				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)														---	---	---	---
RAPGEF1	2889	broad.mit.edu	37	9	134525511	134525511	+	Intron	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134525511C>T	uc004cbc.2	-						RAPGEF1_uc004cbb.2_Intron|RAPGEF1_uc010mzn.2_Intron|RAPGEF1_uc004cbd.2_Intron	NM_005312	NP_005303			guanine nucleotide-releasing factor 2 isoform a						activation of MAPKK activity|nerve growth factor receptor signaling pathway|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|endosome	guanyl-nucleotide exchange factor activity|SH3 domain binding			lung(3)|ovary(2)|breast(1)|skin(1)	7		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;2.19e-05)|Epithelial(140;0.000364)														---	---	---	---
SETX	23064	broad.mit.edu	37	9	135201786	135201786	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135201786C>T	uc004cbk.2	-	10	5382	c.5199G>A	c.(5197-5199)GTG>GTA	p.V1733V	SETX_uc004cbj.2_Silent_p.V1352V|SETX_uc010mzt.2_Silent_p.V1352V	NM_015046	NP_055861	Q7Z333	SETX_HUMAN	senataxin	1733					cell death|double-strand break repair|RNA processing	cytoplasm|nucleolus|nucleoplasm	ATP binding|DNA helicase activity			ovary(2)|skin(1)	3		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)														---	---	---	---
TTF1	7270	broad.mit.edu	37	9	135251410	135251410	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135251410G>A	uc004cbl.2	-	11	2662	c.2610C>T	c.(2608-2610)GAC>GAT	p.D870D	TTF1_uc011mcp.1_RNA|TTF1_uc004cbm.2_Silent_p.D355D	NM_007344	NP_031370	Q15361	TTF1_HUMAN	transcription termination factor, RNA polymerase	870					negative regulation of DNA replication|regulation of transcription, DNA-dependent|termination of RNA polymerase I transcription	nucleolus|nucleoplasm	DNA binding			ovary(2)|upper_aerodigestive_tract(1)|pancreas(1)	4		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;4.25e-06)|Epithelial(140;9.09e-05)														---	---	---	---
DDX31	64794	broad.mit.edu	37	9	135487481	135487481	+	Missense_Mutation	SNP	C	T	T	rs148432033		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135487481C>T	uc004cbq.1	-	19	2454	c.2302G>A	c.(2302-2304)GTG>ATG	p.V768M	DDX31_uc010mzu.1_Missense_Mutation_p.V695M	NM_022779	NP_073616	Q9H8H2	DDX31_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 31	768						nucleolus	ATP binding|ATP-dependent helicase activity|RNA binding			central_nervous_system(1)	1				OV - Ovarian serous cystadenocarcinoma(145;2.67e-06)|Epithelial(140;7.61e-05)														---	---	---	---
C9orf96	169436	broad.mit.edu	37	9	136268949	136268949	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136268949C>T	uc004cdk.2	+	15	1661	c.1600C>T	c.(1600-1602)CTG>TTG	p.L534L	C9orf96_uc004cdl.2_RNA	NM_153710	NP_714921	Q8NE28	SGK71_HUMAN	hypothetical protein LOC169436	534							ATP binding|protein kinase activity			stomach(2)|central_nervous_system(2)	4				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)														---	---	---	---
ADAMTS13	11093	broad.mit.edu	37	9	136320407	136320407	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136320407T>G	uc004cdv.3	+	25	3694	c.3250T>G	c.(3250-3252)TGC>GGC	p.C1084G	ADAMTS13_uc004cdp.3_Missense_Mutation_p.C311G|ADAMTS13_uc004cdt.1_Missense_Mutation_p.C1084G|ADAMTS13_uc004cdu.1_Missense_Mutation_p.C1053G|ADAMTS13_uc004cdw.3_Missense_Mutation_p.C1084G|ADAMTS13_uc004cdx.3_Missense_Mutation_p.C1053G|ADAMTS13_uc004cdz.3_Missense_Mutation_p.C754G|ADAMTS13_uc004cea.1_5'Flank|ADAMTS13_uc004ceb.3_5'Flank	NM_139025	NP_620594	Q76LX8	ATS13_HUMAN	ADAM metallopeptidase with thrombospondin type 1	1084	TSP type-1 8.				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)														---	---	---	---
ADAMTSL2	9719	broad.mit.edu	37	9	136403509	136403509	+	Missense_Mutation	SNP	C	T	T	rs139661631		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136403509C>T	uc011mdl.1	+	4	829	c.272C>T	c.(271-273)ACG>ATG	p.T91M	ADAMTSL2_uc004cei.2_Missense_Mutation_p.T91M	NM_001145320	NP_001138792	Q86TH1	ATL2_HUMAN	ADAMTS-like 2 precursor	91	TSP type-1 1.				negative regulation of transforming growth factor beta receptor signaling pathway	proteinaceous extracellular matrix	metalloendopeptidase activity|protein binding|zinc ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(145;9.31e-08)|Epithelial(140;6.62e-07)|all cancers(34;7.74e-06)														---	---	---	---
VAV2	7410	broad.mit.edu	37	9	136637093	136637093	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136637093G>A	uc004ces.2	-	26	2257	c.2211C>T	c.(2209-2211)TTC>TTT	p.F737F	VAV2_uc004cer.2_Silent_p.F727F|VAV2_uc004cet.1_Silent_p.F276F	NM_001134398	NP_001127870	P52735	VAV2_HUMAN	vav 2 guanine nucleotide exchange factor isoform	737	SH2.				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)														---	---	---	---
CAMSAP1	157922	broad.mit.edu	37	9	138713422	138713422	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138713422C>T	uc004cgr.3	-	11	3085	c.3085G>A	c.(3085-3087)GAA>AAA	p.E1029K	CAMSAP1_uc004cgq.3_Missense_Mutation_p.E919K|CAMSAP1_uc010nbg.2_Missense_Mutation_p.E751K	NM_015447	NP_056262	Q5T5Y3	CAMP1_HUMAN	calmodulin regulated spectrin-associated protein	1029						cytoplasm|microtubule				ovary(1)|central_nervous_system(1)|pancreas(1)	3				OV - Ovarian serous cystadenocarcinoma(145;1.4e-06)|Epithelial(140;1.11e-05)														---	---	---	---
SNAPC4	6621	broad.mit.edu	37	9	139276396	139276396	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139276396G>A	uc004chh.2	-	17	2206	c.2197C>T	c.(2197-2199)CAC>TAC	p.H733Y		NM_003086	NP_003077	Q5SXM2	SNPC4_HUMAN	small nuclear RNA activating complex,	733					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)														---	---	---	---
NOTCH1	4851	broad.mit.edu	37	9	139391870	139391870	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139391870G>A	uc004chz.2	-	34	6321	c.6321C>T	c.(6319-6321)CAC>CAT	p.H2107H		NM_017617	NP_060087	P46531	NOTC1_HUMAN	notch1 preproprotein	2107	Cytoplasmic (Potential).				aortic valve morphogenesis|immune response|negative regulation of BMP signaling pathway|negative regulation of cell-substrate adhesion|negative regulation of myoblast differentiation|negative regulation of osteoblast differentiation|negative regulation of transcription, DNA-dependent|Notch receptor processing	cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane	calcium ion binding|protein binding|receptor activity			haematopoietic_and_lymphoid_tissue(791)|upper_aerodigestive_tract(29)|lung(13)|central_nervous_system(10)|breast(9)|large_intestine(1)|skin(1)|oesophagus(1)|pancreas(1)	856	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)				T|Mis|O	TRB@	T-ALL					HNSCC(8;0.001)			---	---	---	---
TRAF2	7186	broad.mit.edu	37	9	139820309	139820309	+	Missense_Mutation	SNP	G	A	A	rs142412558	byFrequency	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139820309G>A	uc010nbu.2	+	12	1635	c.1462G>A	c.(1462-1464)GAT>AAT	p.D488N	TRAF2_uc004cjv.2_Missense_Mutation_p.D488N|TRAF2_uc011mek.1_Missense_Mutation_p.D477N|TRAF2_uc010nbw.2_Missense_Mutation_p.D463N	NM_021138	NP_066961	Q12933	TRAF2_HUMAN	TNF receptor-associated factor 2	488	MATH.				activation of caspase activity|activation of NF-kappaB-inducing kinase activity|activation of pro-apoptotic gene products|cellular protein complex assembly|induction of apoptosis by extracellular signals|positive regulation of interleukin-2 production|positive regulation of JUN kinase activity|positive regulation of NF-kappaB transcription factor activity|positive regulation of T cell cytokine production|protein autoubiquitination|protein homotrimerization|protein K63-linked ubiquitination|tumor necrosis factor-mediated signaling pathway	CD40 receptor complex|cytosol|internal side of plasma membrane	CD40 receptor binding|enzyme binding|protein binding|signal transducer activity|sphingolipid binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|lung(1)|breast(1)|skin(1)	4	all_cancers(76;0.11)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.229)	OV - Ovarian serous cystadenocarcinoma(145;4.48e-06)|Epithelial(140;9.55e-06)														---	---	---	---
PFKP	5214	broad.mit.edu	37	10	3146003	3146003	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3146003G>A	uc001igp.2	+	5	523	c.487G>A	c.(487-489)GCC>ACC	p.A163T	PFKP_uc001igq.2_Missense_Mutation_p.A155T|PFKP_uc009xhr.2_Missense_Mutation_p.A125T|PFKP_uc009xhs.1_5'Flank	NM_002627	NP_002618	Q01813	K6PP_HUMAN	phosphofructokinase, platelet	163					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)														---	---	---	---
PFKP	5214	broad.mit.edu	37	10	3162244	3162244	+	Intron	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3162244C>T	uc001igp.2	+						PFKP_uc001igq.2_Intron|PFKP_uc009xhr.2_Intron|PFKP_uc009xhs.1_Intron|PFKP_uc009xht.2_Intron|PFKP_uc009xhu.2_Intron	NM_002627	NP_002618			phosphofructokinase, platelet						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)												OREG0019976	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
KIN	22944	broad.mit.edu	37	10	7829837	7829837	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7829837C>T	uc001ijt.2	-	1	108	c.60G>A	c.(58-60)GGG>GGA	p.G20G	KIN_uc010qaz.1_RNA|KIN_uc009xip.2_Silent_p.G20G|KIN_uc010qba.1_5'UTR|ATP5C1_uc010qbb.1_5'Flank|ATP5C1_uc009xiq.1_5'Flank|ATP5C1_uc010qbc.1_5'Flank|ATP5C1_uc001iju.2_5'Flank|ATP5C1_uc001ijv.2_5'Flank	NM_012311	NP_036443	O60870	KIN17_HUMAN	HsKin17 protein	20					DNA recombination|DNA repair|DNA replication|interspecies interaction between organisms|mRNA processing	cytoplasm|nuclear matrix	double-stranded DNA binding|RNA binding|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
TAF3	83860	broad.mit.edu	37	10	8007484	8007484	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:8007484G>A	uc010qbd.1	+	3	2011	c.2011G>A	c.(2011-2013)GCC>ACC	p.A671T		NM_031923	NP_114129	Q5VWG9	TAF3_HUMAN	RNA polymerase II transcription factor TAFII140	671	Lys-rich.				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																		---	---	---	---
FAM188A	80013	broad.mit.edu	37	10	15885239	15885239	+	Silent	SNP	C	T	T	rs140140984		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15885239C>T	uc001iod.1	-	3	428	c.207G>A	c.(205-207)TCG>TCA	p.S69S	FAM188A_uc001ioe.1_5'UTR|FAM188A_uc001iof.1_Silent_p.S69S	NM_024948	NP_079224	Q9H8M7	F188A_HUMAN	chromosome 10 open reading frame 97	69					apoptosis	nucleus	calcium ion binding			ovary(1)	1																		---	---	---	---
NEBL	10529	broad.mit.edu	37	10	21141488	21141488	+	Missense_Mutation	SNP	C	T	T	rs150518045	byFrequency	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21141488C>T	uc001iqi.2	-	10	1391	c.994G>A	c.(994-996)GTC>ATC	p.V332I	NEBL_uc001iqj.2_RNA|NEBL_uc001iqk.2_Intron	NM_006393	NP_006384	O76041	NEBL_HUMAN	nebulette sarcomeric isoform	332	Nebulin 9.				regulation of actin filament length		actin binding|structural constituent of muscle			ovary(2)	2																		---	---	---	---
BMI1	648	broad.mit.edu	37	10	22618263	22618263	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22618263C>T	uc001irh.2	+	10	1412	c.773C>T	c.(772-774)GCC>GTC	p.A258V	BMI1_uc009xkg.2_Missense_Mutation_p.A401V	NM_005180	NP_005171	P35226	BMI1_HUMAN	BMI1 polycomb ring finger oncogene	258	Pro/Ser-rich.				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																		---	---	---	---
KIAA1217	56243	broad.mit.edu	37	10	24833918	24833918	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:24833918C>T	uc001iru.3	+	20	5623	c.5220C>T	c.(5218-5220)AGC>AGT	p.S1740S	KIAA1217_uc001irs.2_Silent_p.S1061S|KIAA1217_uc001irt.3_Silent_p.S1106S|KIAA1217_uc010qcy.1_Silent_p.S1171S|KIAA1217_uc010qcz.1_Silent_p.S1146S|KIAA1217_uc001irw.2_Silent_p.S890S|KIAA1217_uc001irz.2_Silent_p.S824S|KIAA1217_uc001irx.2_Silent_p.S1423S|KIAA1217_uc001iry.2_Silent_p.S864S	NM_019590	NP_062536	Q5T5P2	SKT_HUMAN	sickle tail isoform 1	1740					embryonic skeletal system development	cytoplasm				ovary(5)|skin(2)	7																		---	---	---	---
MYO3A	53904	broad.mit.edu	37	10	26414415	26414415	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:26414415A>G	uc001isn.2	+	19	2352	c.1992A>G	c.(1990-1992)CGA>CGG	p.R664R	MYO3A_uc009xko.1_Silent_p.R664R|MYO3A_uc009xkp.1_RNA|MYO3A_uc009xkq.1_Intron	NM_017433	NP_059129	Q8NEV4	MYO3A_HUMAN	myosin IIIA	664	Myosin head-like.				protein autophosphorylation|response to stimulus|sensory perception of sound|visual perception	cytoplasm|filamentous actin|filopodium|myosin complex	actin binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|plus-end directed microfilament motor activity|protein serine/threonine kinase activity			ovary(6)|stomach(3)|lung(3)|central_nervous_system(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	18																		---	---	---	---
GAD2	2572	broad.mit.edu	37	10	26506539	26506539	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:26506539C>T	uc001isp.2	+	2	580	c.77C>T	c.(76-78)GCG>GTG	p.A26V	GAD2_uc009xkr.2_Missense_Mutation_p.A26V|GAD2_uc001isq.2_Missense_Mutation_p.A26V	NM_001134366	NP_001127838	Q05329	DCE2_HUMAN	glutamate decarboxylase 2	26					glutamate decarboxylation to succinate|neurotransmitter biosynthetic process|neurotransmitter secretion	cell junction|clathrin sculpted gamma-aminobutyric acid transport vesicle membrane|cytosol|Golgi membrane|presynaptic membrane	glutamate decarboxylase activity|protein binding|pyridoxal phosphate binding			central_nervous_system(1)|skin(1)	2					L-Glutamic Acid(DB00142)													---	---	---	---
ACBD5	91452	broad.mit.edu	37	10	27497331	27497331	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27497331C>T	uc010qdp.1	-	10	1439	c.1248G>A	c.(1246-1248)CAG>CAA	p.Q416Q	ACBD5_uc010qdm.1_Silent_p.Q414Q|ACBD5_uc010qdn.1_Silent_p.Q307Q|ACBD5_uc010qdo.1_Silent_p.Q239Q|ACBD5_uc001ito.2_Silent_p.Q381Q|ACBD5_uc001itp.2_Silent_p.Q307Q|ACBD5_uc001itq.2_Silent_p.Q307Q|ACBD5_uc001itr.1_Silent_p.Q205Q	NM_145698	NP_663736	Q5T8D3	ACBD5_HUMAN	acyl-Coenzyme A binding domain containing 5	425					transport	integral to membrane|peroxisomal membrane	fatty-acyl-CoA binding				0																		---	---	---	---
PTCHD3	374308	broad.mit.edu	37	10	27702350	27702350	+	Missense_Mutation	SNP	G	A	A	rs147881350		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27702350G>A	uc001itu.2	-	1	948	c.830C>T	c.(829-831)ACG>ATG	p.T277M		NM_001034842	NP_001030014	Q3KNS1	PTHD3_HUMAN	patched domain containing 3	277					spermatid development	integral to membrane	hedgehog receptor activity			ovary(2)|pancreas(1)|skin(1)	4																		---	---	---	---
MTPAP	55149	broad.mit.edu	37	10	30611528	30611528	+	Silent	SNP	G	A	A	rs139195646	byFrequency	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30611528G>A	uc001iva.3	-	6	1074	c.1011C>T	c.(1009-1011)TCC>TCT	p.S337S	MTPAP_uc001ivb.3_Silent_p.S467S	NM_018109	NP_060579	Q9NVV4	PAPD1_HUMAN	PAP associated domain containing 1 precursor	337					cell death|histone mRNA catabolic process|mRNA polyadenylation|transcription, DNA-dependent	mitochondrion	ATP binding|magnesium ion binding|manganese ion binding|polynucleotide adenylyltransferase activity|protein homodimerization activity|RNA binding|UTP binding			ovary(1)	1																		---	---	---	---
ZNF33A	7581	broad.mit.edu	37	10	38343774	38343774	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38343774A>G	uc001izh.2	+	5	897	c.719A>G	c.(718-720)AAC>AGC	p.N240S	ZNF33A_uc001izg.2_Missense_Mutation_p.N241S|ZNF33A_uc010qev.1_Missense_Mutation_p.N247S|ZNF33A_uc001izi.1_Intron	NM_006974	NP_008905	Q06730	ZN33A_HUMAN	zinc finger protein 33A isoform b	240						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|skin(1)	3																		---	---	---	---
OR13A1	79290	broad.mit.edu	37	10	45798942	45798942	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45798942A>G	uc001jcc.1	-	4	1238	c.929T>C	c.(928-930)TTG>TCG	p.L310S	OR13A1_uc001jcd.1_Missense_Mutation_p.L306S	NM_001004297	NP_001004297	Q8NGR1	O13A1_HUMAN	olfactory receptor, family 13, subfamily A,	310	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0																		---	---	---	---
MARCH8	220972	broad.mit.edu	37	10	45956826	45956826	+	Silent	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45956826G>T	uc001jci.1	-	5	515	c.276C>A	c.(274-276)CCC>CCA	p.P92P	MARCH8_uc001jch.2_Silent_p.P374P|MARCH8_uc001jcj.1_Silent_p.P92P|MARCH8_uc001jck.1_Silent_p.P92P|MARCH8_uc001jcg.1_5'UTR	NM_001002266	NP_001002266	Q5T0T0	MARH8_HUMAN	cellular modulator of immune recognition isoform	92	RING-CH-type.					cytoplasmic vesicle membrane|early endosome membrane|integral to membrane|lysosomal membrane	ubiquitin-protein ligase activity|zinc ion binding				0																		---	---	---	---
RBP3	5949	broad.mit.edu	37	10	48385926	48385926	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:48385926G>A	uc001jez.2	-	2	3280	c.3166C>T	c.(3166-3168)CTC>TTC	p.L1056F		NM_002900	NP_002891	P10745	RET3_HUMAN	retinol-binding protein 3 precursor	1056	4 X approximate tandem repeats.|4.				lipid metabolic process|proteolysis|transport|visual perception	interphotoreceptor matrix	retinal binding|serine-type peptidase activity			large_intestine(1)|central_nervous_system(1)	2					Vitamin A(DB00162)													---	---	---	---
OGDHL	55753	broad.mit.edu	37	10	50959917	50959917	+	Silent	SNP	G	A	A	rs149339959		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50959917G>A	uc001jie.2	-	6	847	c.705C>T	c.(703-705)AGC>AGT	p.S235S	OGDHL_uc009xog.2_Silent_p.S262S|OGDHL_uc010qgt.1_Silent_p.S178S|OGDHL_uc010qgu.1_Silent_p.S26S|OGDHL_uc009xoh.2_Silent_p.S26S	NM_018245	NP_060715	Q9ULD0	OGDHL_HUMAN	oxoglutarate dehydrogenase-like isoform a	235					glycolysis	mitochondrial matrix	oxoglutarate dehydrogenase (succinyl-transferring) activity|thiamine pyrophosphate binding			pancreas(1)	1																		---	---	---	---
CSTF2T	23283	broad.mit.edu	37	10	53458059	53458059	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:53458059C>T	uc001jjp.2	-	1	1297	c.1251G>A	c.(1249-1251)GCG>GCA	p.A417A	PRKG1_uc001jjm.2_Intron|PRKG1_uc001jjn.2_Intron|PRKG1_uc001jjo.2_Intron	NM_015235	NP_056050	Q9H0L4	CSTFT_HUMAN	cleavage stimulation factor, 3' pre-RNA, subunit	417	Gly-rich.				mRNA processing	nucleus	nucleotide binding|RNA binding			ovary(1)	1				COAD - Colon adenocarcinoma(2;0.00736)|Colorectal(2;0.00898)|all cancers(4;0.0188)|GBM - Glioblastoma multiforme(4;0.0778)|Epithelial(53;0.122)														---	---	---	---
PCDH15	65217	broad.mit.edu	37	10	55581920	55581920	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:55581920C>A	uc001jju.1	-	33	5961	c.5566G>T	c.(5566-5568)GAG>TAG	p.E1856*	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_Nonsense_Mutation_p.E1853*|PCDH15_uc010qhw.1_Nonsense_Mutation_p.E1816*|PCDH15_uc010qhx.1_Nonsense_Mutation_p.E1787*|PCDH15_uc010qhy.1_Nonsense_Mutation_p.E1863*|PCDH15_uc010qhz.1_Nonsense_Mutation_p.E1858*|PCDH15_uc010qia.1_Nonsense_Mutation_p.E1836*|PCDH15_uc010qib.1_Nonsense_Mutation_p.E1833*	NM_033056	NP_149045	Q96QU1	PCD15_HUMAN	protocadherin 15 isoform CD1-4 precursor	1856	Cytoplasmic (Potential).				equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound	extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse	calcium ion binding	p.E1856E(1)		pancreas(5)|ovary(4)|upper_aerodigestive_tract(2)|skin(2)	13		Melanoma(3;0.117)|Lung SC(717;0.238)													HNSCC(58;0.16)			---	---	---	---
ANK3	288	broad.mit.edu	37	10	61835822	61835822	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61835822G>A	uc001jky.2	-	37	5009	c.4817C>T	c.(4816-4818)ACG>ATG	p.T1606M	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	1606	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																		---	---	---	---
ARID5B	84159	broad.mit.edu	37	10	63759914	63759914	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:63759914G>A	uc001jlt.1	+	4	593	c.567G>A	c.(565-567)TCG>TCA	p.S189S	ARID5B_uc010qil.1_Silent_p.S189S	NM_032199	NP_115575	Q14865	ARI5B_HUMAN	AT rich interactive domain 5B (MRF1-like)	189					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)																	---	---	---	---
TACR2	6865	broad.mit.edu	37	10	71164698	71164698	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71164698C>T	uc001jpn.2	-	5	1676	c.1081G>A	c.(1081-1083)GGG>AGG	p.G361R	TACR2_uc001jpm.2_Missense_Mutation_p.G149R	NM_001057	NP_001048	P21452	NK2R_HUMAN	tachykinin receptor 2	361	Cytoplasmic (Potential).				excretion|muscle contraction	integral to plasma membrane	tachykinin receptor activity			prostate(1)	1					Clonidine(DB00575)|Octreotide(DB00104)													---	---	---	---
AIFM2	84883	broad.mit.edu	37	10	71880941	71880941	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71880941C>T	uc010qjg.1	-	3	334	c.321G>A	c.(319-321)CTG>CTA	p.L107L	AIFM2_uc001jqp.1_Silent_p.L107L	NM_032797	NP_116186	Q9BRQ8	AIFM2_HUMAN	apoptosis-inducing factor (AIF)-like	107					apoptotic mitochondrial changes|chromosome condensation|induction of apoptosis	cytosol|integral to membrane|mitochondrial outer membrane	DNA binding|electron-transferring-flavoprotein dehydrogenase activity|flavin adenine dinucleotide binding			central_nervous_system(1)	1																		---	---	---	---
NPFFR1	64106	broad.mit.edu	37	10	72025905	72025905	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72025905T>C	uc010qjk.1	-	1	250	c.244A>G	c.(244-246)AAC>GAC	p.N82D		NM_022146	NP_071429	Q9GZQ6	NPFF1_HUMAN	neuropeptide FF receptor 1	84	Helical; Name=2; (Potential).					integral to membrane|plasma membrane	neuropeptide receptor activity				0																		---	---	---	---
CDH23	64072	broad.mit.edu	37	10	73538008	73538008	+	Silent	SNP	C	T	T	rs111033487	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73538008C>T	uc001jrx.3	+	38	5507	c.5130C>T	c.(5128-5130)ATC>ATT	p.I1710I		NM_022124	NP_071407	Q9H251	CAD23_HUMAN	cadherin-like 23 isoform 1 precursor	1710	Cadherin 16.|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																		---	---	---	---
ASCC1	51008	broad.mit.edu	37	10	73912658	73912658	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73912658C>T	uc001jst.1	-	8	907	c.799G>A	c.(799-801)GCC>ACC	p.A267T	ASCC1_uc001jsr.1_Missense_Mutation_p.A154T|ASCC1_uc001jss.1_Missense_Mutation_p.A239T|ASCC1_uc001jsu.1_Missense_Mutation_p.A239T|ASCC1_uc010qju.1_Missense_Mutation_p.A260T			Q8N9N2	ASCC1_HUMAN	RecName: Full=Activating signal cointegrator 1 complex subunit 1; AltName: Full=ASC-1 complex subunit p50; AltName: Full=Trip4 complex subunit p50;	267					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|transcription factor complex	RNA binding				0																		---	---	---	---
CBARA1	10367	broad.mit.edu	37	10	74268011	74268011	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74268011C>T	uc001jtb.1	-	7	693	c.560G>A	c.(559-561)CGA>CAA	p.R187Q	CBARA1_uc010qjw.1_5'UTR|CBARA1_uc010qjx.1_Intron|CBARA1_uc009xqo.1_RNA	NM_006077	NP_006068	Q9BPX6	MICU1_HUMAN	calcium binding atopy-related autoantigen 1	185					calcium ion import|defense response|elevation of mitochondrial calcium ion concentration	integral to membrane|mitochondrial inner membrane	calcium ion binding|protein binding			ovary(1)	1																		---	---	---	---
PLAU	5328	broad.mit.edu	37	10	75674570	75674570	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75674570C>T	uc001jwa.2	+	9	1012	c.866C>T	c.(865-867)GCG>GTG	p.A289V	C10orf55_uc001jvz.1_Intron|PLAU_uc010qkw.1_Missense_Mutation_p.A272V|PLAU_uc010qkx.1_Missense_Mutation_p.A203V|PLAU_uc001jwb.2_RNA|PLAU_uc001jwc.2_Missense_Mutation_p.A289V|PLAU_uc009xrq.1_Missense_Mutation_p.A253V	NM_002658	NP_002649	P00749	UROK_HUMAN	plasminogen activator, urokinase isoform 1	289	Peptidase S1.				blood coagulation|chemotaxis|fibrinolysis|proteolysis|regulation of cell adhesion mediated by integrin|regulation of receptor activity|regulation of smooth muscle cell migration|regulation of smooth muscle cell-matrix adhesion|signal transduction	cell surface|extracellular space|plasma membrane	serine-type endopeptidase activity			ovary(2)|kidney(1)	3	Prostate(51;0.0112)				Amiloride(DB00594)|Urokinase(DB00013)													---	---	---	---
MYST4	23522	broad.mit.edu	37	10	76788343	76788343	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76788343G>A	uc001jwn.1	+	18	4254	c.3761G>A	c.(3760-3762)CGC>CAC	p.R1254H	MYST4_uc001jwo.1_Missense_Mutation_p.R962H|MYST4_uc001jwp.1_Missense_Mutation_p.R1071H	NM_012330	NP_036462	Q8WYB5	MYST4_HUMAN	MYST histone acetyltransferase (monocytic	1254					histone H3 acetylation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	MOZ/MORF histone acetyltransferase complex|nucleosome	DNA binding|histone acetyltransferase activity|transcription factor binding|zinc ion binding			central_nervous_system(5)|ovary(4)|lung(3)|breast(2)|skin(1)|prostate(1)	16	all_cancers(46;0.0347)|all_epithelial(25;0.00236)|Prostate(51;0.0112)|Ovarian(15;0.0964)							T	CREBBP	AML								---	---	---	---
KCNMA1	3778	broad.mit.edu	37	10	78844487	78844487	+	Intron	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:78844487C>T	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)													---	---	---	---
SFTPD	6441	broad.mit.edu	37	10	81701740	81701740	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81701740G>A	uc001kbh.2	-	5	563	c.520C>T	c.(520-522)CGT>TGT	p.R174C	MBL1P_uc001kbf.2_Intron	NM_003019	NP_003010	P35247	SFTPD_HUMAN	pulmonary surfactant-associated protein D	174	Collagen-like.				cell junction assembly|innate immune response|lung alveolus development|macrophage chemotaxis|negative regulation of interleukin-2 biosynthetic process|negative regulation of T cell proliferation|positive regulation of phagocytosis|reactive oxygen species metabolic process|receptor-mediated endocytosis|respiratory gaseous exchange|surfactant homeostasis	collagen|endocytic vesicle|extracellular space|lysosome	bacterial cell surface binding|protein binding|sugar binding			skin(1)	1	Breast(12;0.000615)|Prostate(51;0.0095)|all_epithelial(25;0.027)		Epithelial(14;0.0244)|all cancers(16;0.0558)|Colorectal(32;0.109)															---	---	---	---
NRG3	10718	broad.mit.edu	37	10	84711311	84711311	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:84711311T>C	uc001kco.2	+	5	1168	c.1141T>C	c.(1141-1143)TTC>CTC	p.F381L	NRG3_uc010qlz.1_Missense_Mutation_p.F380L|NRG3_uc001kcp.2_Missense_Mutation_p.F160L|NRG3_uc001kcq.2_Missense_Mutation_p.F31L|NRG3_uc001kcr.2_Missense_Mutation_p.F31L	NM_001010848	NP_001010848	P56975	NRG3_HUMAN	neuregulin 3 isoform 1	381	Helical; Note=Internal signal sequence; (Potential).				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)														---	---	---	---
RGR	5995	broad.mit.edu	37	10	86014126	86014126	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:86014126C>T	uc001kdc.1	+	5	595	c.557C>T	c.(556-558)GCC>GTC	p.A186V	RGR_uc001kdd.1_Missense_Mutation_p.A190V|RGR_uc001kde.1_Missense_Mutation_p.A186V	NM_001012720	NP_001012738	P47804	RGR_HUMAN	retinal G-protein coupled receptor isoform 2	186	Helical; Name=5; (Potential).				phototransduction|protein-chromophore linkage|visual perception	integral to plasma membrane	G-protein coupled receptor activity|photoreceptor activity|protein binding			ovary(1)	1																		---	---	---	---
GRID1	2894	broad.mit.edu	37	10	87407104	87407104	+	Missense_Mutation	SNP	C	T	T	rs76097378	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:87407104C>T	uc001kdl.1	-	13	2149	c.2048G>A	c.(2047-2049)CGG>CAG	p.R683Q	GRID1_uc009xsu.1_RNA|GRID1_uc010qmf.1_Missense_Mutation_p.R254Q|uc001kdm.1_RNA	NM_017551	NP_060021	Q9ULK0	GRID1_HUMAN	glutamate receptor, ionotropic, delta 1	683	Extracellular (Potential).					cell junction|integral to membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(5)|upper_aerodigestive_tract(2)|large_intestine(2)|central_nervous_system(1)	10					L-Glutamic Acid(DB00142)										Multiple Myeloma(13;0.14)			---	---	---	---
PTEN	5728	broad.mit.edu	37	10	89653868	89653868	+	Splice_Site	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:89653868T>C	uc001kfb.2	+	3	1195	c.164_splice	c.e3+2	p.R55_splice		NM_000314	NP_000305			phosphatase and tensin homolog						activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway	cytosol|internal side of plasma membrane|PML body	anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity	p.Y27fs*1(2)|p.?(2)|p.V54fs*29(1)		endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1)	2334		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)			31	D|Mis|N|F|S		glioma| prostate|endometrial	harmartoma|glioma| prostate|endometrial			Proteus_syndrome|Cowden_syndrome|Juvenile_Polyposis|Hereditary_Mixed_Polyposis_Syndrome_type_1|Bannayan-Riley-Ruvalcaba_syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)			---	---	---	---
FAS	355	broad.mit.edu	37	10	90774042	90774042	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90774042G>A	uc001kfr.2	+	9	1189	c.843G>A	c.(841-843)TGG>TGA	p.W281*	FAS_uc010qna.1_RNA|FAS_uc001kfs.2_3'UTR|FAS_uc001kft.2_Nonsense_Mutation_p.W260*|FAS_uc010qnb.1_RNA|FAS_uc010qnc.1_RNA|FAS_uc001kfw.2_3'UTR|FAS_uc010qnd.1_RNA|FAS_uc010qne.1_RNA|FAS_uc009xtp.2_RNA	NM_000043	NP_000034	P25445	TNR6_HUMAN	tumor necrosis factor receptor superfamily,	281	Death.|Interaction with HIPK3 (By similarity).|Cytoplasmic (Potential).				activation of caspase activity|activation of pro-apoptotic gene products|anti-apoptosis|cellular response to mechanical stimulus|positive regulation of necrotic cell death	cytosol|extracellular region|integral to membrane|soluble fraction	identical protein binding|kinase binding			upper_aerodigestive_tract(1)|breast(1)	2		Colorectal(252;0.0161)		Colorectal(12;0.000136)|COAD - Colon adenocarcinoma(12;0.000193)										Autoimmune_Lymphoproliferative_syndrome_type_I				---	---	---	---
EXOC6	54536	broad.mit.edu	37	10	94700473	94700473	+	Intron	SNP	T	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94700473T>G	uc001kig.2	+						EXOC6_uc010qnr.1_Intron|EXOC6_uc001kie.2_Intron|EXOC6_uc009xub.2_Intron|EXOC6_uc009xuc.2_Intron|EXOC6_uc001kih.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)																---	---	---	---
MYOF	26509	broad.mit.edu	37	10	95169361	95169361	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95169361C>T	uc001kin.2	-	6	692	c.569G>A	c.(568-570)CGG>CAG	p.R190Q	MYOF_uc001kio.2_Missense_Mutation_p.R190Q|MYOF_uc001kip.3_Missense_Mutation_p.R190Q|MYOF_uc009xuf.2_Missense_Mutation_p.R172Q	NM_013451	NP_038479	Q9NZM1	MYOF_HUMAN	myoferlin isoform a	190	C2 2.|Cytoplasmic (Potential).|Necessary for interaction with EHD2.				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																		---	---	---	---
SORBS1	10580	broad.mit.edu	37	10	97194450	97194450	+	Missense_Mutation	SNP	C	T	T	rs139115529		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97194450C>T	uc001kkp.2	-	3	146	c.101G>A	c.(100-102)CGC>CAC	p.R34H	SORBS1_uc001kkn.2_Intron|SORBS1_uc001kkm.2_Missense_Mutation_p.R22H|SORBS1_uc001kko.2_Missense_Mutation_p.R34H|SORBS1_uc001kkq.2_Missense_Mutation_p.R34H|SORBS1_uc001kkr.2_Intron|SORBS1_uc001kks.2_Intron|SORBS1_uc001kkt.2_Intron|SORBS1_uc001kku.2_Missense_Mutation_p.R34H|SORBS1_uc001kkv.2_Intron|SORBS1_uc001kkw.2_Missense_Mutation_p.R34H|SORBS1_uc010qoe.1_Intron|SORBS1_uc010qof.1_Intron|SORBS1_uc001kkx.1_Intron	NM_001034954	NP_001030126	Q9BX66	SRBS1_HUMAN	sorbin and SH3 domain containing 1 isoform 3	34					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)														---	---	---	---
TLL2	7093	broad.mit.edu	37	10	98146799	98146799	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98146799C>T	uc001kml.1	-	14	1989	c.1763G>A	c.(1762-1764)TGC>TAC	p.C588Y		NM_012465	NP_036597	Q9Y6L7	TLL2_HUMAN	tolloid-like 2 precursor	588	EGF-like 1; calcium-binding (Potential).			EVDECSWPDHGGCEHRCV -> GKKKKKKKKKKKKKKKKK (in Ref. 5; AAH13871).	cell differentiation|multicellular organismal development|proteolysis	extracellular region	calcium ion binding|metalloendopeptidase activity|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3		Colorectal(252;0.0846)		Epithelial(162;1.51e-07)|all cancers(201;7.59e-06)														---	---	---	---
SLIT1	6585	broad.mit.edu	37	10	98760984	98760984	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98760984C>T	uc001kmw.2	-	37	4742	c.4490G>A	c.(4489-4491)TGC>TAC	p.C1497Y		NM_003061	NP_003052	O75093	SLIT1_HUMAN	slit homolog 1 precursor	1497	CTCK.				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)														---	---	---	---
CRTAC1	55118	broad.mit.edu	37	10	99655720	99655720	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99655720G>A	uc001kou.1	-	10	1595	c.1239C>T	c.(1237-1239)GAC>GAT	p.D413D	CRTAC1_uc001kov.2_Silent_p.D402D|CRTAC1_uc001kot.1_Silent_p.D203D	NM_018058	NP_060528	Q9NQ79	CRAC1_HUMAN	cartilage acidic protein 1 precursor	413	FG-GAP 4; 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)														---	---	---	---
PKD2L1	9033	broad.mit.edu	37	10	102049903	102049903	+	Intron	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102049903G>T	uc001kqx.1	-						PKD2L1_uc009xwm.1_Intron	NM_016112	NP_057196			polycystic kidney disease 2-like 1						signal transduction	integral to membrane	calcium activated cation channel activity|calcium ion binding|cytoskeletal protein binding			ovary(4)	4		Colorectal(252;0.117)		Epithelial(162;6.15e-10)|all cancers(201;5.14e-08)														---	---	---	---
TLX1	3195	broad.mit.edu	37	10	102896641	102896641	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102896641G>A	uc001ksw.2	+	3	1202	c.964G>A	c.(964-966)GTC>ATC	p.V322I		NM_005521	NP_005512	P31314	TLX1_HUMAN	T-cell leukemia homeobox 1	322						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			breast(1)	1				Epithelial(162;6.35e-09)|all cancers(201;3.21e-07)				T	TRB@|TRD@	T-ALL								---	---	---	---
MGEA5	10724	broad.mit.edu	37	10	103563735	103563735	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103563735C>T	uc001ktv.2	-	7	1236	c.793G>A	c.(793-795)GAA>AAA	p.E265K	MGEA5_uc010qqe.1_Missense_Mutation_p.E265K|MGEA5_uc009xws.2_Missense_Mutation_p.E265K|MGEA5_uc001ktw.2_Missense_Mutation_p.E265K|MGEA5_uc009xwt.2_Intron	NM_012215	NP_036347	O60502	NCOAT_HUMAN	meningioma expressed antigen 5 (hyaluronidase)	265					glycoprotein catabolic process	cytoplasm|nucleus	histone acetyltransferase activity|hyalurononglucosaminidase activity			ovary(2)|skin(1)	3		Colorectal(252;0.207)		Epithelial(162;4.67e-09)|all cancers(201;2.54e-07)														---	---	---	---
PPRC1	23082	broad.mit.edu	37	10	103898946	103898946	+	Silent	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103898946C>A	uc001kum.2	+	5	720	c.681C>A	c.(679-681)CCC>CCA	p.P227P	PPRC1_uc001kun.2_Silent_p.P107P|PPRC1_uc010qqj.1_Silent_p.P227P|PPRC1_uc009xxa.2_RNA	NM_015062	NP_055877	Q5VV67	PPRC1_HUMAN	peroxisome proliferator-activated receptor	227					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleotide binding|RNA binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Colorectal(252;0.122)		Epithelial(162;4.97e-08)|all cancers(201;8.99e-07)														---	---	---	---
NT5C2	22978	broad.mit.edu	37	10	104850727	104850727	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104850727C>T	uc001kwo.2	-	17	1424	c.1238G>A	c.(1237-1239)CGT>CAT	p.R413H	NT5C2_uc010qqp.1_Missense_Mutation_p.R384H|NT5C2_uc001kwq.2_Missense_Mutation_p.R413H|NT5C2_uc001kwp.2_Missense_Mutation_p.R260H	NM_012229	NP_036361	P49902	5NTC_HUMAN	5'-nucleotidase, cytosolic II	413					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)													---	---	---	---
INA	9118	broad.mit.edu	37	10	105046873	105046873	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105046873C>T	uc001kws.2	+	2	1196	c.1147C>T	c.(1147-1149)CTC>TTC	p.L383F		NM_032727	NP_116116	Q16352	AINX_HUMAN	internexin neuronal intermediate filament	383	Coil 2.|Rod.				cell differentiation|nervous system development	neurofilament	structural constituent of cytoskeleton			ovary(1)|breast(1)	2				Epithelial(162;3.45e-09)|all cancers(201;9.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.198)														---	---	---	---
SORCS1	114815	broad.mit.edu	37	10	108431115	108431115	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:108431115C>T	uc001kym.2	-	16	2077	c.2069G>A	c.(2068-2070)TGT>TAT	p.C690Y	SORCS1_uc001kyl.2_Missense_Mutation_p.C690Y|SORCS1_uc009xxs.2_Missense_Mutation_p.C690Y|SORCS1_uc001kyn.1_Missense_Mutation_p.C690Y|SORCS1_uc001kyo.2_Missense_Mutation_p.C690Y	NM_052918	NP_443150	Q8WY21	SORC1_HUMAN	SORCS receptor 1 isoform a	690	Lumenal (Potential).					integral to membrane	neuropeptide receptor activity|protein binding			breast(1)|central_nervous_system(1)	2		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)														---	---	---	---
SORCS1	114815	broad.mit.edu	37	10	108439027	108439027	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:108439027T>G	uc001kym.2	-	12	1735	c.1727A>C	c.(1726-1728)AAC>ACC	p.N576T	SORCS1_uc001kyl.2_Missense_Mutation_p.N576T|SORCS1_uc009xxs.2_Missense_Mutation_p.N576T|SORCS1_uc001kyn.1_Missense_Mutation_p.N576T|SORCS1_uc001kyo.2_Missense_Mutation_p.N576T	NM_052918	NP_443150	Q8WY21	SORC1_HUMAN	SORCS receptor 1 isoform a	576	Lumenal (Potential).|BNR 4.					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)														---	---	---	---
HABP2	3026	broad.mit.edu	37	10	115338458	115338458	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115338458C>T	uc001lai.3	+	7	744	c.641C>T	c.(640-642)GCG>GTG	p.A214V	HABP2_uc010qrz.1_RNA|HABP2_uc010qry.1_3'UTR	NM_004132	NP_004123	Q14520	HABP2_HUMAN	hyaluronan binding protein 2 preproprotein	214	Kringle.				cell adhesion|proteolysis	extracellular space	glycosaminoglycan binding|serine-type endopeptidase activity			ovary(2)|skin(1)	3		Colorectal(252;0.0233)|Breast(234;0.0672)		Epithelial(162;0.00319)|all cancers(201;0.0112)														---	---	---	---
VWA2	340706	broad.mit.edu	37	10	116021030	116021030	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116021030C>T	uc001lbl.1	+	5	668	c.347C>T	c.(346-348)GCA>GTA	p.A116V	VWA2_uc001lbk.1_Missense_Mutation_p.A116V|VWA2_uc009xyf.1_5'UTR	NM_198496	NP_940898	Q5GFL6	VWA2_HUMAN	von Willebrand factor A domain containing 2	116	VWFA 1.					extracellular region				ovary(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	5				Epithelial(162;0.036)|all cancers(201;0.0793)														---	---	---	---
INPP5F	22876	broad.mit.edu	37	10	121583376	121583376	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121583376G>A	uc001leo.2	+	19	2377	c.2211G>A	c.(2209-2211)ATG>ATA	p.M737I	INPP5F_uc001lep.2_Missense_Mutation_p.M127I	NM_014937	NP_055752	Q9Y2H2	SAC2_HUMAN	inositol polyphosphate-5-phosphatase F	737							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)														---	---	---	---
DMBT1	1755	broad.mit.edu	37	10	124380630	124380630	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124380630G>A	uc001lgk.1	+	41	5061	c.4955G>A	c.(4954-4956)CGA>CAA	p.R1652Q	DMBT1_uc001lgl.1_Missense_Mutation_p.R1642Q|DMBT1_uc001lgm.1_Missense_Mutation_p.R1024Q|DMBT1_uc009xzz.1_Missense_Mutation_p.R1652Q|DMBT1_uc010qtx.1_Intron|DMBT1_uc009yab.1_Missense_Mutation_p.R355Q|DMBT1_uc009yac.1_5'UTR	NM_007329	NP_015568	Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1 isoform b	1652	SRCR 13.				epithelial cell differentiation|induction of bacterial agglutination|innate immune response|interspecies interaction between organisms|protein transport|response to virus	extrinsic to membrane|phagocytic vesicle membrane|zymogen granule membrane	calcium-dependent protein binding|Gram-negative bacterial cell surface binding|Gram-positive bacterial cell surface binding|pattern recognition receptor activity|scavenger receptor activity|zymogen binding			central_nervous_system(7)	7		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)																---	---	---	---
CHST15	51363	broad.mit.edu	37	10	125801922	125801922	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:125801922C>T	uc001lhl.2	-	3	1441	c.928G>A	c.(928-930)GTG>ATG	p.V310M	CHST15_uc001lhm.2_Missense_Mutation_p.V310M|CHST15_uc001lhn.2_Missense_Mutation_p.V310M|CHST15_uc010que.1_Missense_Mutation_p.V310M|CHST15_uc001lho.2_Missense_Mutation_p.V310M	NM_015892	NP_056976	Q7LFX5	CHSTF_HUMAN	B cell RAG associated protein	310	Lumenal (Potential).				hexose biosynthetic process	Golgi membrane|integral to membrane	3'-phosphoadenosine 5'-phosphosulfate binding|N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase activity			ovary(1)	1																		---	---	---	---
UROS	7390	broad.mit.edu	37	10	127477546	127477546	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127477546C>T	uc001liw.3	-	9	822	c.689G>A	c.(688-690)CGC>CAC	p.R230H	UROS_uc001liv.3_Missense_Mutation_p.R163H|UROS_uc010quh.1_RNA|UROS_uc001lix.3_Missense_Mutation_p.R230H|UROS_uc001liy.3_RNA	NM_000375	NP_000366	P10746	HEM4_HUMAN	uroporphyrinogen III synthase	230					heme biosynthetic process|uroporphyrinogen III biosynthetic process	cytosol|mitochondrion	uroporphyrinogen-III synthase activity				0		all_lung(145;0.00756)|Lung NSC(174;0.0116)|Colorectal(57;0.0855)|all_neural(114;0.0937)|Breast(234;0.203)																---	---	---	---
MGMT	4255	broad.mit.edu	37	10	131506287	131506287	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:131506287A>G	uc001lkh.2	+	3	373	c.347A>G	c.(346-348)CAC>CGC	p.H116R		NM_002412	NP_002403	P16455	MGMT_HUMAN	O-6-methylguanine-DNA methyltransferase	85										ovary(1)|breast(1)	2		all_cancers(35;9.44e-09)|all_epithelial(44;6.98e-08)|Lung NSC(174;0.0157)|all_lung(145;0.0201)|all_neural(114;0.0732)|Colorectal(57;0.0792)|Breast(234;0.167)		OV - Ovarian serous cystadenocarcinoma(35;0.00291)									Direct_reversal_of_damage					---	---	---	---
EBF3	253738	broad.mit.edu	37	10	131639112	131639112	+	Silent	SNP	G	A	A	rs147171591		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:131639112G>A	uc001lki.1	-	14	1589	c.1530C>T	c.(1528-1530)TAC>TAT	p.Y510Y		NM_001005463	NP_001005463	Q9H4W6	COE3_HUMAN	early B-cell factor 3	519	Pro/Ser/Thr-rich.				multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|metal ion binding|protein binding			central_nervous_system(1)|pancreas(1)	2		all_cancers(35;1.8e-08)|all_epithelial(44;8.26e-08)|Lung NSC(174;0.0091)|all_lung(145;0.0123)|Breast(234;0.039)|all_neural(114;0.0722)|Colorectal(57;0.0764)		OV - Ovarian serous cystadenocarcinoma(35;0.00513)														---	---	---	---
JAKMIP3	282973	broad.mit.edu	37	10	133950657	133950657	+	Intron	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133950657A>G	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)														---	---	---	---
NLRP6	171389	broad.mit.edu	37	11	281195	281195	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:281195C>T	uc010qvs.1	+	4	1461	c.1461C>T	c.(1459-1461)GGC>GGT	p.G487G	NLRP6_uc010qvt.1_Silent_p.G487G	NM_138329	NP_612202	P59044	NALP6_HUMAN	NLR family, pyrin domain containing 6	487	NACHT.|LRR 1.					cytoplasm	ATP binding			upper_aerodigestive_tract(1)|skin(1)	2		all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;4.28e-28)|Epithelial(43;2.47e-27)|OV - Ovarian serous cystadenocarcinoma(40;4.66e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.0485)|LUSC - Lung squamous cell carcinoma(625;0.122)														---	---	---	---
ANO9	338440	broad.mit.edu	37	11	418746	418746	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:418746G>A	uc001lpi.2	-	22	2189	c.2104C>T	c.(2104-2106)CGC>TGC	p.R702C	SIGIRR_uc001lpf.2_5'Flank|SIGIRR_uc001lpe.1_5'Flank|ANO9_uc001lph.2_Missense_Mutation_p.R395C|ANO9_uc010qvv.1_Missense_Mutation_p.R558C	NM_001012302	NP_001012302	A1A5B4	ANO9_HUMAN	tumor protein p53 inducible protein 5	702	Extracellular (Potential).					chloride channel complex	chloride channel activity			central_nervous_system(2)|ovary(1)|skin(1)	4																		---	---	---	---
PTDSS2	81490	broad.mit.edu	37	11	487453	487453	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:487453C>A	uc001lpj.2	+	6	780	c.604C>A	c.(604-606)CTT>ATT	p.L202I		NM_030783	NP_110410	Q9BVG9	PTSS2_HUMAN	phosphatidylserine synthase 2	202	Extracellular (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)													---	---	---	---
TALDO1	6888	broad.mit.edu	37	11	763457	763457	+	Missense_Mutation	SNP	G	A	A	rs151052416		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:763457G>A	uc001lqz.2	+	5	625	c.575G>A	c.(574-576)CGC>CAC	p.R192H	TALDO1_uc001lra.2_Missense_Mutation_p.R192H	NM_006755	NP_006746	P37837	TALDO_HUMAN	transaldolase 1	192					energy reserve metabolic process|xylulose biosynthetic process	cytosol	protein binding|sedoheptulose-7-phosphate:D-glyceraldehyde-3-phosphate glyceronetransferase activity				0		all_cancers(49;1.13e-08)|all_epithelial(84;2.95e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.159)|all_lung(207;0.198)		all cancers(45;4.66e-26)|Epithelial(43;2.97e-25)|OV - Ovarian serous cystadenocarcinoma(40;1.48e-19)|BRCA - Breast invasive adenocarcinoma(625;4.41e-05)|Lung(200;0.0595)|LUSC - Lung squamous cell carcinoma(625;0.0712)														---	---	---	---
LRDD	55367	broad.mit.edu	37	11	799897	799897	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:799897G>A	uc001lro.1	-	15	2534	c.2392C>T	c.(2392-2394)CGT>TGT	p.R798C	SLC25A22_uc009yci.2_5'Flank|SLC25A22_uc001lrj.2_5'Flank|LRDD_uc009yck.1_RNA|LRDD_uc001lrk.1_Missense_Mutation_p.R781C|LRDD_uc001lrl.1_Missense_Mutation_p.R641C|LRDD_uc001lrm.1_Missense_Mutation_p.R485C|LRDD_uc001lrn.1_Missense_Mutation_p.R641C|LRDD_uc001lrp.1_3'UTR	NM_145886	NP_665893	Q9HB75	PIDD_HUMAN	leucine rich repeat and death domain containing	798	Death.				apoptosis|signal transduction	cytoplasm|nucleus	death receptor binding				0		all_cancers(49;1.13e-08)|all_epithelial(84;2.95e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.159)|all_lung(207;0.198)		all cancers(45;1.45e-25)|Epithelial(43;1.17e-24)|OV - Ovarian serous cystadenocarcinoma(40;6.76e-19)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)														---	---	---	---
MUC6	4588	broad.mit.edu	37	11	1015764	1015764	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1015764G>T	uc001lsw.2	-	31	7088	c.7037C>A	c.(7036-7038)CCC>CAC	p.P2346H		NM_005961	NP_005952	Q6W4X9	MUC6_HUMAN	mucin 6, gastric	2346					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	1263879	1263879	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1263879G>A	uc009ycr.1	+	47	7974	c.7848G>A	c.(7846-7848)ACG>ACA	p.T2616T	MUC5B_uc001ltb.2_Silent_p.T1926T	NM_017511	NP_059981	Q9HC84	MUC5B_HUMAN	SubName: Full=Mucin 5AC, oligomeric mucus/gel-forming;	1923	7 X Cys-rich subdomain repeats.|11 X approximate tandem repeats, Ser/Thr- rich.|Thr-rich.				cell adhesion	extracellular region	extracellular matrix structural constituent|protein binding				0		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)														---	---	---	---
BRSK2	9024	broad.mit.edu	37	11	1467040	1467040	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1467040C>T	uc001lti.2	+	12	1515	c.1129C>T	c.(1129-1131)CGG>TGG	p.R377W	BRSK2_uc009ycv.1_Missense_Mutation_p.R377W|BRSK2_uc001lth.1_Missense_Mutation_p.R377W|BRSK2_uc001ltj.2_Missense_Mutation_p.R377W|BRSK2_uc001ltk.2_RNA|BRSK2_uc001ltl.2_Missense_Mutation_p.R377W|BRSK2_uc001ltm.2_Missense_Mutation_p.R423W|BRSK2_uc001ltn.2_RNA|BRSK2_uc010qwx.1_RNA	NM_003957	NP_003948	Q8IWQ3	BRSK2_HUMAN	BR serine/threonine kinase 2	377					establishment of cell polarity|neuron differentiation		ATP binding|magnesium ion binding|protein serine/threonine kinase activity				0		all_epithelial(84;4.17e-05)|Breast(177;0.000307)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00144)|Lung(200;0.0713)|LUSC - Lung squamous cell carcinoma(625;0.0842)														---	---	---	---
NAP1L4	4676	broad.mit.edu	37	11	2985125	2985125	+	Intron	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2985125C>A	uc001lxc.2	-						NAP1L4_uc010qxm.1_Intron|NAP1L4_uc010qxn.1_Intron|SNORA54_uc001lxd.1_5'Flank	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)														---	---	---	---
OSBPL5	114879	broad.mit.edu	37	11	3111807	3111807	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3111807C>T	uc001lxk.2	-	20	2537	c.2379G>A	c.(2377-2379)CAG>CAA	p.Q793Q	OSBPL5_uc010qxq.1_Silent_p.Q704Q|OSBPL5_uc009ydw.2_Silent_p.Q725Q|OSBPL5_uc001lxl.2_Silent_p.Q725Q|OSBPL5_uc001lxj.2_Silent_p.Q247Q	NM_020896	NP_065947	Q9H0X9	OSBL5_HUMAN	oxysterol-binding protein-like protein 5 isoform	793					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)														---	---	---	---
ART5	116969	broad.mit.edu	37	11	3661166	3661166	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3661166G>A	uc001lyb.1	-	2	886	c.493C>T	c.(493-495)CTT>TTT	p.L165F	ART5_uc001lyc.1_Missense_Mutation_p.L165F|ART5_uc001lyd.2_Missense_Mutation_p.L165F|ART5_uc009yea.2_Missense_Mutation_p.L165F	NM_053017	NP_443750	Q96L15	NAR5_HUMAN	ADP-ribosyltransferase 5 precursor	165						extracellular region	NAD(P)+-protein-arginine ADP-ribosyltransferase activity			ovary(1)	1		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0336)|LUSC - Lung squamous cell carcinoma(625;0.19)														---	---	---	---
CHRNA10	57053	broad.mit.edu	37	11	3687420	3687420	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3687420G>T	uc001lyf.2	-	5	1342	c.1270C>A	c.(1270-1272)CGT>AGT	p.R424S	CHRNA10_uc010qxt.1_Missense_Mutation_p.R218S|CHRNA10_uc010qxu.1_Missense_Mutation_p.R218S	NM_020402	NP_065135	Q9GZZ6	ACH10_HUMAN	cholinergic receptor, nicotinic, alpha 10	424	Cytoplasmic (Potential).				elevation of cytosolic calcium ion concentration|regulation of cell proliferation|synaptic transmission, cholinergic	cell junction|postsynaptic membrane	calcium channel activity|receptor activity|receptor binding			ovary(1)	1		Medulloblastoma(188;0.0075)|Breast(177;0.0164)|all_neural(188;0.0577)		BRCA - Breast invasive adenocarcinoma(625;0.0344)|LUSC - Lung squamous cell carcinoma(625;0.192)	Chloroprocaine(DB01161)|Methadone(DB00333)|Nicotine(DB00184)|Pentolinium(DB01090)|Procaine(DB00721)|Trimethaphan(DB01116)													---	---	---	---
STIM1	6786	broad.mit.edu	37	11	4103494	4103494	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4103494G>A	uc001lyv.2	+	8	1618	c.1050G>A	c.(1048-1050)TGG>TGA	p.W350*	STIM1_uc009yef.2_Nonsense_Mutation_p.W350*|STIM1_uc009yeg.2_Nonsense_Mutation_p.W177*	NM_003156	NP_003147	Q13586	STIM1_HUMAN	stromal interaction molecule 1 precursor	350	Cytoplasmic (Potential).|Potential.				activation of store-operated calcium channel activity|calcium ion transport|detection of calcium ion|platelet activation	integral to endoplasmic reticulum membrane|integral to plasma membrane|microtubule	calcium ion binding|microtubule plus-end binding			pancreas(1)	1		Breast(177;0.00159)|Medulloblastoma(188;0.00258)|all_neural(188;0.0233)		BRCA - Breast invasive adenocarcinoma(625;0.114)|LUSC - Lung squamous cell carcinoma(625;0.141)														---	---	---	---
STIM1	6786	broad.mit.edu	37	11	4112533	4112533	+	Silent	SNP	G	A	A	rs148209416		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4112533G>A	uc001lyv.2	+	12	2131	c.1563G>A	c.(1561-1563)TCG>TCA	p.S521S	STIM1_uc009yef.2_Missense_Mutation_p.G534R|STIM1_uc009yeg.2_Silent_p.S348S	NM_003156	NP_003147	Q13586	STIM1_HUMAN	stromal interaction molecule 1 precursor	521	Cytoplasmic (Potential).				activation of store-operated calcium channel activity|calcium ion transport|detection of calcium ion|platelet activation	integral to endoplasmic reticulum membrane|integral to plasma membrane|microtubule	calcium ion binding|microtubule plus-end binding			pancreas(1)	1		Breast(177;0.00159)|Medulloblastoma(188;0.00258)|all_neural(188;0.0233)		BRCA - Breast invasive adenocarcinoma(625;0.114)|LUSC - Lung squamous cell carcinoma(625;0.141)														---	---	---	---
TRIM68	55128	broad.mit.edu	37	11	4621714	4621714	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4621714G>A	uc001lzf.1	-	7	1488	c.1250C>T	c.(1249-1251)CCG>CTG	p.P417L	TRIM68_uc001lzg.1_Missense_Mutation_p.P194L|TRIM68_uc010qyj.1_RNA	NM_018073	NP_060543	Q6AZZ1	TRI68_HUMAN	ring finger protein 137	417	B30.2/SPRY.				protein autoubiquitination|regulation of androgen receptor signaling pathway	Golgi apparatus|nucleolus|perinuclear region of cytoplasm	androgen receptor binding|histone acetyltransferase binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1		Medulloblastoma(188;0.0025)|Breast(177;0.0101)|all_neural(188;0.0227)		Epithelial(150;9.49e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0288)|LUSC - Lung squamous cell carcinoma(625;0.192)														---	---	---	---
OR51E1	143503	broad.mit.edu	37	11	4674693	4674693	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4674693A>G	uc001lzi.3	+	2	1081	c.937A>G	c.(937-939)ACA>GCA	p.T313A		NM_152430	NP_689643	Q8TCB6	O51E1_HUMAN	olfactory receptor, family 51, subfamily E,	312	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			large_intestine(3)|pancreas(1)	4		Medulloblastoma(188;0.0025)|Breast(177;0.0101)|all_neural(188;0.0227)		Epithelial(150;7.37e-14)|GBM - Glioblastoma multiforme(2;2.85e-05)|BRCA - Breast invasive adenocarcinoma(625;0.00222)|LUSC - Lung squamous cell carcinoma(625;0.19)														---	---	---	---
TRIM5	85363	broad.mit.edu	37	11	5699619	5699619	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5699619G>A	uc001mbm.1	-	4	816	c.559C>T	c.(559-561)CAA>TAA	p.Q187*	TRIM5_uc001mbq.1_Nonsense_Mutation_p.Q187*|TRIM5_uc001mbl.1_RNA|TRIM5_uc001mbn.2_Nonsense_Mutation_p.Q187*|TRIM5_uc001mbo.2_Nonsense_Mutation_p.Q187*|TRIM5_uc001mbp.2_Nonsense_Mutation_p.Q187*	NM_033034	NP_149023	Q9C035	TRIM5_HUMAN	tripartite motif protein TRIM5 isoform alpha	187	Potential.				interspecies interaction between organisms|protein trimerization|response to virus	cytoplasm|cytoplasmic mRNA processing body	ligase activity|protein binding|protein homodimerization activity|zinc ion binding			ovary(1)	1		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)|Lung NSC(207;0.138)|all_lung(207;0.221)		Epithelial(150;7.21e-09)|BRCA - Breast invasive adenocarcinoma(625;0.139)														---	---	---	---
CCKBR	887	broad.mit.edu	37	11	6291537	6291537	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6291537G>A	uc001mcp.2	+	3	816	c.623G>A	c.(622-624)CGC>CAC	p.R208H	CCKBR_uc001mcq.2_Missense_Mutation_p.R136H|CCKBR_uc001mcr.2_Missense_Mutation_p.R208H|CCKBR_uc001mcs.2_Missense_Mutation_p.R208H|CCKBR_uc001mct.1_5'Flank	NM_176875	NP_795344	P32239	GASR_HUMAN	cholecystokinin B receptor	208	Extracellular (Potential).				activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|cell proliferation|digestion|elevation of cytosolic calcium ion concentration|feeding behavior|positive regulation of cell proliferation|sensory perception		1-phosphatidylinositol-3-kinase regulator activity|gastrin receptor activity|phosphatidylinositol phospholipase C activity|type B gastrin/cholecystokinin receptor binding			lung(5)|ovary(2)|breast(1)	8		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;2.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.139)	Pentagastrin(DB00183)													---	---	---	---
CCKBR	887	broad.mit.edu	37	11	6292725	6292725	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6292725G>A	uc001mcp.2	+	5	1489	c.1296G>A	c.(1294-1296)TCG>TCA	p.S432S	CCKBR_uc001mcq.2_Silent_p.S360S|CCKBR_uc001mcr.2_Silent_p.S415S|CCKBR_uc001mcs.2_Silent_p.S501S	NM_176875	NP_795344	P32239	GASR_HUMAN	cholecystokinin B receptor	432	Cytoplasmic (Potential).				activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|cell proliferation|digestion|elevation of cytosolic calcium ion concentration|feeding behavior|positive regulation of cell proliferation|sensory perception		1-phosphatidylinositol-3-kinase regulator activity|gastrin receptor activity|phosphatidylinositol phospholipase C activity|type B gastrin/cholecystokinin receptor binding			lung(5)|ovary(2)|breast(1)	8		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;2.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.139)	Pentagastrin(DB00183)													---	---	---	---
APBB1	322	broad.mit.edu	37	11	6424925	6424925	+	Silent	SNP	G	T	T	rs139929849		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6424925G>T	uc001mdb.1	-	3	949	c.849C>A	c.(847-849)CCC>CCA	p.P283P	APBB1_uc001mcz.1_5'Flank|APBB1_uc001mdd.3_Silent_p.P63P|APBB1_uc001mda.2_Intron|APBB1_uc001mdc.1_Silent_p.P283P|APBB1_uc010rab.1_5'Flank|APBB1_uc010rac.1_5'Flank|APBB1_uc010rad.1_5'Flank|APBB1_uc010rae.1_Silent_p.P48P|APBB1_uc010raf.1_Silent_p.P24P|APBB1_uc009yfa.2_Silent_p.P24P|APBB1_uc009yey.2_Silent_p.P24P|APBB1_uc010rag.1_Silent_p.P24P|APBB1_uc009yfb.2_Silent_p.P24P|APBB1_uc001mde.2_Silent_p.P24P|APBB1_uc010rah.1_Silent_p.P24P	NM_001164	NP_001155	O00213	APBB1_HUMAN	amyloid beta A4 precursor protein-binding,	283	WW.				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)														---	---	---	---
DCHS1	8642	broad.mit.edu	37	11	6655115	6655115	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6655115C>T	uc001mem.1	-	4	2533	c.2123G>A	c.(2122-2124)CGT>CAT	p.R708H		NM_003737	NP_003728	Q96JQ0	PCD16_HUMAN	dachsous 1 precursor	708	Cadherin 7.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|large_intestine(1)|pancreas(1)	5		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)														---	---	---	---
DCHS1	8642	broad.mit.edu	37	11	6661810	6661810	+	Silent	SNP	C	T	T	rs143172918	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6661810C>T	uc001mem.1	-	2	1445	c.1035G>A	c.(1033-1035)TCG>TCA	p.S345S		NM_003737	NP_003728	Q96JQ0	PCD16_HUMAN	dachsous 1 precursor	345	Extracellular (Potential).|Cadherin 3.				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|large_intestine(1)|pancreas(1)	5		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)														---	---	---	---
RBMXL2	27288	broad.mit.edu	37	11	7111248	7111248	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7111248G>A	uc001mfc.2	+	1	1084	c.897G>A	c.(895-897)CCG>CCA	p.P299P		NM_014469	NP_055284	O75526	HNRGT_HUMAN	testes-specific heterogenous nuclear	299	Arg/Gly/Pro-rich.					nucleus|ribonucleoprotein complex	nucleotide binding|RNA binding				0				Epithelial(150;5.14e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)														---	---	---	---
CTR9	9646	broad.mit.edu	37	11	10793117	10793117	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10793117G>T	uc001mja.2	+	19	2547	c.2398G>T	c.(2398-2400)GGA>TGA	p.G800*		NM_014633	NP_055448	Q6PD62	CTR9_HUMAN	SH2 domain binding protein 1	800					histone H2B ubiquitination|histone monoubiquitination	Cdc73/Paf1 complex|nuclear speck				ovary(2)	2				all cancers(16;1.64e-07)|Epithelial(150;2.47e-07)|BRCA - Breast invasive adenocarcinoma(625;0.111)														---	---	---	---
PIK3C2A	5286	broad.mit.edu	37	11	17134211	17134211	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17134211C>T	uc001mmq.3	-	20	3390	c.3324G>A	c.(3322-3324)TCG>TCA	p.S1108S	PIK3C2A_uc009ygu.1_Translation_Start_Site|PIK3C2A_uc010rcw.1_Silent_p.S728S|PIK3C2A_uc001mmr.3_Intron	NM_002645	NP_002636	O00443	P3C2A_HUMAN	phosphoinositide-3-kinase, class 2 alpha	1108					cell communication|phosphatidylinositol biosynthetic process|phosphatidylinositol-mediated signaling	clathrin-coated vesicle|Golgi apparatus|nucleus|phosphatidylinositol 3-kinase complex|plasma membrane	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity			lung(4)|central_nervous_system(4)|stomach(1)|ovary(1)	10					Phosphatidylserine(DB00144)													---	---	---	---
ABCC8	6833	broad.mit.edu	37	11	17483300	17483300	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17483300G>T	uc001mnc.2	-	5	778	c.652C>A	c.(652-654)CTG>ATG	p.L218M	ABCC8_uc010rcy.1_Missense_Mutation_p.L218M	NM_000352	NP_000343	Q09428	ABCC8_HUMAN	ATP-binding cassette, sub-family C, member 8	218	Cytoplasmic (By similarity).				carbohydrate metabolic process|energy reserve metabolic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances|potassium ion transmembrane transporter activity|sulfonylurea receptor activity			ovary(1)	1				READ - Rectum adenocarcinoma(2;0.0325)|Colorectal(2;0.1)	Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)|Gliclazide(DB01120)|Mitiglinide(DB01252)|Nateglinide(DB00731)|Repaglinide(DB00912)													---	---	---	---
MYOD1	4654	broad.mit.edu	37	11	17741380	17741380	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17741380C>T	uc001mni.2	+	1	271	c.51C>T	c.(49-51)GAC>GAT	p.D17D		NM_002478	NP_002469	P15172	MYOD1_HUMAN	myogenic differentiation 1	17					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																		---	---	---	---
E2F8	79733	broad.mit.edu	37	11	19256468	19256468	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:19256468C>T	uc001mpm.2	-	5	1111	c.589G>A	c.(589-591)GGG>AGG	p.G197R	E2F8_uc009yhv.2_RNA|E2F8_uc001mpn.3_Missense_Mutation_p.G197R	NM_024680	NP_078956	A0AVK6	E2F8_HUMAN	E2F family member 8	197					cell cycle	transcription factor complex	DNA binding|sequence-specific DNA binding transcription factor activity			skin(1)	1																		---	---	---	---
SLC17A6	57084	broad.mit.edu	37	11	22363070	22363070	+	Intron	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:22363070G>A	uc001mqk.2	+							NM_020346	NP_065079			solute carrier family 17 (sodium-dependent						sodium ion transport	cell junction|integral to membrane|synaptic vesicle membrane|synaptosome	L-glutamate transmembrane transporter activity|symporter activity			ovary(3)|breast(1)	4																		---	---	---	---
KIF18A	81930	broad.mit.edu	37	11	28045380	28045380	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:28045380G>A	uc001msc.2	-	16	2704	c.2522C>T	c.(2521-2523)TCG>TTG	p.S841L		NM_031217	NP_112494	Q8NI77	KI18A_HUMAN	kinesin family member 18A	841					blood coagulation|microtubule depolymerization|microtubule-based movement|mitotic metaphase plate congression|mitotic prometaphase|protein transport	caveola|cytosol|kinetochore microtubule|microtubule organizing center|nucleus|ruffle	actin binding|ATP binding|microtubule plus-end binding|plus-end-directed microtubule motor activity|tubulin-dependent ATPase activity|ubiquitin binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	30926645	30926645	+	RNA	SNP	G	A	A	rs144668195		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:30926645G>A	uc001mss.1	-	9		c.1274C>T			uc009yjk.1_Missense_Mutation_p.R839W|uc009yjj.1_RNA					Homo sapiens mRNA for KIAA1493 protein, partial cds.																														---	---	---	---
CCDC73	493860	broad.mit.edu	37	11	32636061	32636061	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32636061G>A	uc001mtv.2	-	16	1847	c.1803C>T	c.(1801-1803)TTC>TTT	p.F601F		NM_001008391	NP_001008392	Q6ZRK6	CCD73_HUMAN	sarcoma antigen NY-SAR-79	601										ovary(1)|central_nervous_system(1)	2	Breast(20;0.112)																	---	---	---	---
C11orf41	25758	broad.mit.edu	37	11	33566554	33566554	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33566554A>G	uc001mup.3	+	2	2266	c.2142A>G	c.(2140-2142)CCA>CCG	p.P714P	C11orf41_uc001mun.1_Silent_p.P714P	NM_012194	NP_036326	Q6ZVL6	CK041_HUMAN	hypothetical protein LOC25758	708						integral to membrane				ovary(2)	2																		---	---	---	---
CAT	847	broad.mit.edu	37	11	34482794	34482794	+	Intron	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34482794G>A	uc001mvm.2	+						CAT_uc009ykc.1_Intron|CAT_uc001mvn.2_5'UTR	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)													---	---	---	---
PDHX	8050	broad.mit.edu	37	11	35006241	35006241	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35006241C>T	uc001mvt.2	+	9	1674	c.1148C>T	c.(1147-1149)GCT>GTT	p.A383V	PDHX_uc010rep.1_Missense_Mutation_p.A368V|PDHX_uc010req.1_Missense_Mutation_p.A156V	NM_003477	NP_003468	O00330	ODPX_HUMAN	pyruvate dehydrogenase complex, component X	383					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)															---	---	---	---
CD44	960	broad.mit.edu	37	11	35211585	35211585	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35211585G>A	uc001mvu.2	+	5	1074	c.640G>A	c.(640-642)GAC>AAC	p.D214N	CD44_uc001mvv.2_Missense_Mutation_p.D214N|CD44_uc001mvw.2_Missense_Mutation_p.D214N|CD44_uc001mvx.2_Missense_Mutation_p.D214N|CD44_uc001mvy.2_Intron|CD44_uc001mwc.3_Missense_Mutation_p.D214N|CD44_uc010rer.1_Missense_Mutation_p.D214N|CD44_uc009ykh.2_RNA|CD44_uc010res.1_5'UTR|CD44_uc010ret.1_RNA|CD44_uc010reu.1_5'UTR	NM_000610	NP_000601	P16070	CD44_HUMAN	CD44 antigen isoform 1 precursor	214	Extracellular (Potential).				cell-cell adhesion|cell-matrix adhesion|interferon-gamma-mediated signaling pathway|negative regulation of apoptosis|negative regulation of DNA damage response, signal transduction by p53 class mediator|positive regulation of ERK1 and ERK2 cascade|positive regulation of peptidyl-serine phosphorylation|positive regulation of peptidyl-tyrosine phosphorylation	cell surface|Golgi apparatus|integral to plasma membrane	collagen binding|hyaluronic acid binding|receptor activity			pancreas(1)	1	all_cancers(35;0.212)|all_lung(20;0.0874)|all_epithelial(35;0.112)	all_hematologic(20;0.107)	STAD - Stomach adenocarcinoma(6;0.00731)		Hyaluronidase(DB00070)													---	---	---	---
ACCSL	390110	broad.mit.edu	37	11	44073280	44073280	+	Intron	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44073280G>A	uc001mxw.1	+						ACCSL_uc009ykr.2_Intron	NM_001031854	NP_001027025			1-aminocyclopropane-1-carboxylate synthase								1-aminocyclopropane-1-carboxylate synthase activity|pyridoxal phosphate binding|transferase activity, transferring nitrogenous groups			ovary(5)	5																		---	---	---	---
ACCS	84680	broad.mit.edu	37	11	44105261	44105261	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44105261G>A	uc009yks.1	+	15	1569	c.1425G>A	c.(1423-1425)CAG>CAA	p.Q475Q	EXT2_uc010rfo.1_Intron|ACCS_uc001mxx.2_Silent_p.Q475Q	NM_001127219	NP_001120691	Q96QU6	1A1L1_HUMAN	1-aminocyclopropane-1-carboxylate synthase	475							1-aminocyclopropane-1-carboxylate synthase activity|protein homodimerization activity|pyridoxal phosphate binding|transferase activity, transferring nitrogenous groups			breast(2)|ovary(1)|lung(1)	4																		---	---	---	---
EXT2	2132	broad.mit.edu	37	11	44135753	44135753	+	Silent	SNP	C	T	T	rs111364140		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44135753C>T	uc001mxz.2	+	4	979	c.645C>T	c.(643-645)GGC>GGT	p.G215G	EXT2_uc010rfo.1_Silent_p.G243G|EXT2_uc001mxy.2_Silent_p.G228G|EXT2_uc009ykt.2_Silent_p.G215G|EXT2_uc001mya.2_Silent_p.G248G	NM_207122	NP_997005	Q93063	EXT2_HUMAN	exostosin 2 isoform 2	215	Lumenal (Potential).				glycosaminoglycan biosynthetic process|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|ossification|signal transduction	Golgi membrane|integral to membrane|intrinsic to endoplasmic reticulum membrane	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|heparan sulfate N-acetylglucosaminyltransferase activity|N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity|protein heterodimerization activity			lung(2)|breast(2)|skin(1)	5								Mis|N|F|S			exostoses|osteosarcoma			Hereditary_Multiple_Exostoses				---	---	---	---
ACP2	53	broad.mit.edu	37	11	47264454	47264454	+	Intron	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47264454G>T	uc001nei.2	-						ACP2_uc010rhe.1_Intron|ACP2_uc009ylj.2_Intron|ACP2_uc010rhf.1_Intron|ACP2_uc010rhg.1_Intron|ACP2_uc010rhh.1_Intron|ACP2_uc010rhi.1_Intron|ACP2_uc009ylk.2_Intron	NM_001610	NP_001601			acid phosphatase 2, lysosomal isoform 1							integral to membrane|lysosomal lumen|lysosomal membrane	acid phosphatase activity			ovary(1)	1																		---	---	---	---
MADD	8567	broad.mit.edu	37	11	47298400	47298400	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47298400G>A	uc001ner.1	+	5	1272	c.1081G>A	c.(1081-1083)GCA>ACA	p.A361T	MADD_uc001neq.2_Missense_Mutation_p.A361T|MADD_uc001nev.1_Missense_Mutation_p.A361T|MADD_uc001nes.1_Missense_Mutation_p.A361T|MADD_uc001net.1_Missense_Mutation_p.A361T|MADD_uc009yln.1_Missense_Mutation_p.A361T|MADD_uc001neu.1_Missense_Mutation_p.A361T|MADD_uc001nex.2_Missense_Mutation_p.A361T|MADD_uc001nez.2_Missense_Mutation_p.A361T|MADD_uc001new.2_Missense_Mutation_p.A361T	NM_003682	NP_003673	Q8WXG6	MADD_HUMAN	MAP-kinase activating death domain-containing	361	DENN.				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)														---	---	---	---
PTPRJ	5795	broad.mit.edu	37	11	48134376	48134376	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48134376G>A	uc001ngp.3	+	3	548	c.193G>A	c.(193-195)GCA>ACA	p.A65T	PTPRJ_uc001ngo.3_Missense_Mutation_p.A65T	NM_002843	NP_002834	Q12913	PTPRJ_HUMAN	protein tyrosine phosphatase, receptor type, J	65	Extracellular (Potential).				contact inhibition|negative regulation of cell growth|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of MAP kinase activity|negative regulation of platelet-derived growth factor receptor signaling pathway|negative regulation of protein kinase B signaling cascade|negative regulation of T cell receptor signaling pathway|negative regulation of vascular permeability|platelet-derived growth factor receptor signaling pathway|positive chemotaxis|positive regulation of focal adhesion assembly|positive regulation of protein kinase B signaling cascade|positive regulation of survival gene product expression	cell surface|cell-cell junction|immunological synapse|integral to plasma membrane|ruffle membrane	beta-catenin binding|delta-catenin binding|gamma-catenin binding|mitogen-activated protein kinase binding|platelet-derived growth factor receptor binding|protein tyrosine phosphatase activity			breast(3)|kidney(3)|ovary(1)|skin(1)	8																		---	---	---	---
OR4C15	81309	broad.mit.edu	37	11	55322311	55322311	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55322311G>A	uc010rig.1	+	1	529	c.529G>A	c.(529-531)GTG>ATG	p.V177M		NM_001001920	NP_001001920	Q8NGM1	OR4CF_HUMAN	olfactory receptor, family 4, subfamily C,	123	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2															HNSCC(20;0.049)			---	---	---	---
OR5L1	219437	broad.mit.edu	37	11	55579394	55579394	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55579394G>T	uc001nhw.1	+	1	452	c.452G>T	c.(451-453)TGT>TTT	p.C151F		NM_001004738	NP_001004738	Q8NGL2	OR5L1_HUMAN	olfactory receptor, family 5, subfamily L,	151	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(3)|ovary(2)	5		all_epithelial(135;0.208)																---	---	---	---
OR5D16	390144	broad.mit.edu	37	11	55606783	55606783	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55606783C>A	uc010rio.1	+	1	556	c.556C>A	c.(556-558)CTG>ATG	p.L186M		NM_001005496	NP_001005496	Q8NGK9	OR5DG_HUMAN	olfactory receptor, family 5, subfamily D,	186	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(4)|skin(1)	5		all_epithelial(135;0.208)																---	---	---	---
Unknown	0	broad.mit.edu	37	11	56143445	56143445	+	IGR	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56143445G>A								OR8J1 (14774 upstream) : OR5R1 (41291 downstream)																																			---	---	---	---
OR5M8	219484	broad.mit.edu	37	11	56258583	56258583	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56258583C>A	uc001nix.1	-	1	264	c.264G>T	c.(262-264)AAG>AAT	p.K88N		NM_001005282	NP_001005282	Q8NGP6	OR5M8_HUMAN	olfactory receptor, family 5, subfamily M,	88	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1	Esophageal squamous(21;0.00352)																	---	---	---	---
OR5M10	390167	broad.mit.edu	37	11	56345140	56345140	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56345140C>T	uc001niz.1	-	1	58	c.58G>A	c.(58-60)GAC>AAC	p.D20N		NM_001004741	NP_001004741	Q6IEU7	OR5MA_HUMAN	olfactory receptor, family 5, subfamily M,	20	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0																		---	---	---	---
OR9I1	219954	broad.mit.edu	37	11	57886596	57886596	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57886596A>G	uc001nml.1	-	1	321	c.321T>C	c.(319-321)TGT>TGC	p.C107C	OR9Q1_uc001nmj.2_Intron	NM_001005211	NP_001005211	Q8NGQ6	OR9I1_HUMAN	olfactory receptor, family 9, subfamily I,	107	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			pancreas(1)	1		Breast(21;0.0589)																---	---	---	---
CNTF	1270	broad.mit.edu	37	11	58391500	58391500	+	Intron	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58391500C>T	uc001nna.3	+						ZFP91-CNTF_uc010rkm.1_Intron	NM_000614	NP_000605			ciliary neurotrophic factor						ciliary neurotrophic factor-mediated signaling pathway|growth|negative regulation of neuron apoptosis|positive regulation of tyrosine phosphorylation of Stat3 protein		ciliary neurotrophic factor receptor binding|growth factor activity|interleukin-6 receptor binding			ovary(1)	1		Breast(21;0.00725)|all_epithelial(135;0.0101)|all_lung(304;0.24)																---	---	---	---
GLYATL2	219970	broad.mit.edu	37	11	58604809	58604809	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58604809T>C	uc001nnd.3	-	4	379	c.248A>G	c.(247-249)GAC>GGC	p.D83G	GLYATL2_uc009ymq.2_Missense_Mutation_p.D83G	NM_145016	NP_659453	Q8WU03	GLYL2_HUMAN	glycine-N-acyltransferase-like 2	83						mitochondrion	glycine N-acyltransferase activity			ovary(1)|skin(1)	2		Breast(21;0.0044)|all_epithelial(135;0.0216)			Glycine(DB00145)													---	---	---	---
OR10V1	390201	broad.mit.edu	37	11	59480554	59480554	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59480554G>A	uc001nof.1	-	1	765	c.765C>T	c.(763-765)TGC>TGT	p.C255C		NM_001005324	NP_001005324	Q8NGI7	O10V1_HUMAN	olfactory receptor, family 10, subfamily V,	255	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0																		---	---	---	---
MRPL16	54948	broad.mit.edu	37	11	59574080	59574080	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59574080G>A	uc001noh.2	-	4	710	c.496C>T	c.(496-498)CGT>TGT	p.R166C		NM_017840	NP_060310	Q9NX20	RM16_HUMAN	mitochondrial ribosomal protein L16 precursor	166							rRNA binding			central_nervous_system(1)	1																		---	---	---	---
TMEM132A	54972	broad.mit.edu	37	11	60704376	60704376	+	Silent	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60704376C>A	uc001nqj.2	+	11	3262	c.3069C>A	c.(3067-3069)TCC>TCA	p.S1023S	TMEM132A_uc001nqi.2_Silent_p.S1024S|TMEM132A_uc001nqm.2_Silent_p.S233S	NM_178031	NP_821174	Q24JP5	T132A_HUMAN	transmembrane protein 132A isoform b	1023	Cytoplasmic (Potential).|Confers cellular localization similar to full-length form (By similarity).					endoplasmic reticulum membrane|Golgi membrane|integral to membrane				skin(1)	1																		---	---	---	---
SLC15A3	51296	broad.mit.edu	37	11	60707056	60707056	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60707056T>C	uc001nqn.2	-	6	1565	c.1331A>G	c.(1330-1332)CAG>CGG	p.Q444R	SLC15A3_uc001nqo.2_Missense_Mutation_p.S388G	NM_016582	NP_057666	Q8IY34	S15A3_HUMAN	solute carrier family 15, member 3	444					oligopeptide transport|protein transport	integral to membrane|lysosomal membrane	peptide:hydrogen symporter activity				0																		---	---	---	---
CD6	923	broad.mit.edu	37	11	60783258	60783258	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60783258G>A	uc001nqq.2	+	9	1684	c.1461G>A	c.(1459-1461)GAG>GAA	p.E487E	CD6_uc001nqp.2_Silent_p.E487E|CD6_uc001nqr.2_Silent_p.E455E|CD6_uc001nqs.2_RNA|CD6_uc001nqt.2_Intron	NM_006725	NP_006716	P30203	CD6_HUMAN	CD6 molecule precursor	487	Cytoplasmic (Potential).				cell adhesion	cell surface|integral to plasma membrane	scavenger receptor activity			pancreas(1)	1																		---	---	---	---
DAK	26007	broad.mit.edu	37	11	61110231	61110231	+	Silent	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61110231C>A	uc001nre.2	+	10	1037	c.780C>A	c.(778-780)TCC>TCA	p.S260S	DDB1_uc010rlf.1_5'Flank|DAK_uc009ynm.1_Silent_p.S190S	NM_015533	NP_056348	Q3LXA3	DHAK_HUMAN	dihydroxyacetone kinase 2	260	DhaK.				glycerol metabolic process	cytosol	ATP binding|FAD-AMP lyase (cyclizing) activity|glycerone kinase activity|metal ion binding				0																		---	---	---	---
AHNAK	79026	broad.mit.edu	37	11	62289124	62289124	+	Silent	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62289124G>T	uc001ntl.2	-	5	13065	c.12765C>A	c.(12763-12765)CCC>CCA	p.P4255P	AHNAK_uc001ntk.1_Intron	NM_001620	NP_001611	Q09666	AHNK_HUMAN	AHNAK nucleoprotein isoform 1	4255					nervous system development	nucleus	protein binding			ovary(10)|pancreas(4)|skin(4)|upper_aerodigestive_tract(1)	19		Melanoma(852;0.155)																---	---	---	---
AHNAK	79026	broad.mit.edu	37	11	62292451	62292451	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62292451C>T	uc001ntl.2	-	5	9738	c.9438G>A	c.(9436-9438)TGG>TGA	p.W3146*	AHNAK_uc001ntk.1_Intron	NM_001620	NP_001611	Q09666	AHNK_HUMAN	AHNAK nucleoprotein isoform 1	3146					nervous system development	nucleus	protein binding			ovary(10)|pancreas(4)|skin(4)|upper_aerodigestive_tract(1)	19		Melanoma(852;0.155)																---	---	---	---
METTL12	751071	broad.mit.edu	37	11	62433383	62433383	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62433383C>T	uc001nug.1	+	2	291	c.32C>T	c.(31-33)CCG>CTG	p.P11L	C11orf48_uc001nue.2_Intron|C11orf48_uc001nuf.2_Intron|METTL12_uc001nuh.2_5'UTR|METTL12_uc010rmc.1_RNA	NM_001043229	NP_001036694	A8MUP2	MTL12_HUMAN	methyltransferase like 12 precursor	11						mitochondrion	methyltransferase activity				0																		---	---	---	---
UBXN1	51035	broad.mit.edu	37	11	62446025	62446025	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62446025A>G	uc001nul.1	-	3	294	c.162T>C	c.(160-162)ACT>ACC	p.T54T	UBXN1_uc001nuj.2_Silent_p.T54T|UBXN1_uc001num.1_Silent_p.T54T|UBXN1_uc001nuk.2_Silent_p.T19T|UBXN1_uc010rme.1_Silent_p.T54T|UBXN1_uc010rmf.1_Silent_p.T54T	NM_015853	NP_056937	Q04323	UBXN1_HUMAN	UBX domain protein 1	54	Interaction with BRCA1.				negative regulation of proteasomal ubiquitin-dependent protein catabolic process|negative regulation of protein ubiquitination|proteasomal ubiquitin-dependent protein catabolic process	cytoplasm	ATPase binding|K6-linked polyubiquitin binding				0																		---	---	---	---
PLCB3	5331	broad.mit.edu	37	11	64026040	64026040	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64026040C>T	uc001nzb.2	+	11	1108	c.1108C>T	c.(1108-1110)CCG>TCG	p.P370S	PLCB3_uc009ypg.1_Missense_Mutation_p.P370S|PLCB3_uc009yph.1_Missense_Mutation_p.P303S|PLCB3_uc009ypi.2_Missense_Mutation_p.P370S	NM_000932	NP_000923	Q01970	PLCB3_HUMAN	phospholipase C beta 3	370	PI-PLC X-box.				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																		---	---	---	---
GPR137	56834	broad.mit.edu	37	11	64054479	64054479	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64054479C>T	uc001nzg.1	+	3	708	c.400C>T	c.(400-402)CGA>TGA	p.R134*	BAD_uc001nzd.2_5'Flank|BAD_uc001nzc.2_5'Flank|GPR137_uc009ypj.1_Nonsense_Mutation_p.R140*|BAD_uc009ypk.2_5'Flank|GPR137_uc010rni.1_Nonsense_Mutation_p.R192*|GPR137_uc001nze.1_Nonsense_Mutation_p.R134*|GPR137_uc001nzf.2_Nonsense_Mutation_p.R134*|GPR137_uc001nzh.1_Nonsense_Mutation_p.R134*|GPR137_uc001nzi.2_Nonsense_Mutation_p.R134*|GPR137_uc010rnj.1_Nonsense_Mutation_p.R134*	NM_020155	NP_064540	Q96N19	G137A_HUMAN	G protein-coupled receptor 137	134	Cytoplasmic (Potential).					integral to membrane				central_nervous_system(1)	1																		---	---	---	---
SLC22A11	55867	broad.mit.edu	37	11	64329603	64329603	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64329603G>A	uc001oai.2	+	3	999	c.625G>A	c.(625-627)GGC>AGC	p.G209S	SLC22A11_uc001oah.1_Missense_Mutation_p.R174Q|SLC22A11_uc001oaj.2_Missense_Mutation_p.G209S|SLC22A11_uc009ypq.2_Missense_Mutation_p.G209S|SLC22A11_uc001oak.1_Missense_Mutation_p.G38S	NM_018484	NP_060954	Q9NSA0	S22AB_HUMAN	solute carrier family 22 member 11	209	Helical; (Potential).				urate metabolic process	apical plasma membrane|external side of plasma membrane|integral to plasma membrane	inorganic anion exchanger activity|protein binding|sodium-independent organic anion transmembrane transporter activity			ovary(1)|central_nervous_system(1)	2					Probenecid(DB01032)											OREG0004030	type=REGULATORY REGION|Gene=SLC22A11|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	---	---	---	---
NRXN2	9379	broad.mit.edu	37	11	64428294	64428294	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64428294G>A	uc001oar.2	-	11	2555	c.2116C>T	c.(2116-2118)CGA>TGA	p.R706*	NRXN2_uc001oas.2_Nonsense_Mutation_p.R675*|NRXN2_uc001oaq.2_Nonsense_Mutation_p.R373*	NM_015080	NP_055895	P58401	NRX2B_HUMAN	neurexin 2 isoform alpha-1 precursor	Error:Variant_position_missing_in_P58401_after_alignment					cell adhesion	integral to membrane				upper_aerodigestive_tract(2)|central_nervous_system(2)|skin(2)|ovary(2)|kidney(1)|pancreas(1)	10																		---	---	---	---
MAP4K2	5871	broad.mit.edu	37	11	64563866	64563866	+	Intron	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64563866C>T	uc001obh.2	-						MAP4K2_uc001obg.2_RNA|MAP4K2_uc001obi.2_Intron	NM_004579	NP_004570			mitogen-activated protein kinase kinase kinase						activation of JUN kinase activity|immune response|positive regulation of JNK cascade|vesicle targeting	basolateral plasma membrane|Golgi membrane|soluble fraction	ATP binding|mitogen-activated protein kinase kinase kinase binding|protein serine/threonine kinase activity|small GTPase regulator activity			ovary(1)|pancreas(1)	2																		---	---	---	---
C11orf2	738	broad.mit.edu	37	11	64878997	64878997	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64878997C>T	uc001ocr.1	+	10	2327	c.2287C>T	c.(2287-2289)CGC>TGC	p.R763C	TM7SF2_uc001oct.2_5'Flank|TM7SF2_uc010rny.1_5'Flank|TM7SF2_uc001ocu.2_5'Flank|TM7SF2_uc001ocv.2_5'Flank|C11orf2_uc001ocs.1_Missense_Mutation_p.R639C	NM_013265	NP_037397	Q9UID3	FFR_HUMAN	chromosome 11 open reading frame 2	763					lipid transport|protein transport	Golgi apparatus|integral to membrane					0																		---	---	---	---
EIF1AD	84285	broad.mit.edu	37	11	65766220	65766220	+	Intron	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65766220C>T	uc001ogm.1	-						EIF1AD_uc001ogn.1_Intron	NM_032325	NP_115701			eukaryotic translation initiation factor 1A							nucleus	translation initiation factor activity				0																		---	---	---	---
PELI3	246330	broad.mit.edu	37	11	66241301	66241301	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66241301G>A	uc001oic.3	+	7	909	c.745G>A	c.(745-747)GAG>AAG	p.E249K	PELI3_uc001oib.2_Missense_Mutation_p.E249K|PELI3_uc001oid.3_Missense_Mutation_p.E225K|PELI3_uc001oie.3_Missense_Mutation_p.E100K|PELI3_uc010rpd.1_Missense_Mutation_p.E90K	NM_145065	NP_659502	Q8N2H9	PELI3_HUMAN	pellino 3 alpha isoform 1	249						cytosol	protein binding			ovary(1)	1																		---	---	---	---
DPP3	10072	broad.mit.edu	37	11	66262922	66262922	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66262922C>T	uc001oig.1	+	14	1601	c.1539C>T	c.(1537-1539)AGC>AGT	p.S513S	DPP3_uc001oif.1_Silent_p.S513S|DPP3_uc010rpe.1_Silent_p.S502S|DPP3_uc001oih.1_5'Flank	NM_005700	NP_005691	Q9NY33	DPP3_HUMAN	dipeptidyl peptidase III	513					proteolysis	cytoplasm	aminopeptidase activity|dipeptidyl-peptidase activity|metal ion binding|metallopeptidase activity			ovary(1)|skin(1)	2																		---	---	---	---
SPTBN2	6712	broad.mit.edu	37	11	66475139	66475139	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66475139G>A	uc001ojd.2	-	12	1573	c.1501C>T	c.(1501-1503)CGC>TGC	p.R501C		NM_006946	NP_008877	O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2	501	Spectrin 2.				actin filament capping|axon guidance|cell death|vesicle-mediated transport	cytosol|spectrin	actin binding|structural constituent of cytoskeleton			large_intestine(1)|pancreas(1)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
SSH3	54961	broad.mit.edu	37	11	67076941	67076941	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67076941C>T	uc001okj.2	+	11	1313	c.1135C>T	c.(1135-1137)CGC>TGC	p.R379C	SSH3_uc001okk.2_RNA|SSH3_uc001okl.2_Missense_Mutation_p.R233C	NM_017857	NP_060327	Q8TE77	SSH3_HUMAN	slingshot homolog 3	379	Tyrosine-protein phosphatase.				regulation of actin polymerization or depolymerization|regulation of axonogenesis|regulation of lamellipodium assembly	cytoplasm|cytoskeleton|nucleus	actin binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(15;2.26e-06)															---	---	---	---
CARNS1	57571	broad.mit.edu	37	11	67191613	67191613	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67191613C>T	uc009yrp.2	+	9	2477	c.2025C>T	c.(2023-2025)AAC>AAT	p.N675N	PPP1CA_uc001okx.1_5'Flank|CARNS1_uc001olc.3_Silent_p.N814N	NM_020811	NP_065862	A5YM72	CRNS1_HUMAN	ATP-grasp domain containing 1	675	ATP-grasp.				carnosine biosynthetic process		ATP binding|carnosine synthase activity|metal ion binding				0																		---	---	---	---
NUMA1	4926	broad.mit.edu	37	11	71725087	71725087	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71725087C>T	uc001orl.1	-	15	3634	c.3462G>A	c.(3460-3462)CGG>CGA	p.R1154R	NUMA1_uc009ysw.1_Silent_p.R717R|NUMA1_uc001ork.1_Intron|NUMA1_uc001orm.1_Silent_p.R1154R|NUMA1_uc001orn.2_Silent_p.R717R|NUMA1_uc009ysx.1_Silent_p.R1154R|NUMA1_uc001oro.1_Silent_p.R1154R	NM_006185	NP_006176	Q14980	NUMA1_HUMAN	nuclear mitotic apparatus protein 1	1154	Potential.				G2/M transition of mitotic cell cycle|mitotic anaphase|nucleus organization	chromosome|cytosol|nucleoplasm|spindle microtubule|spindle pole	protein binding|structural molecule activity			ovary(3)|lung(2)|skin(2)|central_nervous_system(1)	8								T	RARA	APL								---	---	---	---
NUMA1	4926	broad.mit.edu	37	11	71725245	71725245	+	Missense_Mutation	SNP	C	T	T	rs140741340	byFrequency;by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71725245C>T	uc001orl.1	-	15	3476	c.3304G>A	c.(3304-3306)GCA>ACA	p.A1102T	NUMA1_uc009ysw.1_Missense_Mutation_p.A665T|NUMA1_uc001ork.1_Intron|NUMA1_uc001orm.1_Missense_Mutation_p.A1102T|NUMA1_uc001orn.2_Missense_Mutation_p.A665T|NUMA1_uc009ysx.1_Missense_Mutation_p.A1102T|NUMA1_uc001oro.1_Missense_Mutation_p.A1102T	NM_006185	NP_006176	Q14980	NUMA1_HUMAN	nuclear mitotic apparatus protein 1	1102	Potential.				G2/M transition of mitotic cell cycle|mitotic anaphase|nucleus organization	chromosome|cytosol|nucleoplasm|spindle microtubule|spindle pole	protein binding|structural molecule activity			ovary(3)|lung(2)|skin(2)|central_nervous_system(1)	8								T	RARA	APL								---	---	---	---
C11orf51	25906	broad.mit.edu	37	11	71821248	71821248	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71821248C>A	uc001orw.2	-	5	426	c.204G>T	c.(202-204)GAG>GAT	p.E68D	LRTOMT_uc010rqv.1_3'UTR|LRTOMT_uc010rqw.1_3'UTR|LRTOMT_uc001ors.3_3'UTR|C11orf51_uc009ytc.1_Missense_Mutation_p.E59D|C11orf51_uc001orv.2_Missense_Mutation_p.E68D	NM_014042	NP_054761	P60006	CK051_HUMAN	hypothetical protein LOC25906	68	Asp-rich.					intracellular					0																		---	---	---	---
RELT	84957	broad.mit.edu	37	11	73106159	73106159	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73106159G>A	uc001otv.2	+	10	1239	c.1074G>A	c.(1072-1074)CAG>CAA	p.Q358Q	RELT_uc001otw.2_Silent_p.Q358Q|RELT_uc001otx.2_RNA	NM_152222	NP_689408	Q969Z4	TR19L_HUMAN	RELT tumor necrosis factor receptor precursor	358	Cytoplasmic (Potential).					cytoplasm|integral to membrane|plasma membrane	binding|receptor activity			upper_aerodigestive_tract(1)	1																		---	---	---	---
DNAJB13	374407	broad.mit.edu	37	11	73679454	73679454	+	Missense_Mutation	SNP	G	A	A	rs147921001	byFrequency	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73679454G>A	uc001ouo.2	+	6	1422	c.671G>A	c.(670-672)CGC>CAC	p.R224H		NM_153614	NP_705842	P59910	DJB13_HUMAN	testis spermatogenesis apoptosis-related protein	224					apoptosis|protein folding|spermatogenesis		heat shock protein binding|unfolded protein binding				0	Breast(11;7.42e-05)																	---	---	---	---
RSF1	51773	broad.mit.edu	37	11	77386207	77386207	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77386207G>A	uc001oyn.2	-	14	3556	c.3436C>T	c.(3436-3438)CGT>TGT	p.R1146C	RSF1_uc001oym.2_Missense_Mutation_p.R894C	NM_016578	NP_057662	Q96T23	RSF1_HUMAN	remodeling and spacing factor 1	1146	Arg-rich.				CenH3-containing nucleosome assembly at centromere|negative regulation of DNA binding|negative regulation of transcription, DNA-dependent|nucleosome positioning|positive regulation of transcription, DNA-dependent|positive regulation of viral transcription|transcription initiation, DNA-dependent	RSF complex	histone binding|protein binding|zinc ion binding			ovary(2)|central_nervous_system(2)	4	all_cancers(14;1.54e-17)|all_epithelial(13;4.06e-20)|Ovarian(111;0.152)		Epithelial(5;3e-50)|all cancers(3;6.37e-47)|BRCA - Breast invasive adenocarcinoma(5;9.82e-31)															---	---	---	---
KCTD21	283219	broad.mit.edu	37	11	77884897	77884897	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77884897C>T	uc001ozb.2	-	2	779	c.704G>A	c.(703-705)GGC>GAC	p.G235D		NM_001029859	NP_001025030	Q4G0X4	KCD21_HUMAN	potassium channel tetramerisation domain	235						voltage-gated potassium channel complex	voltage-gated potassium channel activity			pancreas(1)	1	all_cancers(14;3.77e-18)|all_epithelial(13;6.16e-21)|Breast(9;5.6e-16)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;1.46e-24)															---	---	---	---
PRCP	5547	broad.mit.edu	37	11	82560971	82560971	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82560971G>A	uc001ozs.2	-	5	849	c.736C>T	c.(736-738)CGA>TGA	p.R246*	PRCP_uc001ozr.2_Nonsense_Mutation_p.R267*	NM_005040	NP_005031	P42785	PCP_HUMAN	prolylcarboxypeptidase isoform 1 preproprotein	246	SKS domain.				blood coagulation, intrinsic pathway|proteolysis	lysosome|plasma membrane	protein binding|serine-type carboxypeptidase activity			skin(1)	1																		---	---	---	---
DLG2	1740	broad.mit.edu	37	11	83984291	83984291	+	Intron	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:83984291C>T	uc001paj.2	-						DLG2_uc001pai.2_Missense_Mutation_p.R3Q|DLG2_uc010rsy.1_Missense_Mutation_p.R3Q|DLG2_uc010rsz.1_Intron|DLG2_uc010rta.1_Intron|DLG2_uc001pak.2_Intron|DLG2_uc010rtb.1_Missense_Mutation_p.R3Q|DLG2_uc001pal.1_Intron|DLG2_uc001pam.1_Intron	NM_001364	NP_001355			chapsyn-110 isoform 2							cell junction|postsynaptic density|postsynaptic membrane	guanylate kinase activity|protein binding|protein binding			ovary(3)|pancreas(2)|skin(1)	6		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)																---	---	---	---
SYTL2	54843	broad.mit.edu	37	11	85436047	85436047	+	Intron	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85436047C>T	uc010rth.1	-						SYTL2_uc010rtg.1_Intron|SYTL2_uc010rti.1_Intron|SYTL2_uc010rtj.1_Intron|SYTL2_uc009yvj.2_RNA|SYTL2_uc001pbd.2_Missense_Mutation_p.A485T|SYTL2_uc001pbb.2_Missense_Mutation_p.A485T|SYTL2_uc001pbc.2_Missense_Mutation_p.A485T|SYTL2_uc010rtf.1_Intron	NM_001162951	NP_001156423			synaptotagmin-like 2 isoform g						intracellular protein transport|vesicle docking involved in exocytosis	exocytic vesicle|extrinsic to plasma membrane|melanosome|membrane fraction	neurexin binding|phosphatidylinositol-4,5-bisphosphate binding|phosphatidylserine binding|Rab GTPase binding			ovary(2)|large_intestine(1)	3		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)														---	---	---	---
CCDC83	220047	broad.mit.edu	37	11	85622403	85622403	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85622403A>T	uc001pbh.1	+	8	1264	c.752A>T	c.(751-753)GAT>GTT	p.D251V	CCDC83_uc001pbg.1_Missense_Mutation_p.D251V|CCDC83_uc001pbi.1_RNA|CCDC83_uc001pbj.1_Missense_Mutation_p.D152V	NM_173556	NP_775827	Q8IWF9	CCD83_HUMAN	coiled-coil domain containing 83	251	Potential.									skin(1)	1		Acute lymphoblastic leukemia(157;4.88e-06)|all_hematologic(158;0.00572)																---	---	---	---
PICALM	8301	broad.mit.edu	37	11	85689112	85689112	+	Intron	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85689112C>T	uc001pbm.2	-						PICALM_uc001pbl.2_Splice_Site_p.Y551_splice|PICALM_uc001pbn.2_Intron|PICALM_uc010rtl.1_Intron|PICALM_uc001pbk.2_Intron|PICALM_uc010rtk.1_Splice_Site_p.Y178_splice|PICALM_uc001pbo.1_Splice_Site_p.Y233_splice	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|								---	---	---	---
CCDC81	60494	broad.mit.edu	37	11	86123507	86123507	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86123507C>A	uc001pbx.1	+	11	1725	c.1297C>A	c.(1297-1299)CTG>ATG	p.L433M	CCDC81_uc001pbw.1_Missense_Mutation_p.L343M|CCDC81_uc010rtq.1_Missense_Mutation_p.L216M|CCDC81_uc001pby.1_Missense_Mutation_p.L168M	NM_001156474	NP_001149946	Q6ZN84	CCD81_HUMAN	coiled-coil domain containing 81 isoform 1	433										skin(1)	1		Acute lymphoblastic leukemia(157;5.51e-06)|all_hematologic(158;0.00535)																---	---	---	---
TYR	7299	broad.mit.edu	37	11	88960990	88960990	+	Splice_Site	SNP	G	T	T	rs61754382		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:88960990G>T	uc001pcs.2	+	3	1119	c.1037_splice	c.e3-1	p.G346_splice		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				---	---	---	---
CEP57	9702	broad.mit.edu	37	11	95564282	95564282	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:95564282A>G	uc001pfp.1	+	11	1586	c.1365A>G	c.(1363-1365)GGA>GGG	p.G455G	CEP57_uc010ruh.1_Silent_p.G446G|CEP57_uc010rui.1_Silent_p.G429G|CEP57_uc009ywn.1_Silent_p.G303G|CEP57_uc001pfq.1_Silent_p.G429G|CEP57_uc001pfr.1_Silent_p.G303G	NM_014679	NP_055494	Q86XR8	CEP57_HUMAN	translokin	455	Mediates interaction with microtubules (By similarity).|Potential.				fibroblast growth factor receptor signaling pathway|G2/M transition of mitotic cell cycle|protein import into nucleus, translocation|spermatid development	centrosome|cytosol|Golgi apparatus|microtubule|nucleus	fibroblast growth factor binding|protein homodimerization activity			ovary(1)	1		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)												Mosaic_Variegated_Aneuploidy_Syndrome				---	---	---	---
CNTN5	53942	broad.mit.edu	37	11	100211310	100211310	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:100211310C>T	uc001pga.2	+	22	3185	c.2846C>T	c.(2845-2847)ACA>ATA	p.T949I	CNTN5_uc001pgb.2_Missense_Mutation_p.T875I|CNTN5_uc010ruk.1_Missense_Mutation_p.T220I	NM_014361	NP_055176	O94779	CNTN5_HUMAN	contactin 5 isoform long	949	Fibronectin type-III 3.				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)														---	---	---	---
DYNC2H1	79659	broad.mit.edu	37	11	103090682	103090682	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103090682G>T	uc001pho.2	+	56	9015	c.8871G>T	c.(8869-8871)AAG>AAT	p.K2957N	DYNC2H1_uc001phn.1_Missense_Mutation_p.K2957N|DYNC2H1_uc009yxe.1_Intron	NM_001080463	NP_001073932	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	2957	Potential.|Stalk (By similarity).				cell projection organization|Golgi organization|microtubule-based movement|multicellular organismal development	cilium axoneme|dynein complex|Golgi apparatus|microtubule|plasma membrane	ATP binding|ATPase activity|microtubule motor activity				0		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)														---	---	---	---
DYNC2H1	79659	broad.mit.edu	37	11	103128425	103128425	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103128425G>A	uc001pho.2	+	69	10694	c.10550G>A	c.(10549-10551)CGT>CAT	p.R3517H	DYNC2H1_uc001phn.1_Missense_Mutation_p.R3524H|DYNC2H1_uc009yxe.1_Intron	NM_001080463	NP_001073932	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	3517					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)														---	---	---	---
NPAT	4863	broad.mit.edu	37	11	108031665	108031665	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108031665C>T	uc001pjz.3	-	17	4250	c.4148G>A	c.(4147-4149)CGT>CAT	p.R1383H	NPAT_uc010rvv.1_Missense_Mutation_p.R439H	NM_002519	NP_002510	Q14207	NPAT_HUMAN	nuclear protein,  ataxia-telangiectasia locus	1383					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)														---	---	---	---
DLAT	1737	broad.mit.edu	37	11	111922036	111922036	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111922036G>A	uc001pmo.2	+	11	2136	c.1477G>A	c.(1477-1479)GAA>AAA	p.E493K	DLAT_uc009yyk.1_Missense_Mutation_p.E388K|DLAT_uc010rwr.1_Missense_Mutation_p.E366K	NM_001931	NP_001922	P10515	ODP2_HUMAN	dihydrolipoamide S-acetyltransferase precursor	493	Catalytic (By similarity).				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)													---	---	---	---
NCAM1	4684	broad.mit.edu	37	11	113075153	113075153	+	5'UTR	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113075153C>T	uc009yyq.1	+	3					NCAM1_uc001pno.2_5'UTR	NM_001076682	NP_001070150			neural cell adhesion molecule 1 isoform 3						axon guidance|interferon-gamma-mediated signaling pathway	anchored to membrane|extracellular region|Golgi membrane|integral to membrane				ovary(1)	1		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)														---	---	---	---
DRD2	1813	broad.mit.edu	37	11	113286314	113286314	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113286314A>G	uc001pnz.2	-	4	873	c.552T>C	c.(550-552)ATT>ATC	p.I184I	DRD2_uc010rwv.1_Silent_p.I183I|DRD2_uc001poa.3_Silent_p.I184I|DRD2_uc001pob.3_Silent_p.I184I|DRD2_uc009yyr.1_Silent_p.I184I	NM_000795	NP_000786	P14416	DRD2_HUMAN	dopamine receptor D2 isoform long	184	Extracellular (By similarity).				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)													---	---	---	---
NNMT	4837	broad.mit.edu	37	11	114168792	114168792	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114168792C>T	uc001por.1	+	4	538	c.274C>T	c.(274-276)CAG>TAG	p.Q92*	NNMT_uc001pos.1_Nonsense_Mutation_p.Q92*	NM_006169	NP_006160	P40261	NNMT_HUMAN	nicotinamide N-methyltransferase	92					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)													---	---	---	---
DSCAML1	57453	broad.mit.edu	37	11	117302447	117302447	+	Intron	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117302447G>T	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	117651330	117651330	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117651330G>A	uc001prh.1	-	2	424	c.422C>T	c.(421-423)ACG>ATG	p.T141M	DSCAML1_uc001pri.1_Translation_Start_Site	NM_020693	NP_065744	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	81	Extracellular (Potential).|Ig-like C2-type 1.				axonogenesis|brain development|cell fate determination|dorsal/ventral pattern formation|embryonic skeletal system morphogenesis|homophilic cell adhesion	cell surface|integral to membrane|plasma membrane	protein homodimerization activity			ovary(3)|large_intestine(2)|skin(2)|upper_aerodigestive_tract(1)	8	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)														---	---	---	---
TMPRSS4	56649	broad.mit.edu	37	11	117985906	117985906	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117985906C>T	uc010rxo.1	+	11	1354	c.1063C>T	c.(1063-1065)CGG>TGG	p.R355W	TMPRSS4_uc010rxp.1_Missense_Mutation_p.R350W|TMPRSS4_uc010rxq.1_Missense_Mutation_p.R208W|TMPRSS4_uc010rxr.1_Missense_Mutation_p.R330W|TMPRSS4_uc010rxs.1_Missense_Mutation_p.R315W|TMPRSS4_uc009yzu.2_Intron|TMPRSS4_uc010rxt.1_Missense_Mutation_p.R330W	NM_019894	NP_063947	Q9NRS4	TMPS4_HUMAN	transmembrane protease, serine 4 isoform 1	355	Extracellular (Potential).|Peptidase S1.				proteolysis	integral to membrane	scavenger receptor activity|serine-type endopeptidase activity			large_intestine(1)|central_nervous_system(1)	2	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0431)|all_hematologic(192;0.164)|Breast(348;0.183)|all_neural(223;0.238)		BRCA - Breast invasive adenocarcinoma(274;4.16e-05)|Epithelial(105;0.00204)														---	---	---	---
CD3E	916	broad.mit.edu	37	11	118183570	118183570	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118183570T>C	uc001psq.3	+	6	597	c.341T>C	c.(340-342)CTG>CCG	p.L114P	CD3E_uc010rya.1_Missense_Mutation_p.L114P	NM_000733	NP_000724	P07766	CD3E_HUMAN	CD3E antigen, epsilon polypeptide precursor	114	Extracellular (Potential).				G-protein coupled receptor protein signaling pathway|signal complex assembly|T cell costimulation|T cell receptor signaling pathway|transmembrane receptor protein tyrosine kinase signaling pathway	external side of plasma membrane|integral to plasma membrane	protein heterodimerization activity|protein kinase binding|receptor signaling complex scaffold activity|receptor signaling protein activity|SH3 domain binding|T cell receptor binding|transmembrane receptor activity			ovary(2)	2	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.09e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0251)	Muromonab(DB00075)													---	---	---	---
FOXR1	283150	broad.mit.edu	37	11	118850143	118850143	+	Intron	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118850143C>T	uc001pui.2	+						FOXR1_uc001puj.2_Intron|FOXR1_uc001puk.2_Intron	NM_181721	NP_859072			forkhead box R1						embryo development|organ development|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			skin(1)	1	all_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)														---	---	---	---
OAF	220323	broad.mit.edu	37	11	120096485	120096485	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120096485C>T	uc001pxb.2	+	2	588	c.347C>T	c.(346-348)GCC>GTC	p.A116V		NM_178507	NP_848602	Q86UD1	OAF_HUMAN	OAF homolog precursor	116											0		Breast(109;0.00663)|Medulloblastoma(222;0.0523)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)														---	---	---	---
GRIK4	2900	broad.mit.edu	37	11	120702613	120702613	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120702613G>A	uc001pxn.2	+	7	851	c.564G>A	c.(562-564)ACG>ACA	p.T188T	GRIK4_uc009zav.1_Silent_p.T188T|GRIK4_uc009zaw.1_Silent_p.T188T|GRIK4_uc009zax.1_Silent_p.T188T	NM_014619	NP_055434	Q16099	GRIK4_HUMAN	glutamate receptor KA1 precursor	188	Extracellular (Potential).				glutamate signaling pathway|synaptic transmission	cell junction|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			ovary(2)|central_nervous_system(1)	3		Breast(109;0.000868)|Medulloblastoma(222;0.0453)|all_neural(223;0.116)|all_hematologic(192;0.21)		BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.116)	L-Glutamic Acid(DB00142)													---	---	---	---
TBCEL	219899	broad.mit.edu	37	11	120925921	120925921	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120925921G>A	uc009zay.2	+	5	694	c.616G>A	c.(616-618)GTC>ATC	p.V206I	TBCEL_uc001pxo.2_Missense_Mutation_p.V206I|TBCEL_uc001pxp.2_Missense_Mutation_p.V62I|TBCEL_uc001pxq.2_Intron	NM_001130047	NP_001123519	Q5QJ74	TBCEL_HUMAN	tubulin folding cofactor E-like	206	LRR 6.					cytoplasm|cytoskeleton				skin(1)	1		Breast(109;0.00526)|Medulloblastoma(222;0.0523)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;5.89e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.121)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	124120712	124120712	+	IGR	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124120712G>A								OR8G2 (24402 upstream) : OR8D1 (59025 downstream)																																			---	---	---	---
KCNJ1	3758	broad.mit.edu	37	11	128709289	128709289	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128709289A>G	uc001qeo.1	-	2	958	c.907T>C	c.(907-909)TCC>CCC	p.S303P	KCNJ1_uc001qep.1_Missense_Mutation_p.S284P|KCNJ1_uc001qeq.1_Missense_Mutation_p.S284P|KCNJ1_uc001qer.1_Missense_Mutation_p.S284P|KCNJ1_uc001qes.1_Missense_Mutation_p.S284P	NM_000220	NP_000211	P48048	IRK1_HUMAN	potassium inwardly-rectifying channel J1 isoform	303	Cytoplasmic (By similarity).				excretion	voltage-gated potassium channel complex	ATP binding|inward rectifier potassium channel activity			ovary(3)|breast(1)	4	all_hematologic(175;0.0641)	all_lung(97;4.89e-06)|Lung NSC(97;9.34e-06)|Breast(109;0.00123)|all_hematologic(192;0.00793)|Renal(330;0.0112)|all_neural(223;0.0189)|Medulloblastoma(222;0.0425)		OV - Ovarian serous cystadenocarcinoma(99;4.05e-06)|LUSC - Lung squamous cell carcinoma(976;0.008)|Lung(977;0.00942)	Acetohexamide(DB00414)|Chlorpropamide(DB00672)|Glibenclamide(DB01016)|Gliclazide(DB01120)|Glimepiride(DB00222)|Glipizide(DB01067)|Glycodiazine(DB01382)|Minoxidil(DB00350)|Nateglinide(DB00731)|Repaglinide(DB00912)|Tolazamide(DB00839)|Tolbutamide(DB01124)													---	---	---	---
ARHGAP32	9743	broad.mit.edu	37	11	128842510	128842510	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128842510A>G	uc009zcp.2	-	21	3849	c.3849T>C	c.(3847-3849)GCT>GCC	p.A1283A	ARHGAP32_uc009zcq.1_3'UTR|ARHGAP32_uc009zco.2_Silent_p.A242A|ARHGAP32_uc001qez.2_Silent_p.A934A	NM_001142685	NP_001136157	A7KAX9	RHG32_HUMAN	Rho GTPase-activating protein isoform 1	1283					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																		---	---	---	---
APLP2	334	broad.mit.edu	37	11	129992333	129992333	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129992333T>C	uc010sby.1	+	6	1004	c.847T>C	c.(847-849)TAC>CAC	p.Y283H	APLP2_uc001qfp.2_Missense_Mutation_p.Y283H|APLP2_uc001qfq.2_Missense_Mutation_p.Y283H|APLP2_uc010sbz.1_Missense_Mutation_p.Y127H|APLP2_uc001qfr.2_Missense_Mutation_p.Y105H|APLP2_uc001qfs.2_Intron|APLP2_uc001qfv.2_Missense_Mutation_p.Y230H	NM_001642	NP_001633	Q06481	APLP2_HUMAN	amyloid beta (A4) precursor-like protein 2	283	Extracellular (Potential).				G-protein coupled receptor protein signaling pathway	integral to membrane|nucleus|plasma membrane	DNA binding|identical protein binding|serine-type endopeptidase inhibitor activity			ovary(3)	3	all_hematologic(175;0.0429)	Breast(109;0.00586)|Lung NSC(97;0.00785)|all_lung(97;0.0154)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.0197)|Lung(977;0.24)														---	---	---	---
LRTM2	654429	broad.mit.edu	37	12	1943444	1943444	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1943444G>A	uc001qjt.2	+	5	1476	c.670G>A	c.(670-672)GAC>AAC	p.D224N	CACNA2D4_uc001qjp.2_Intron|CACNA2D4_uc009zds.1_Intron|CACNA2D4_uc009zdt.1_Intron|CACNA2D4_uc009zdr.1_Intron|LRTM2_uc001qju.2_Missense_Mutation_p.D224N|LRTM2_uc010sdx.1_Missense_Mutation_p.D224N|LRTM2_uc001qjv.2_5'UTR	NM_001039029	NP_001034118	Q8N967	LRTM2_HUMAN	leucine-rich repeats and transmembrane domains 2	224	LRRCT.|Extracellular (Potential).					integral to membrane				large_intestine(1)	1	Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.000834)															---	---	---	---
CACNA1C	775	broad.mit.edu	37	12	2566787	2566787	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2566787C>T	uc009zdu.1	+	5	985	c.672C>T	c.(670-672)CTC>CTT	p.L224L	CACNA1C_uc009zdv.1_Silent_p.L224L|CACNA1C_uc001qkb.2_Silent_p.L224L|CACNA1C_uc001qkc.2_Silent_p.L224L|CACNA1C_uc001qke.2_Silent_p.L224L|CACNA1C_uc001qkf.2_Silent_p.L224L|CACNA1C_uc001qjz.2_Silent_p.L224L|CACNA1C_uc001qkd.2_Silent_p.L224L|CACNA1C_uc001qkg.2_Silent_p.L224L|CACNA1C_uc009zdw.1_Silent_p.L224L|CACNA1C_uc001qkh.2_Silent_p.L224L|CACNA1C_uc001qkl.2_Silent_p.L224L|CACNA1C_uc001qkn.2_Silent_p.L224L|CACNA1C_uc001qko.2_Silent_p.L224L|CACNA1C_uc001qkp.2_Silent_p.L224L|CACNA1C_uc001qkr.2_Silent_p.L224L|CACNA1C_uc001qku.2_Silent_p.L224L|CACNA1C_uc001qkq.2_Silent_p.L224L|CACNA1C_uc001qks.2_Silent_p.L224L|CACNA1C_uc001qkt.2_Silent_p.L224L|CACNA1C_uc001qka.1_5'UTR|CACNA1C_uc001qki.1_5'UTR|CACNA1C_uc001qkj.1_5'UTR|CACNA1C_uc001qkk.1_5'UTR|CACNA1C_uc001qkm.1_5'UTR	NM_199460	NP_955630	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type,	224	Extracellular (Potential).|I.				axon guidance|calcium ion transport into cytosol|energy reserve metabolic process|regulation of insulin secretion	cytoplasm|postsynaptic density|voltage-gated calcium channel complex	calmodulin binding|voltage-gated calcium channel activity			ovary(10)|central_nervous_system(1)	11			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Nicardipine(DB00622)|Verapamil(DB00661)													---	---	---	---
CACNA1C	775	broad.mit.edu	37	12	2602496	2602496	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2602496A>G	uc009zdu.1	+	7	1370	c.1057A>G	c.(1057-1059)ATG>GTG	p.M353V	CACNA1C_uc009zdv.1_Missense_Mutation_p.M350V|CACNA1C_uc001qkb.2_Missense_Mutation_p.M353V|CACNA1C_uc001qkc.2_Missense_Mutation_p.M353V|CACNA1C_uc001qke.2_Missense_Mutation_p.M353V|CACNA1C_uc001qkf.2_Missense_Mutation_p.M353V|CACNA1C_uc001qjz.2_Missense_Mutation_p.M353V|CACNA1C_uc001qkd.2_Missense_Mutation_p.M353V|CACNA1C_uc001qkg.2_Missense_Mutation_p.M353V|CACNA1C_uc009zdw.1_Missense_Mutation_p.M353V|CACNA1C_uc001qkh.2_Missense_Mutation_p.M353V|CACNA1C_uc001qkl.2_Missense_Mutation_p.M353V|CACNA1C_uc001qkn.2_Missense_Mutation_p.M353V|CACNA1C_uc001qko.2_Missense_Mutation_p.M353V|CACNA1C_uc001qkp.2_Missense_Mutation_p.M353V|CACNA1C_uc001qkr.2_Missense_Mutation_p.M353V|CACNA1C_uc001qku.2_Missense_Mutation_p.M353V|CACNA1C_uc001qkq.2_Missense_Mutation_p.M353V|CACNA1C_uc001qks.2_Missense_Mutation_p.M353V|CACNA1C_uc001qkt.2_Missense_Mutation_p.M353V|CACNA1C_uc001qka.1_5'UTR|CACNA1C_uc001qki.1_Missense_Mutation_p.M89V|CACNA1C_uc001qkj.1_Missense_Mutation_p.M89V|CACNA1C_uc001qkk.1_Missense_Mutation_p.M89V|CACNA1C_uc001qkm.1_Missense_Mutation_p.M89V	NM_199460	NP_955630	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type,	353	I.|Extracellular (Potential).				axon guidance|calcium ion transport into cytosol|energy reserve metabolic process|regulation of insulin secretion	cytoplasm|postsynaptic density|voltage-gated calcium channel complex	calmodulin binding|voltage-gated calcium channel activity			ovary(10)|central_nervous_system(1)	11			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Nicardipine(DB00622)|Verapamil(DB00661)													---	---	---	---
ITFG2	55846	broad.mit.edu	37	12	2921981	2921981	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2921981T>G	uc001qlb.1	+	1	119	c.55T>G	c.(55-57)TTC>GTC	p.F19V	ITFG2_uc001qla.1_Missense_Mutation_p.F19V|ITFG2_uc010seb.1_5'UTR|ITFG2_uc010sec.1_RNA	NM_018463	NP_060933	Q969R8	ITFG2_HUMAN	integrin alpha FG-GAP repeat containing 2	19	FG-GAP 1; atypical.										0			OV - Ovarian serous cystadenocarcinoma(31;0.000818)															---	---	---	---
CCND2	894	broad.mit.edu	37	12	4385203	4385203	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4385203C>T	uc001qmo.2	+	2	533	c.228C>T	c.(226-228)GTC>GTT	p.V76V		NM_001759	NP_001750	P30279	CCND2_HUMAN	cyclin D2	76	Cyclin N-terminal.				cell division|positive regulation of cyclin-dependent protein kinase activity|positive regulation of protein phosphorylation	cyclin-dependent protein kinase holoenzyme complex|cytoplasm|membrane|nucleus	protein kinase binding			haematopoietic_and_lymphoid_tissue(1)|breast(1)|kidney(1)	3			all cancers(3;4.15e-10)|GBM - Glioblastoma multiforme(3;6.34e-05)|Colorectal(7;0.00245)|OV - Ovarian serous cystadenocarcinoma(31;0.00301)|COAD - Colon adenocarcinoma(12;0.0264)|STAD - Stomach adenocarcinoma(119;0.206)					T	IGL@	NHL,CLL								---	---	---	---
ACRBP	84519	broad.mit.edu	37	12	6752705	6752705	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6752705C>T	uc001qpu.1	-	6	1125	c.1077G>A	c.(1075-1077)TCG>TCA	p.S359S	ACRBP_uc010sfg.1_Silent_p.S326S	NM_032489	NP_115878	Q8NEB7	ACRBP_HUMAN	proacrosin binding protein sp32 precursor	359						acrosomal vesicle|extracellular region				central_nervous_system(1)	1																		---	---	---	---
MLF2	8079	broad.mit.edu	37	12	6861114	6861114	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6861114G>A	uc010sfi.1	-	3	220	c.157C>T	c.(157-159)CCT>TCT	p.P53S	MLF2_uc001qqp.2_Missense_Mutation_p.P53S|MLF2_uc009zey.1_Missense_Mutation_p.P53S	NM_005439	NP_005430	Q15773	MLF2_HUMAN	myeloid leukemia factor 2	53					defense response	cytoplasm|nucleus	protein binding			large_intestine(1)	1																		---	---	---	---
TPI1	7167	broad.mit.edu	37	12	6978878	6978878	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6978878G>A	uc001qrk.2	+	5	522	c.484G>A	c.(484-486)GTC>ATC	p.V162I	TPI1_uc010sfo.1_Missense_Mutation_p.V80I	NM_000365	NP_000356	P60174	TPIS_HUMAN	triosephosphate isomerase 1 isoform 1	162					fatty acid biosynthetic process|gluconeogenesis|glycolysis|pentose-phosphate shunt	cytosol	triose-phosphate isomerase activity				0																OREG0021638	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
LRRC23	10233	broad.mit.edu	37	12	7014793	7014793	+	5'UTR	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7014793G>A	uc001qrt.3	+	2					LRRC23_uc001qrn.1_5'UTR|LRRC23_uc009zfg.2_Intron|LRRC23_uc001qrp.2_5'UTR|LRRC23_uc001qrq.2_5'UTR|LRRC23_uc001qrr.2_5'UTR|LRRC23_uc001qrs.2_5'UTR|LRRC23_uc009zfh.2_5'UTR	NM_001135217	NP_001128689			leucine rich repeat containing 23 isoform a											ovary(1)	1																		---	---	---	---
NECAP1	25977	broad.mit.edu	37	12	8245544	8245544	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8245544C>T	uc001qtx.2	+	6	647	c.569C>T	c.(568-570)CCG>CTG	p.P190L	NECAP1_uc001qty.2_Missense_Mutation_p.P48L	NM_015509	NP_056324	Q8NC96	NECP1_HUMAN	NECAP endocytosis associated 1	190					endocytosis|protein transport	clathrin coated vesicle membrane|plasma membrane				ovary(1)	1				Kidney(36;0.0915)														---	---	---	---
RIMKLB	57494	broad.mit.edu	37	12	8926004	8926004	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8926004G>A	uc001quu.2	+	6	1036	c.785G>A	c.(784-786)GGC>GAC	p.G262D	RIMKLB_uc009zgf.1_RNA|RIMKLB_uc001qux.2_Missense_Mutation_p.G262D|RIMKLB_uc010sgl.1_Missense_Mutation_p.G262D|RIMKLB_uc001quw.2_Missense_Mutation_p.G262D	NM_020734	NP_065785	Q9ULI2	RIMKB_HUMAN	ribosomal modification protein rimK-like family	262	ATP-grasp.				protein modification process	cytoplasm	acid-amino acid ligase activity|ATP binding|metal ion binding				0																		---	---	---	---
A2M	2	broad.mit.edu	37	12	9246138	9246138	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9246138C>T	uc001qvk.1	-	18	2276	c.2163G>A	c.(2161-2163)GTG>GTA	p.V721V	A2M_uc009zgk.1_Silent_p.V571V	NM_000014	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin precursor	721	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	9305467	9305467	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9305467G>A	uc001qvl.2	-	31	4103	c.4074C>T	c.(4072-4074)TGC>TGT	p.C1358C	PZP_uc009zgl.2_Silent_p.C1144C	NM_002864	NP_002855			pregnancy-zone protein precursor											ovary(3)|upper_aerodigestive_tract(1)|large_intestine(1)	5																		---	---	---	---
CLEC12A	160364	broad.mit.edu	37	12	10131562	10131562	+	Intron	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10131562C>T	uc001qwr.3	+						CLEC12A_uc001qwq.2_Intron|CLEC12A_uc001qws.3_Intron|CLEC12A_uc001qwt.2_Intron	NM_138337	NP_612210			myeloid inhibitory C-type lectin-like receptor							integral to membrane|plasma membrane	receptor activity|sugar binding			skin(1)	1																		---	---	---	---
GABARAPL1	23710	broad.mit.edu	37	12	10374385	10374385	+	Splice_Site	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10374385G>A	uc001qxs.2	+	4	529	c.289_splice	c.e4-1	p.D97_splice	GABARAPL1_uc001qxt.2_Splice_Site|GABARAPL1_uc001qxu.2_Splice_Site	NM_031412	NP_113600			GABA(A) receptor-associated protein like 1							autophagic vacuole|endoplasmic reticulum|Golgi apparatus|membrane|microtubule	beta-tubulin binding|GABA receptor binding				0																		---	---	---	---
CSDA	8531	broad.mit.edu	37	12	10856642	10856642	+	Intron	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10856642C>T	uc001qyt.2	-						CSDA_uc001qyu.2_Intron	NM_003651	NP_003642			cold shock domain protein A isoform a						negative regulation of transcription from RNA polymerase II promoter|response to cold	cytoplasm|nucleus	double-stranded DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(2)|lung(1)|large_intestine(1)	4	Glioma(1;0.155)																	---	---	---	---
TAS2R50	259296	broad.mit.edu	37	12	11139175	11139175	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11139175G>A	uc001qzl.2	-	1	337	c.285C>T	c.(283-285)AGC>AGT	p.S95S	PRR4_uc009zhp.2_Intron|PRH1_uc001qzb.3_Intron|PRH1_uc001qzc.2_Intron|PRB4_uc001qzf.1_Intron|PRH1_uc001qzj.2_Intron	NM_176890	NP_795371	P59544	T2R50_HUMAN	taste receptor, type 2, member 50	95	Helical; Name=3; (Potential).				sensory perception of taste	integral to membrane	G-protein coupled receptor activity			ovary(2)	2																		---	---	---	---
PRB1	5542	broad.mit.edu	37	12	11506766	11506766	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11506766G>A	uc001qzw.1	-	3	308	c.271C>T	c.(271-273)CGA>TGA	p.R91*	PRB1_uc001qzu.1_Nonsense_Mutation_p.R91*|PRB1_uc001qzv.1_Nonsense_Mutation_p.R91*	NM_005039	NP_005030	P04280	PRP1_HUMAN	proline-rich protein BstNI subfamily 1 isoform 1	152	5.|15 X 20 AA approximate tandem repeats of P-P-G-K-P-Q-G-P-P-[PAQ]-Q-[GE]-[GD]- [NKS]-[KSQRN]-[PRQS]-[QS] [GPS]-[PQAR]- [PSR].		Missing (in clone CP-4).|Missing (in clone CP-5).|Missing (in allele S).|Missing (in allele M).			extracellular region					0			OV - Ovarian serous cystadenocarcinoma(49;0.185)															---	---	---	---
MANSC1	54682	broad.mit.edu	37	12	12491444	12491444	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12491444G>A	uc001rai.1	-	3	532	c.274C>T	c.(274-276)CAA>TAA	p.Q92*	MANSC1_uc010shm.1_Nonsense_Mutation_p.Q26*|MANSC1_uc001raj.1_Nonsense_Mutation_p.Q58*|MANSC1_uc009zht.1_Nonsense_Mutation_p.Q11*	NM_018050	NP_060520	Q9H8J5	MANS1_HUMAN	MANSC domain containing 1 precursor	92	MANSC.|Extracellular (Potential).					integral to membrane					0		Prostate(47;0.0865)		BRCA - Breast invasive adenocarcinoma(232;0.185)														---	---	---	---
ATF7IP	55729	broad.mit.edu	37	12	14650841	14650841	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14650841T>C	uc001rbw.2	+	15	3805	c.3647T>C	c.(3646-3648)ATT>ACT	p.I1216T	ATF7IP_uc001rbx.2_Missense_Mutation_p.I1215T|ATF7IP_uc001rby.3_Missense_Mutation_p.I1216T|ATF7IP_uc001rca.2_Missense_Mutation_p.I1216T	NM_018179	NP_060649	Q6VMQ6	MCAF1_HUMAN	activating transcription factor 7 interacting	1216	Interaction with MBD1.|Fibronectin type-III.				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																		---	---	---	---
STRAP	11171	broad.mit.edu	37	12	16047083	16047083	+	Intron	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:16047083T>C	uc001rdc.3	+						STRAP_uc010shw.1_Intron|STRAP_uc001rdd.3_Intron	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)																---	---	---	---
ABCC9	10060	broad.mit.edu	37	12	22005044	22005044	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22005044T>C	uc001rfi.1	-	22	2776	c.2756A>G	c.(2755-2757)CAA>CGA	p.Q919R	ABCC9_uc001rfh.2_Missense_Mutation_p.Q919R|ABCC9_uc001rfj.1_Missense_Mutation_p.Q883R	NM_005691	NP_005682	O60706	ABCC9_HUMAN	ATP-binding cassette, sub-family C, member 9	919	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)													---	---	---	---
ABCC9	10060	broad.mit.edu	37	12	22015949	22015949	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22015949A>G	uc001rfi.1	-	18	2297	c.2277T>C	c.(2275-2277)CCT>CCC	p.P759P	ABCC9_uc001rfh.2_Silent_p.P759P|ABCC9_uc001rfj.1_Silent_p.P723P	NM_005691	NP_005682	O60706	ABCC9_HUMAN	ATP-binding cassette, sub-family C, member 9	759	Cytoplasmic (Potential).|ABC transporter 1.				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	23893839	23893839	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:23893839G>A	uc001rfw.2	-	5	805	c.703C>T	c.(703-705)CGT>TGT	p.R235C	SOX5_uc001rfx.2_Missense_Mutation_p.R222C|SOX5_uc001rfy.2_Missense_Mutation_p.R222C|SOX5_uc010siv.1_Missense_Mutation_p.R222C|SOX5_uc010siw.1_RNA|SOX5_uc001rfz.1_Missense_Mutation_p.R187C	NM_006940	NP_008871	P35711	SOX5_HUMAN	SRY (sex determining region Y)-box 5 isoform a	235	Potential.				transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(5)|lung(1)	6																		---	---	---	---
CASC1	55259	broad.mit.edu	37	12	25267796	25267796	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25267796A>G	uc001rgl.2	-	12	1469	c.1387T>C	c.(1387-1389)TGG>CGG	p.W463R	CASC1_uc001rgk.2_Missense_Mutation_p.W469R|CASC1_uc001rgm.3_Missense_Mutation_p.W527R|CASC1_uc001rgj.2_Missense_Mutation_p.W423R|CASC1_uc010sje.1_Missense_Mutation_p.W404R|CASC1_uc010sjf.1_Missense_Mutation_p.W351R|CASC1_uc010sjg.1_3'UTR	NM_001082973	NP_001076442	Q6TDU7	CASC1_HUMAN	cancer susceptibility candidate 1 isoform b	463										ovary(2)	2	Acute lymphoblastic leukemia(6;0.00112)|all_hematologic(7;0.00152)|Melanoma(3;0.0301)|Colorectal(261;0.11)		OV - Ovarian serous cystadenocarcinoma(3;7.42e-20)|Epithelial(3;7.58e-16)|all cancers(3;1.07e-13)															---	---	---	---
KRAS	3845	broad.mit.edu	37	12	25398281	25398281	+	Missense_Mutation	SNP	C	T	T	rs112445441		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25398281C>T	uc001rgp.1	-	2	219	c.38G>A	c.(37-39)GGC>GAC	p.G13D	KRAS_uc001rgq.1_Missense_Mutation_p.G13D|KRAS_uc001rgr.2_RNA	NM_033360	NP_203524	P01116	RASK_HUMAN	c-K-ras2 protein isoform a precursor	13	GTP.		G -> R (in pylocytic astrocytoma; somatic mutation; increase activation of the Ras pathway).|G -> D (in a breast carcinoma cell line and GASC; somatic mutation).		activation of MAPKK activity|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction	plasma membrane	GTP binding|GTPase activity|protein binding	p.G13D(2647)|p.G13C(182)|p.G13S(58)|p.G13R(41)|p.G13V(27)|p.G13A(24)|p.G13G(11)|p.G13E(4)|p.G12_G13insG(4)|p.G13N(3)|p.G13I(1)|p.G13_V14>DI(1)		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)			G13D(NCIH647_LUNG)|G13D(MDAMB231_BREAST)|G13D(NCIH747_LARGE_INTESTINE)|G13D(T84_LARGE_INTESTINE)|G13D(LOVO_LARGE_INTESTINE)|G13D(DLD1_LARGE_INTESTINE)|G13D(DV90_LUNG)|G13D(HCT15_LARGE_INTESTINE)|G13D(HCT116_LARGE_INTESTINE)|G13D(TOLEDO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G13D(NOMO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)	119	Mis		pancreatic|colorectal|lung|thyroid|AML|others				Cardiofaciocutaneous_syndrome|Noonan_syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)			---	---	---	---
IFLTD1	160492	broad.mit.edu	37	12	25679780	25679780	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25679780G>T	uc001rgs.2	-	4	688	c.538C>A	c.(538-540)CAA>AAA	p.Q180K	IFLTD1_uc001rgt.1_Missense_Mutation_p.Q83K|IFLTD1_uc010sji.1_Missense_Mutation_p.Q201K|IFLTD1_uc010sjj.1_Missense_Mutation_p.Q117K|IFLTD1_uc009zjc.2_Missense_Mutation_p.Q201K	NM_152590	NP_689803	Q8N9Z9	ILFT1_HUMAN	intermediate filament tail domain containing 1	180						intermediate filament	structural molecule activity			ovary(2)|central_nervous_system(1)	3	all_lung(3;2.75e-22)|Lung NSC(3;1.77e-21)|all_hematologic(7;0.00656)|Colorectal(261;0.0847)																	---	---	---	---
ARNTL2	56938	broad.mit.edu	37	12	27568857	27568857	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27568857A>G	uc001rht.1	+	15	1660	c.1642A>G	c.(1642-1644)ACT>GCT	p.T548A	ARNTL2_uc001rhw.2_Missense_Mutation_p.T511A|ARNTL2_uc010sjp.1_Missense_Mutation_p.T511A|ARNTL2_uc001rhu.1_Missense_Mutation_p.T534A|ARNTL2_uc009zji.1_Missense_Mutation_p.T514A|ARNTL2_uc001rhv.1_Missense_Mutation_p.T500A|uc001rhx.2_Intron	NM_020183	NP_064568	Q8WYA1	BMAL2_HUMAN	aryl hydrocarbon receptor nuclear	548					circadian rhythm|entrainment of circadian clock|regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			ovary(1)|skin(1)	2	Colorectal(261;0.0847)|Lung SC(9;0.184)																	---	---	---	---
PKP2	5318	broad.mit.edu	37	12	32996207	32996207	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32996207G>A	uc001rlj.3	-	6	1534	c.1419C>T	c.(1417-1419)GGC>GGT	p.G473G	PKP2_uc001rlk.3_Intron|PKP2_uc010skj.1_Intron	NM_004572	NP_004563	Q99959	PKP2_HUMAN	plakophilin 2 isoform 2b	473					cell-cell adhesion	desmosome|integral to membrane|nucleus	binding			ovary(1)|pancreas(1)	2	Lung NSC(5;9.35e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)																	---	---	---	---
ALG10	84920	broad.mit.edu	37	12	34179081	34179081	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:34179081A>T	uc001rlm.2	+	3	972	c.653A>T	c.(652-654)GAC>GTC	p.D218V		NM_032834	NP_116223	Q5BKT4	AG10A_HUMAN	asparagine-linked glycosylation 10 homolog	218	Cytoplasmic (Potential).				dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|integral to membrane	dolichyl-phosphate-glucose-glycolipid alpha-glucosyltransferase activity			skin(1)	1	Lung NSC(5;3.82e-05)|Acute lymphoblastic leukemia(23;0.0142)|all_hematologic(23;0.0429)	Lung NSC(34;0.204)|all_lung(34;0.235)																---	---	---	---
ADAMTS20	80070	broad.mit.edu	37	12	43846079	43846079	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:43846079T>G	uc010skx.1	-	14	2077	c.2077A>C	c.(2077-2079)ATG>CTG	p.M693L		NM_025003	NP_079279	P59510	ATS20_HUMAN	a disintegrin-like and metalloprotease with	693	Cys-rich.					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)														---	---	---	---
PLEKHA9	51054	broad.mit.edu	37	12	45567083	45567083	+	Missense_Mutation	SNP	C	T	T	rs150051178	byFrequency	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:45567083C>T	uc001rom.1	-	3	1603	c.1066G>A	c.(1066-1068)GTA>ATA	p.V356I	PLEKHA9_uc009zke.2_Missense_Mutation_p.V356I	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	45567160	45567160	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:45567160C>T	uc001rom.1	-	3	1526	c.989G>A	c.(988-990)GGC>GAC	p.G330D	PLEKHA9_uc009zke.2_Missense_Mutation_p.G330D	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)														---	---	---	---
ANO6	196527	broad.mit.edu	37	12	45803165	45803165	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:45803165T>C	uc001roo.2	+	16	2241	c.1906T>C	c.(1906-1908)TTT>CTT	p.F636L	ANO6_uc010sld.1_Missense_Mutation_p.F636L|ANO6_uc010sle.1_Missense_Mutation_p.F636L|ANO6_uc010slf.1_Missense_Mutation_p.F657L|ANO6_uc010slg.1_Missense_Mutation_p.F618L	NM_001025356	NP_001020527	Q4KMQ2	ANO6_HUMAN	anoctamin 6 isoform a	636	Extracellular (Potential).				activation of blood coagulation via clotting cascade|phosphatidylserine exposure on blood platelet	chloride channel complex|plasma membrane	chloride channel activity			ovary(1)|kidney(1)	2																		---	---	---	---
SLC38A1	81539	broad.mit.edu	37	12	46622973	46622973	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46622973C>T	uc001rpa.2	-	5	535	c.277G>A	c.(277-279)GCC>ACC	p.A93T	SLC38A1_uc001rpb.2_Missense_Mutation_p.A93T|SLC38A1_uc001rpc.2_Missense_Mutation_p.A93T|SLC38A1_uc001rpd.2_Missense_Mutation_p.A93T|SLC38A1_uc001rpe.2_Missense_Mutation_p.A93T|SLC38A1_uc010slh.1_Missense_Mutation_p.A66T|SLC38A1_uc009zkj.1_Missense_Mutation_p.A93T	NM_030674	NP_109599	Q9H2H9	S38A1_HUMAN	amino acid transporter system A1	93	Helical; (Potential).				cellular nitrogen compound metabolic process|neurotransmitter uptake	integral to membrane|plasma membrane	sodium:amino acid symporter activity			ovary(2)|skin(2)|central_nervous_system(1)	5	Lung SC(27;0.137)|Renal(347;0.236)		all cancers(1;0.00805)|OV - Ovarian serous cystadenocarcinoma(5;0.0106)|Epithelial(2;0.0344)															---	---	---	---
AMIGO2	347902	broad.mit.edu	37	12	47471213	47471213	+	3'UTR	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:47471213C>T	uc001rpm.2	-	3					FAM113B_uc001rpn.2_5'Flank|AMIGO2_uc001rpk.2_3'UTR|AMIGO2_uc001rpl.2_3'UTR	NM_001143668	NP_001137140			adhesion molecule with Ig-like domain 2						heterophilic cell-cell adhesion|homophilic cell adhesion	integral to membrane|nucleus|plasma membrane				ovary(1)|skin(1)	2	Renal(347;0.138)|Lung SC(27;0.192)																	---	---	---	---
FAM113B	91523	broad.mit.edu	37	12	47629502	47629502	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:47629502G>A	uc001rpn.2	+	4	1387	c.656G>A	c.(655-657)CGC>CAC	p.R219H	FAM113B_uc010slj.1_Missense_Mutation_p.R99H|FAM113B_uc001rpq.2_Missense_Mutation_p.R219H	NM_138371	NP_612380	Q96HM7	F113B_HUMAN	hypothetical protein LOC91523	219							hydrolase activity			skin(3)|ovary(2)	5	Renal(347;0.138)|Lung SC(27;0.192)																	---	---	---	---
VDR	7421	broad.mit.edu	37	12	48238574	48238574	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48238574C>T	uc001rqm.2	-	11	1521	c.1239G>A	c.(1237-1239)AAG>AAA	p.K413K	VDR_uc001rql.2_Silent_p.K463K|VDR_uc001rqn.2_Silent_p.K413K|VDR_uc010slq.1_Silent_p.K381K	NM_001017535	NP_001017535	P11473	VDR_HUMAN	vitamin D (1,25-dihydroxyvitamin D3) receptor	413	Ligand-binding.				decidualization|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of vitamin D 24-hydroxylase activity|regulation of calcidiol 1-monooxygenase activity|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	retinoid X receptor binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|vitamin D3 receptor activity|zinc ion binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Acute lymphoblastic leukemia(13;0.109)|all_hematologic(14;0.214)		GBM - Glioblastoma multiforme(48;0.17)	Calcidiol(DB00146)|Calcipotriol(DB02300)|Calcitriol(DB00136)|Dihydrotachysterol(DB01070)|Ergocalciferol(DB00153)|Paricalcitol(DB00910)													---	---	---	---
WNT10B	7480	broad.mit.edu	37	12	49361733	49361733	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49361733C>T	uc001rss.2	-	4	1053	c.707G>A	c.(706-708)CGC>CAC	p.R236H	WNT10B_uc001rst.2_Missense_Mutation_p.A189T	NM_003394	NP_003385	O00744	WN10B_HUMAN	wingless-type MMTV integration site family,	236					axis specification|bone trabecula formation|canonical Wnt receptor signaling pathway|cellular response to retinoic acid|chondrocyte differentiation|female gonad development|hemopoietic stem cell proliferation|midbrain-hindbrain boundary development|myoblast cell differentiation involved in skeletal muscle regeneration|negative regulation of epithelial cell proliferation|negative regulation of fat cell differentiation|neuron differentiation|positive regulation of anagen|positive regulation of apoptosis|positive regulation of bone mineralization|positive regulation of cell proliferation|positive regulation of epithelial cell differentiation|positive regulation of osteoblast differentiation|protein stabilization|regulation of skeletal muscle tissue development|skeletal muscle fiber development|smoothened signaling pathway|Wnt receptor signaling pathway, calcium modulating pathway	extracellular space|plasma membrane|proteinaceous extracellular matrix	G-protein-coupled receptor binding|signal transducer activity			skin(4)|lung(3)	7																		---	---	---	---
MLL2	8085	broad.mit.edu	37	12	49424718	49424718	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49424718G>A	uc001rta.3	-	40	13629	c.13629C>T	c.(13627-13629)GAC>GAT	p.D4543D		NM_003482	NP_003473	O14686	MLL2_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 2	4543					chromatin silencing|histone H3-K4 methylation|oocyte growth|positive regulation of cell proliferation|positive regulation of estrogen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|response to estrogen stimulus|transcription, DNA-dependent	histone methyltransferase complex	histone-lysine N-methyltransferase activity|protein binding|transcription regulatory region DNA binding|zinc ion binding			kidney(16)|central_nervous_system(12)|lung(4)|skin(4)|ovary(3)|pancreas(2)	41								N|F|Mis		medulloblastoma|renal					HNSCC(34;0.089)			---	---	---	---
MLL2	8085	broad.mit.edu	37	12	49434552	49434552	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49434552C>T	uc001rta.3	-	31	7001	c.7001G>A	c.(7000-7002)CGG>CAG	p.R2334Q		NM_003482	NP_003473	O14686	MLL2_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 2	2334	Pro-rich.				chromatin silencing|histone H3-K4 methylation|oocyte growth|positive regulation of cell proliferation|positive regulation of estrogen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|response to estrogen stimulus|transcription, DNA-dependent	histone methyltransferase complex	histone-lysine N-methyltransferase activity|protein binding|transcription regulatory region DNA binding|zinc ion binding			kidney(16)|central_nervous_system(12)|lung(4)|skin(4)|ovary(3)|pancreas(2)	41								N|F|Mis		medulloblastoma|renal					HNSCC(34;0.089)			---	---	---	---
DHH	50846	broad.mit.edu	37	12	49484980	49484980	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49484980C>T	uc001rtf.2	-	2	803	c.496G>A	c.(496-498)GCA>ACA	p.A166T		NM_021044	NP_066382	O43323	DHH_HUMAN	desert hedgehog preproprotein	166					cell-cell signaling|proteolysis	extracellular space|plasma membrane	calcium ion binding|peptidase activity|zinc ion binding			lung(1)|breast(1)	2																		---	---	---	---
DNAJC22	79962	broad.mit.edu	37	12	49743155	49743155	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49743155G>A	uc001rua.2	+	2	901	c.500G>A	c.(499-501)CGC>CAC	p.R167H	DNAJC22_uc001rub.2_Missense_Mutation_p.R167H	NM_024902	NP_079178	Q8N4W6	DJC22_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 22	167					protein folding	integral to membrane	heat shock protein binding|unfolded protein binding			ovary(1)	1																		---	---	---	---
ACCN2	41	broad.mit.edu	37	12	50452564	50452564	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50452564C>T	uc001rvw.2	+	2	244	c.15C>T	c.(13-15)GCC>GCT	p.A5A	ACCN2_uc001rvv.2_Silent_p.A5A|ACCN2_uc009zln.2_5'UTR|ACCN2_uc009zlo.2_Silent_p.A5A	NM_001095	NP_001086	P78348	ACCN2_HUMAN	amiloride-sensitive cation channel 2, neuronal	5	Cytoplasmic (By similarity).				calcium ion transport|response to pH|signal transduction	integral to plasma membrane	ligand-gated sodium channel activity|protein binding			ovary(1)	1					Amiloride(DB00594)													---	---	---	---
SMARCD1	6602	broad.mit.edu	37	12	50484376	50484376	+	Intron	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50484376A>G	uc001rvx.3	+						SMARCD1_uc001rvy.3_Intron|SMARCD1_uc009zlp.2_Intron	NM_003076	NP_003067			SWI/SNF-related matrix-associated						chromatin-mediated maintenance of transcription|nervous system development|regulation of transcription from RNA polymerase II promoter	nBAF complex|npBAF complex|nucleoplasm|SWI/SNF complex	protein complex scaffold|transcription coactivator activity			ovary(1)	1																		---	---	---	---
SLC11A2	4891	broad.mit.edu	37	12	51393164	51393164	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51393164C>T	uc001rxe.3	-	7	668	c.571G>A	c.(571-573)GCA>ACA	p.A191T	SLC11A2_uc001rxd.3_Missense_Mutation_p.A40T|SLC11A2_uc001rxc.3_Missense_Mutation_p.A191T|SLC11A2_uc001rxf.2_RNA|SLC11A2_uc010smx.1_Missense_Mutation_p.A187T|SLC11A2_uc001rxh.1_Missense_Mutation_p.A191T|SLC11A2_uc001rxj.1_Missense_Mutation_p.A191T|SLC11A2_uc001rxi.2_Missense_Mutation_p.A191T|SLC11A2_uc001rxk.1_Missense_Mutation_p.A220T|SLC11A2_uc010smy.1_Missense_Mutation_p.A154T	NM_000617	NP_000608	P49281	NRAM2_HUMAN	solute carrier family 11 (proton-coupled	191	Helical; (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																		---	---	---	---
SLC11A2	4891	broad.mit.edu	37	12	51393180	51393180	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51393180G>A	uc001rxe.3	-	7	652	c.555C>T	c.(553-555)GGC>GGT	p.G185G	SLC11A2_uc001rxd.3_Silent_p.G34G|SLC11A2_uc001rxc.3_Silent_p.G185G|SLC11A2_uc001rxf.2_RNA|SLC11A2_uc010smx.1_Silent_p.G181G|SLC11A2_uc001rxh.1_Silent_p.G185G|SLC11A2_uc001rxj.1_Silent_p.G185G|SLC11A2_uc001rxi.2_Silent_p.G185G|SLC11A2_uc001rxk.1_Silent_p.G214G|SLC11A2_uc010smy.1_Silent_p.G148G	NM_000617	NP_000608	P49281	NRAM2_HUMAN	solute carrier family 11 (proton-coupled	185	Helical; (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																		---	---	---	---
KRT75	9119	broad.mit.edu	37	12	52826943	52826943	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52826943G>A	uc001saj.2	-	2	614	c.592C>T	c.(592-594)CCC>TCC	p.P198S		NM_004693	NP_004684	O95678	K2C75_HUMAN	keratin 75	198	Linker 1.|Rod.					keratin filament	structural molecule activity				0				BRCA - Breast invasive adenocarcinoma(357;0.192)														---	---	---	---
KRT74	121391	broad.mit.edu	37	12	52962173	52962173	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52962173G>A	uc001sap.1	-	7	1183	c.1135C>T	c.(1135-1137)CGT>TGT	p.R379C		NM_175053	NP_778223	Q7RTS7	K2C74_HUMAN	keratin 6 irs4	379	Rod.|Coil 2.					keratin filament	structural molecule activity			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(357;0.191)														---	---	---	---
ESPL1	9700	broad.mit.edu	37	12	53680232	53680232	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53680232C>A	uc001sck.2	+	18	3803	c.3712C>A	c.(3712-3714)CCA>ACA	p.P1238T	ESPL1_uc001scj.2_Missense_Mutation_p.P913T|ESPL1_uc010soe.1_Intron	NM_012291	NP_036423	Q14674	ESPL1_HUMAN	separase	1238					apoptosis|cytokinesis|establishment of mitotic spindle localization|mitotic sister chromatid segregation|negative regulation of sister chromatid cohesion|positive regulation of mitotic metaphase/anaphase transition|proteolysis	centrosome|nucleus	cysteine-type peptidase activity|protein binding			lung(1)|kidney(1)|skin(1)	3																		---	---	---	---
ESPL1	9700	broad.mit.edu	37	12	53681832	53681832	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53681832G>A	uc001sck.2	+	19	4344	c.4253G>A	c.(4252-4254)CGG>CAG	p.R1418Q	ESPL1_uc001scj.2_Missense_Mutation_p.R1093Q|ESPL1_uc010soe.1_3'UTR	NM_012291	NP_036423	Q14674	ESPL1_HUMAN	separase	1418					apoptosis|cytokinesis|establishment of mitotic spindle localization|mitotic sister chromatid segregation|negative regulation of sister chromatid cohesion|positive regulation of mitotic metaphase/anaphase transition|proteolysis	centrosome|nucleus	cysteine-type peptidase activity|protein binding			lung(1)|kidney(1)|skin(1)	3																OREG0021863	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
ESPL1	9700	broad.mit.edu	37	12	53681905	53681905	+	Silent	SNP	A	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53681905A>T	uc001sck.2	+	19	4417	c.4326A>T	c.(4324-4326)CCA>CCT	p.P1442P	ESPL1_uc001scj.2_Silent_p.P1117P|ESPL1_uc010soe.1_3'UTR	NM_012291	NP_036423	Q14674	ESPL1_HUMAN	separase	1442					apoptosis|cytokinesis|establishment of mitotic spindle localization|mitotic sister chromatid segregation|negative regulation of sister chromatid cohesion|positive regulation of mitotic metaphase/anaphase transition|proteolysis	centrosome|nucleus	cysteine-type peptidase activity|protein binding			lung(1)|kidney(1)|skin(1)	3																OREG0021863	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
ESPL1	9700	broad.mit.edu	37	12	53681913	53681913	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53681913C>T	uc001sck.2	+	19	4425	c.4334C>T	c.(4333-4335)GCC>GTC	p.A1445V	ESPL1_uc001scj.2_Missense_Mutation_p.A1120V|ESPL1_uc010soe.1_3'UTR	NM_012291	NP_036423	Q14674	ESPL1_HUMAN	separase	1445					apoptosis|cytokinesis|establishment of mitotic spindle localization|mitotic sister chromatid segregation|negative regulation of sister chromatid cohesion|positive regulation of mitotic metaphase/anaphase transition|proteolysis	centrosome|nucleus	cysteine-type peptidase activity|protein binding			lung(1)|kidney(1)|skin(1)	3																OREG0021863	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
C12orf10	60314	broad.mit.edu	37	12	53700549	53700549	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53700549C>A	uc001scp.3	+	6	903	c.851C>A	c.(850-852)TCC>TAC	p.S284Y	C12orf10_uc009zmx.2_Missense_Mutation_p.S233Y|C12orf10_uc001scq.3_Missense_Mutation_p.S169Y	NM_021640	NP_067653	Q86UA3	Q86UA3_HUMAN	MYG1 protein precursor	284										ovary(2)	2																		---	---	---	---
AAAS	8086	broad.mit.edu	37	12	53701642	53701642	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53701642G>A	uc001scr.3	-	15	1566	c.1403C>T	c.(1402-1404)GCC>GTC	p.A468V	AAAS_uc001scs.3_Missense_Mutation_p.A435V	NM_015665	NP_056480	Q9NRG9	AAAS_HUMAN	achalasia, adrenocortical insufficiency,	468					carbohydrate metabolic process|glucose transport|nucleocytoplasmic transport|regulation of glucose transport|regulation of nucleocytoplasmic transport|transmembrane transport|viral reproduction	nuclear pore				ovary(1)	1																		---	---	---	---
SILV	6490	broad.mit.edu	37	12	56348059	56348059	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56348059C>T	uc001sip.2	-	11	1956	c.1925G>A	c.(1924-1926)CGC>CAC	p.R642H	SILV_uc001siq.2_Missense_Mutation_p.R649H|SILV_uc010spx.1_Missense_Mutation_p.R556H|SILV_uc001sir.2_Missense_Mutation_p.R642H	NM_006928	NP_008859	P40967	PMEL_HUMAN	silver homolog	642	Cytoplasmic (Potential).				melanin biosynthetic process|melanosome organization	endoplasmic reticulum membrane|extracellular region|Golgi apparatus|integral to membrane|melanosome|multivesicular body membrane|plasma membrane	protein binding				0																		---	---	---	---
MIP	4284	broad.mit.edu	37	12	56847512	56847512	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56847512C>T	uc001slh.2	-	2	420	c.388G>A	c.(388-390)GCA>ACA	p.A130T		NM_012064	NP_036196	P30301	MIP_HUMAN	major intrinsic protein of lens fiber	130	Helical; (By similarity).				response to stimulus|visual perception	gap junction|integral to plasma membrane	structural constituent of eye lens			skin(1)	1																		---	---	---	---
NACA	4666	broad.mit.edu	37	12	57111870	57111870	+	Intron	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57111870G>T	uc001slz.2	-						NACA_uc001sly.2_Intron|NACA_uc009zoy.1_Silent_p.A1148A|NACA_uc001smc.2_Intron|NACA_uc001sma.2_Intron|NACA_uc001smb.2_Intron|NACA_uc010squ.1_Intron	NM_001113201	NP_001106672			nascent polypeptide-associated complex alpha						interspecies interaction between organisms|protein transport|transcription, DNA-dependent|translation	nascent polypeptide-associated complex|nucleus	DNA binding			ovary(1)	1								T	BCL6	NHL								---	---	---	---
SDR9C7	121214	broad.mit.edu	37	12	57323219	57323219	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57323219G>A	uc010sqw.1	-	3	679	c.679C>T	c.(679-681)CCT>TCT	p.P227S		NM_148897	NP_683695	Q8NEX9	DR9C7_HUMAN	short chain dehydrogenase/reductase family 9C,	227						cytoplasm	binding|oxidoreductase activity			central_nervous_system(1)	1																		---	---	---	---
NAB2	4665	broad.mit.edu	37	12	57486328	57486328	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57486328G>A	uc001smz.2	+	3	1433	c.1055G>A	c.(1054-1056)CGA>CAA	p.R352Q		NM_005967	NP_005958	Q15742	NAB2_HUMAN	NGFI-A binding protein 2	352	NCD2.				cell proliferation|negative regulation of transcription from RNA polymerase III promoter|transcription, DNA-dependent	nucleus	transcription corepressor activity			upper_aerodigestive_tract(1)|ovary(1)	2																		---	---	---	---
LRP1	4035	broad.mit.edu	37	12	57574224	57574224	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57574224G>A	uc001snd.2	+	32	5814	c.5348G>A	c.(5347-5349)CGG>CAG	p.R1783Q		NM_002332	NP_002323	Q07954	LRP1_HUMAN	low density lipoprotein-related protein 1	1783	Extracellular (Potential).|LDL-receptor class B 16.				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)													---	---	---	---
MBD6	114785	broad.mit.edu	37	12	57921419	57921419	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57921419C>A	uc001soj.1	+	8	2436	c.2212C>A	c.(2212-2214)CCT>ACT	p.P738T	MBD6_uc001sok.1_Missense_Mutation_p.P605T|MBD6_uc001sol.1_RNA	NM_052897	NP_443129	Q96DN6	MBD6_HUMAN	methyl-CpG binding domain protein 6	738	Pro-rich.					chromosome|nucleus	chromatin binding|DNA binding			central_nervous_system(3)|ovary(1)	4																		---	---	---	---
SLC26A10	65012	broad.mit.edu	37	12	58015593	58015593	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:58015593C>A	uc001spe.2	+	4	987	c.676C>A	c.(676-678)CTA>ATA	p.L226I	SLC26A10_uc001spf.2_RNA|SLC26A10_uc009zpz.1_5'Flank	NM_133489	NP_597996	Q8NG04	S2610_HUMAN	solute carrier family 26, member 10	226						integral to membrane	antiporter activity			large_intestine(1)|central_nervous_system(1)	2	Melanoma(17;0.122)															OREG0021948	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
AGAP2	116986	broad.mit.edu	37	12	58121846	58121846	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:58121846G>A	uc001spq.2	-	15	2640	c.2640C>T	c.(2638-2640)ATC>ATT	p.I880I	AGAP2_uc001spo.1_5'Flank|AGAP2_uc001spp.2_Silent_p.I879I|AGAP2_uc001spr.2_Silent_p.I524I|LOC100130776_uc001sps.3_3'UTR	NM_001122772	NP_001116244	Q99490	AGAP2_HUMAN	centaurin, gamma 1 isoform PIKE-L	880	PH.				axon guidance|negative regulation of neuron apoptosis|negative regulation of protein catabolic process|protein transport|regulation of ARF GTPase activity|small GTPase mediated signal transduction	mitochondrion|nucleolus	ARF GTPase activator activity|GTP binding|zinc ion binding			central_nervous_system(3)|breast(2)	5																		---	---	---	---
SLC16A7	9194	broad.mit.edu	37	12	60168435	60168435	+	Intron	SNP	T	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:60168435T>A	uc001sqs.2	+						SLC16A7_uc001sqt.2_Intron|SLC16A7_uc001squ.2_Intron|SLC16A7_uc009zqi.2_Intron|SLC16A7_uc010ssi.1_Intron	NM_004731	NP_004722			solute carrier family 16, member 7							integral to plasma membrane|membrane fraction	pyruvate secondary active transmembrane transporter activity|secondary active monocarboxylate transmembrane transporter activity|symporter activity			ovary(1)	1				GBM - Glioblastoma multiforme(3;0.0303)	Pyruvic acid(DB00119)													---	---	---	---
MON2	23041	broad.mit.edu	37	12	62979234	62979234	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:62979234T>C	uc001sre.2	+	33	5251	c.4860T>C	c.(4858-4860)CAT>CAC	p.H1620H	MON2_uc009zqj.2_Silent_p.H1620H|MON2_uc010ssl.1_Silent_p.H1548H|MON2_uc010ssm.1_Silent_p.H1591H|MON2_uc010ssn.1_Silent_p.H1614H|MON2_uc001srf.2_Silent_p.H1383H|MON2_uc001srg.2_Silent_p.H489H	NM_015026	NP_055841	Q7Z3U7	MON2_HUMAN	MON2 homolog	1621					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)														---	---	---	---
XPOT	11260	broad.mit.edu	37	12	64812728	64812728	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64812728A>G	uc001ssb.2	+	6	769	c.343A>G	c.(343-345)ACA>GCA	p.T115A	XPOT_uc009zqm.1_Missense_Mutation_p.T25A	NM_007235	NP_009166	O43592	XPOT_HUMAN	tRNA exportin	115	Necessary for interaction with Ran, nuclear localization and nuclear import.				intracellular protein transport|tRNA export from nucleus	cytoplasm|nucleoplasm	protein transporter activity|tRNA binding			ovary(2)	2				GBM - Glioblastoma multiforme(28;0.0404)														---	---	---	---
XPOT	11260	broad.mit.edu	37	12	64812733	64812733	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64812733G>A	uc001ssb.2	+	6	774	c.348G>A	c.(346-348)GAG>GAA	p.E116E	XPOT_uc009zqm.1_Silent_p.E26E	NM_007235	NP_009166	O43592	XPOT_HUMAN	tRNA exportin	116	Necessary for interaction with Ran, nuclear localization and nuclear import.				intracellular protein transport|tRNA export from nucleus	cytoplasm|nucleoplasm	protein transporter activity|tRNA binding			ovary(2)	2				GBM - Glioblastoma multiforme(28;0.0404)														---	---	---	---
XPOT	11260	broad.mit.edu	37	12	64812808	64812808	+	Silent	SNP	C	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64812808C>G	uc001ssb.2	+	6	849	c.423C>G	c.(421-423)CTC>CTG	p.L141L	XPOT_uc009zqm.1_Silent_p.L51L	NM_007235	NP_009166	O43592	XPOT_HUMAN	tRNA exportin	141	Necessary for interaction with Ran, nuclear localization and nuclear import.				intracellular protein transport|tRNA export from nucleus	cytoplasm|nucleoplasm	protein transporter activity|tRNA binding			ovary(2)	2				GBM - Glioblastoma multiforme(28;0.0404)														---	---	---	---
NUP107	57122	broad.mit.edu	37	12	69109410	69109410	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69109410C>A	uc001suf.2	+	12	1088	c.973C>A	c.(973-975)CCT>ACT	p.P325T	NUP107_uc001sug.2_Missense_Mutation_p.P172T|NUP107_uc010stj.1_Missense_Mutation_p.P296T	NM_020401	NP_065134	P57740	NU107_HUMAN	nucleoporin 107kDa	325					carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA export from nucleus|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|Nup107-160 complex	nucleocytoplasmic transporter activity|protein binding			skin(1)	1	Breast(13;6.25e-06)		Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.00694)															---	---	---	---
CPM	1368	broad.mit.edu	37	12	69279677	69279677	+	Intron	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69279677G>A	uc001sup.2	-						CPM_uc001sur.2_Intron|CPM_uc001suq.2_Intron	NM_198320	NP_938079			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)															---	---	---	---
CCT2	10576	broad.mit.edu	37	12	69980567	69980567	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69980567T>C	uc001svb.1	+	3	207	c.113T>C	c.(112-114)TTG>TCG	p.L38S	CCT2_uc009zrm.1_RNA|CCT2_uc009zrn.1_Missense_Mutation_p.L38S|CCT2_uc010stl.1_5'UTR	NM_006431	NP_006422	P78371	TCPB_HUMAN	chaperonin containing TCP1, subunit 2	38					'de novo' posttranslational protein folding	nucleus	ATP binding|unfolded protein binding			ovary(1)|central_nervous_system(1)|skin(1)	3	all_cancers(2;7.7e-106)|Breast(13;2.15e-06)|Esophageal squamous(21;0.187)		Epithelial(6;2.72e-18)|GBM - Glioblastoma multiforme(2;2.58e-10)|Lung(24;0.000185)|OV - Ovarian serous cystadenocarcinoma(12;0.00126)|STAD - Stomach adenocarcinoma(21;0.00501)|Kidney(9;0.143)|LUSC - Lung squamous cell carcinoma(43;0.24)															---	---	---	---
TBC1D15	64786	broad.mit.edu	37	12	72307610	72307610	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:72307610T>C	uc001swu.2	+	13	1431	c.1422T>C	c.(1420-1422)TAT>TAC	p.Y474Y	TBC1D15_uc010stt.1_Silent_p.Y443Y|TBC1D15_uc001swv.2_Silent_p.Y457Y|TBC1D15_uc001sww.2_Silent_p.Y206Y	NM_022771	NP_073608	Q8TC07	TBC15_HUMAN	TBC1 domain family, member 15 isoform 1	452	Rab-GAP TBC.						protein binding|Rab GTPase activator activity				0																		---	---	---	---
E2F7	144455	broad.mit.edu	37	12	77444494	77444494	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:77444494C>T	uc001sym.3	-	4	636	c.400G>A	c.(400-402)GAA>AAA	p.E134K	E2F7_uc001syn.2_Missense_Mutation_p.E134K	NM_203394	NP_976328	Q96AV8	E2F7_HUMAN	E2F transcription factor 7	134					cell cycle	transcription factor complex	DNA binding|identical protein binding			upper_aerodigestive_tract(1)|ovary(1)|kidney(1)	3																		---	---	---	---
PPP1R12A	4659	broad.mit.edu	37	12	80328667	80328667	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80328667T>C	uc001syz.2	-	1	312	c.45A>G	c.(43-45)AAA>AAG	p.K15K	PPP1R12A_uc001sza.2_Silent_p.K15K|PPP1R12A_uc010sud.1_Silent_p.K15K|PPP1R12A_uc001szb.2_Silent_p.K15K|PPP1R12A_uc001szc.2_Silent_p.K15K	NM_002480	NP_002471	O14974	MYPT1_HUMAN	protein phosphatase 1, regulatory (inhibitor)	15						contractile fiber	protein binding|signal transducer activity			ovary(2)|breast(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	7																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	80750652	80750652	+	5'UTR	SNP	C	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80750652C>G	uc009zsg.1	+	2					uc001szd.2_Missense_Mutation_p.Q3E					RecName: Full=Uncharacterized protein C12orf64;																														---	---	---	---
DUSP6	1848	broad.mit.edu	37	12	89744647	89744647	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:89744647G>A	uc001tay.2	-	2	1036	c.556C>T	c.(556-558)CGA>TGA	p.R186*	DUSP6_uc001taz.2_Intron	NM_001946	NP_001937	Q16828	DUS6_HUMAN	dual specificity phosphatase 6 isoform a	186					dorsal/ventral pattern formation|inactivation of MAPK activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of ERK1 and ERK2 cascade|nerve growth factor receptor signaling pathway|positive regulation of apoptosis|regulation of endodermal cell fate specification|regulation of fibroblast growth factor receptor signaling pathway|regulation of heart growth|response to nitrosative stress|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	MAP kinase tyrosine/serine/threonine phosphatase activity|protein tyrosine phosphatase activity				0																		---	---	---	---
DCN	1634	broad.mit.edu	37	12	91552114	91552114	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:91552114C>T	uc001tbs.2	-	3	591	c.497G>A	c.(496-498)CGA>CAA	p.R166Q	DCN_uc001tbo.2_Intron|DCN_uc001tbp.2_Intron|DCN_uc001tbq.2_Intron|DCN_uc001tbr.2_Intron|DCN_uc001tbt.2_Missense_Mutation_p.R166Q|DCN_uc001tbu.2_Missense_Mutation_p.R166Q	NM_133503	NP_598010	P07585	PGS2_HUMAN	decorin isoform a preproprotein	166	LRR 5.				organ morphogenesis	extracellular space				central_nervous_system(2)|ovary(1)|lung(1)	4																		---	---	---	---
C12orf63	374467	broad.mit.edu	37	12	97079013	97079013	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:97079013C>T	uc001tet.1	+	9	1364	c.1286C>T	c.(1285-1287)GCA>GTA	p.A429V		NM_198520	NP_940922	Q6ZTY8	CL063_HUMAN	hypothetical protein LOC374467	429										skin(6)|ovary(1)	7																		---	---	---	---
UHRF1BP1L	23074	broad.mit.edu	37	12	100452815	100452815	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100452815A>G	uc001tgq.2	-	14	2469	c.2240T>C	c.(2239-2241)GTA>GCA	p.V747A	UHRF1BP1L_uc001tgp.2_Missense_Mutation_p.V397A	NM_015054	NP_055869	A0JNW5	UH1BL_HUMAN	UHRF1 (ICBP90) binding protein 1-like isoform a	747										ovary(2)	2																		---	---	---	---
SLC17A8	246213	broad.mit.edu	37	12	100790165	100790165	+	Silent	SNP	A	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100790165A>C	uc010svi.1	+	5	959	c.646A>C	c.(646-648)AGA>CGA	p.R216R	SLC17A8_uc009ztx.2_Silent_p.R216R	NM_139319	NP_647480	Q8NDX2	VGLU3_HUMAN	solute carrier family 17 (sodium-dependent	216	Cytoplasmic (Potential).				neurotransmitter transport|sensory perception of sound|sodium ion transport	cell junction|integral to membrane|synaptic vesicle membrane|synaptosome	L-glutamate transmembrane transporter activity|symporter activity			ovary(3)	3																		---	---	---	---
UTP20	27340	broad.mit.edu	37	12	101750726	101750726	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101750726C>A	uc001tia.1	+	43	5713	c.5557C>A	c.(5557-5559)CTA>ATA	p.L1853I		NM_014503	NP_055318	O75691	UTP20_HUMAN	down-regulated in metastasis	1853	HEAT 2.				endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|negative regulation of cell proliferation	90S preribosome|cytoplasm|nucleolus|nucleoplasm|preribosome, small subunit precursor|small-subunit processome	protein binding			ovary(2)|breast(2)	4																		---	---	---	---
STAB2	55576	broad.mit.edu	37	12	104118879	104118879	+	Intron	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104118879C>T	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																		---	---	---	---
TCP11L2	255394	broad.mit.edu	37	12	106715425	106715425	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106715425C>T	uc001tln.2	+	5	750	c.576C>T	c.(574-576)CCC>CCT	p.P192P	TCP11L2_uc001tll.2_Silent_p.P192P|TCP11L2_uc001tlm.2_Silent_p.P192P	NM_152772	NP_689985	Q8N4U5	T11L2_HUMAN	t-complex 11 (mouse) like 2	192										ovary(3)	3																		---	---	---	---
BTBD11	121551	broad.mit.edu	37	12	108011205	108011205	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108011205C>T	uc001tmk.1	+	9	2744	c.2223C>T	c.(2221-2223)CAC>CAT	p.H741H	BTBD11_uc009zut.1_Intron|BTBD11_uc001tmj.2_Silent_p.H741H|BTBD11_uc001tml.1_Silent_p.H278H	NM_001018072	NP_001018082	A6QL63	BTBDB_HUMAN	BTB (POZ) domain containing 11 isoform a	741	ANK 4.					integral to membrane	DNA binding			skin(2)|ovary(1)	3																		---	---	---	---
WSCD2	9671	broad.mit.edu	37	12	108603945	108603945	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108603945G>A	uc001tms.2	+	4	1289	c.545G>A	c.(544-546)GGC>GAC	p.G182D	WSCD2_uc001tmt.2_Missense_Mutation_p.G182D	NM_014653	NP_055468	Q2TBF2	WSCD2_HUMAN	WSC domain containing 2	182	WSC 1.					integral to membrane				ovary(1)|large_intestine(1)|breast(1)	3																		---	---	---	---
SART3	9733	broad.mit.edu	37	12	108942899	108942899	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108942899C>T	uc001tmz.1	-	2	639	c.404G>A	c.(403-405)CGC>CAC	p.R135H	SART3_uc009zux.1_5'UTR|SART3_uc010swx.1_Missense_Mutation_p.R135H|SART3_uc010swy.1_Missense_Mutation_p.R3H|SART3_uc010swz.1_Missense_Mutation_p.R135H|SART3_uc001tna.1_RNA	NM_014706	NP_055521	Q15020	SART3_HUMAN	squamous cell carcinoma antigen recognized by T	135	HAT 1.				RNA processing	cytoplasm|nuclear speck	nucleotide binding|protein binding|RNA binding			pancreas(1)	1														Porokeratosis				---	---	---	---
SART3	9733	broad.mit.edu	37	12	108954646	108954646	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108954646C>T	uc001tmz.1	-	1	520	c.285G>A	c.(283-285)CAG>CAA	p.Q95Q	SART3_uc009zux.1_5'UTR|SART3_uc010swx.1_Silent_p.Q95Q|SART3_uc010swz.1_Silent_p.Q95Q|SART3_uc001tna.1_RNA|SART3_uc001tnb.2_Silent_p.Q95Q|ISCU_uc010sxa.1_5'Flank|ISCU_uc010sxb.1_5'Flank|ISCU_uc001tnc.3_5'Flank|ISCU_uc010sxc.1_5'Flank|ISCU_uc009zuy.2_5'Flank|ISCU_uc010sxd.1_5'Flank	NM_014706	NP_055521	Q15020	SART3_HUMAN	squamous cell carcinoma antigen recognized by T	95	Potential.				RNA processing	cytoplasm|nuclear speck	nucleotide binding|protein binding|RNA binding			pancreas(1)	1														Porokeratosis				---	---	---	---
ATP2A2	488	broad.mit.edu	37	12	110777297	110777297	+	Intron	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110777297A>G	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																		---	---	---	---
GPN3	51184	broad.mit.edu	37	12	110897617	110897617	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110897617G>A	uc001tqr.2	-	3	264	c.208C>T	c.(208-210)CGA>TGA	p.R70*	GPN3_uc001tqs.2_Nonsense_Mutation_p.R80*	NM_016301	NP_057385	Q9UHW5	GPN3_HUMAN	GPN-loop GTPase 3 isoform 1	70						protein complex	GTP binding				0																		---	---	---	---
TCTN1	79600	broad.mit.edu	37	12	111085688	111085688	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111085688G>A	uc009zvs.2	+	14	1863	c.1755G>A	c.(1753-1755)CCG>CCA	p.P585P	TCTN1_uc001trp.3_Silent_p.P571P|TCTN1_uc001trn.3_Silent_p.P590P|TCTN1_uc001trk.3_RNA|HVCN1_uc001trq.1_Intron	NM_001082537	NP_001076006	Q2MV58	TECT1_HUMAN	tectonic family member 1 isoform 2	585					multicellular organismal development	extracellular region					0																		---	---	---	---
ACAD10	80724	broad.mit.edu	37	12	112171759	112171759	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112171759C>T	uc001tsq.2	+	11	1627	c.1427C>T	c.(1426-1428)CCA>CTA	p.P476L	ACAD10_uc001tsp.2_Missense_Mutation_p.P476L|ACAD10_uc009zvx.2_Missense_Mutation_p.P507L|ACAD10_uc001tss.1_RNA	NM_025247	NP_079523	Q6JQN1	ACD10_HUMAN	acyl-Coenzyme A dehydrogenase family, member 10	476							acyl-CoA dehydrogenase activity|flavin adenine dinucleotide binding|hydrolase activity|transferase activity, transferring phosphorus-containing groups			ovary(2)	2																		---	---	---	---
NOS1	4842	broad.mit.edu	37	12	117710317	117710317	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117710317G>A	uc001twm.1	-	10	2398	c.1712C>T	c.(1711-1713)GCC>GTC	p.A571V		NM_000620	NP_000611	P29475	NOS1_HUMAN	nitric oxide synthase 1, neuronal	571					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	117723955	117723955	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117723955C>T	uc001twm.1	-	6	1930	c.1244G>A	c.(1243-1245)CGG>CAG	p.R415Q		NM_000620	NP_000611	P29475	NOS1_HUMAN	nitric oxide synthase 1, neuronal	415					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)													---	---	---	---
GCN1L1	10985	broad.mit.edu	37	12	120589033	120589033	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120589033C>T	uc001txo.2	-	34	4238	c.4225G>A	c.(4225-4227)GGC>AGC	p.G1409S		NM_006836	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis	1409					regulation of translation	ribosome	protein binding|translation factor activity, nucleic acid binding			ovary(4)	4	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
SIRT4	23409	broad.mit.edu	37	12	120750802	120750802	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120750802G>A	uc001tyc.2	+	4	928	c.908G>A	c.(907-909)CGT>CAT	p.R303H		NM_012240	NP_036372	Q9Y6E7	SIRT4_HUMAN	sirtuin 4	303	Deacetylase sirtuin-type.				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)																	---	---	---	---
C12orf43	64897	broad.mit.edu	37	12	121448638	121448638	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121448638G>A	uc001tzh.1	-	3	303	c.280C>T	c.(280-282)CTG>TTG	p.L94L	C12orf43_uc009zxa.1_Silent_p.L125L|C12orf43_uc010szo.1_Silent_p.L52L|C12orf43_uc010szp.1_Silent_p.L94L|C12orf43_uc001tzi.1_Silent_p.L94L	NM_022895	NP_075046	Q96C57	CL043_HUMAN	hypothetical protein LOC64897	94											0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)																	---	---	---	---
LRRC43	254050	broad.mit.edu	37	12	122677528	122677528	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122677528T>A	uc009zxm.2	+	7	1351	c.1326T>A	c.(1324-1326)GAT>GAA	p.D442E	LRRC43_uc001ubw.3_Missense_Mutation_p.D257E|LRRC43_uc009zxn.2_Missense_Mutation_p.D203E	NM_001098519	NP_001091989	Q8N309	LRC43_HUMAN	leucine rich repeat containing 43 isoform 1	442											0	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000312)|Epithelial(86;0.000539)|BRCA - Breast invasive adenocarcinoma(302;0.225)														---	---	---	---
KNTC1	9735	broad.mit.edu	37	12	123060124	123060124	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123060124C>T	uc001ucv.2	+	28	2580	c.2417C>T	c.(2416-2418)GCG>GTG	p.A806V	KNTC1_uc010taf.1_Intron	NM_014708	NP_055523	P50748	KNTC1_HUMAN	Rough Deal homolog, centromere/kinetochore	806					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)														---	---	---	---
NCOR2	9612	broad.mit.edu	37	12	124979699	124979699	+	Silent	SNP	C	T	T	rs143791421	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124979699C>T	uc010tba.1	-	1	216	c.99G>A	c.(97-99)ACG>ACA	p.T33T	NCOR2_uc010tay.1_Silent_p.T33T|NCOR2_uc010taz.1_Silent_p.T33T|NCOR2_uc010tbb.1_Silent_p.T33T|NCOR2_uc010tbc.1_Silent_p.T33T|NCOR2_uc001ugj.1_Silent_p.T33T|NCOR2_uc001ugk.1_Silent_p.T33T	NM_001077261	NP_001070729	Q9Y618	NCOR2_HUMAN	nuclear receptor co-repressor 2 isoform 2	33					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)														---	---	---	---
AACS	65985	broad.mit.edu	37	12	125613986	125613986	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125613986C>T	uc001uhc.2	+	14	1735	c.1529C>T	c.(1528-1530)GCG>GTG	p.A510V	AACS_uc001uhd.2_Missense_Mutation_p.A510V|AACS_uc009zyh.2_Intron|AACS_uc009zyi.2_Missense_Mutation_p.A108V	NM_023928	NP_076417	Q86V21	AACS_HUMAN	acetoacetyl-CoA synthetase	510					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)														---	---	---	---
TMEM132B	114795	broad.mit.edu	37	12	126004054	126004054	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:126004054G>A	uc001uhe.1	+	4	1169	c.1161G>A	c.(1159-1161)GGG>GGA	p.G387G		NM_052907	NP_443139	Q14DG7	T132B_HUMAN	transmembrane protein 132B	387	Extracellular (Potential).					integral to membrane				skin(11)|ovary(5)|large_intestine(1)|pancreas(1)|breast(1)	19	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000423)|Epithelial(86;0.00394)|all cancers(50;0.0362)														---	---	---	---
TMEM132D	121256	broad.mit.edu	37	12	130184915	130184915	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130184915G>A	uc009zyl.1	-	2	736	c.408C>T	c.(406-408)GAC>GAT	p.D136D		NM_133448	NP_597705	Q14C87	T132D_HUMAN	transmembrane protein 132D precursor	136	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)														---	---	---	---
SFRS8	6433	broad.mit.edu	37	12	132238992	132238992	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132238992G>A	uc001uja.1	+	9	1542	c.1402G>A	c.(1402-1404)GCC>ACC	p.A468T	SFRS8_uc010tbn.1_Missense_Mutation_p.A468T|SFRS8_uc001ujb.1_Missense_Mutation_p.A261T|SFRS8_uc001uiz.1_Missense_Mutation_p.A342T	NM_004592	NP_004583	Q12872	SFSWA_HUMAN	splicing factor, arginine/serine-rich 8	468	SURP motif 2.				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)														---	---	---	---
SFRS8	6433	broad.mit.edu	37	12	132281835	132281835	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132281835G>A	uc001uja.1	+	16	2787	c.2647G>A	c.(2647-2649)GCG>ACG	p.A883T	SFRS8_uc010tbn.1_Missense_Mutation_p.A935T	NM_004592	NP_004583	Q12872	SFSWA_HUMAN	splicing factor, arginine/serine-rich 8	883	Arg/Ser-rich (RS domain).				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)														---	---	---	---
EP400	57634	broad.mit.edu	37	12	132514298	132514298	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132514298C>T	uc001ujn.2	+	27	5469	c.5434C>T	c.(5434-5436)CCG>TCG	p.P1812S	EP400_uc001ujl.2_Missense_Mutation_p.P1811S|EP400_uc001ujm.2_Missense_Mutation_p.P1731S|SNORA49_uc001ujo.2_5'Flank	NM_015409	NP_056224	Q96L91	EP400_HUMAN	E1A binding protein p400	1848					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)														---	---	---	---
ZMYM5	9205	broad.mit.edu	37	13	20399055	20399055	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20399055C>T	uc010tcn.1	-	8	1837	c.1572G>A	c.(1570-1572)ACG>ACA	p.T524T	ZMYM5_uc001umm.1_Silent_p.T348T	NM_001142684	NP_001136156	Q9UJ78	ZMYM5_HUMAN	zinc finger protein 237 isoform 3	524						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)														---	---	---	---
ZMYM5	9205	broad.mit.edu	37	13	20426142	20426142	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20426142A>T	uc010tcn.1	-	3	444	c.179T>A	c.(178-180)GTT>GAT	p.V60D	ZMYM5_uc001umm.1_Translation_Start_Site|ZMYM5_uc001umn.2_Missense_Mutation_p.V60D|ZMYM5_uc001umo.2_Missense_Mutation_p.V60D	NM_001142684	NP_001136156	Q9UJ78	ZMYM5_HUMAN	zinc finger protein 237 isoform 3	60						nucleus	zinc ion binding				0		all_cancers(29;2.96e-22)|all_epithelial(30;3.76e-20)|all_lung(29;4.38e-20)|Lung NSC(5;5.8e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.61e-05)|Epithelial(112;4.89e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00171)|Lung(94;0.00942)|LUSC - Lung squamous cell carcinoma(192;0.0431)														---	---	---	---
ZMYM2	7750	broad.mit.edu	37	13	20577064	20577064	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20577064G>A	uc001umr.2	+	5	1220	c.922G>A	c.(922-924)GCC>ACC	p.A308T	ZMYM2_uc001umq.2_Missense_Mutation_p.A221T|ZMYM2_uc001ums.2_Missense_Mutation_p.A308T|ZMYM2_uc001umt.2_Missense_Mutation_p.A308T|ZMYM2_uc009zzn.1_Missense_Mutation_p.A243T	NM_003453	NP_003444	Q9UBW7	ZMYM2_HUMAN	zinc finger protein 198	308					regulation of transcription, DNA-dependent|transcription, DNA-dependent	PML body	ubiquitin conjugating enzyme binding|zinc ion binding			lung(3)|ovary(2)|prostate(1)	6		all_cancers(29;8.65e-21)|all_epithelial(30;1.04e-18)|all_lung(29;6.75e-18)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;0.000148)|Epithelial(112;0.000249)|OV - Ovarian serous cystadenocarcinoma(117;0.00816)|Lung(94;0.0173)|LUSC - Lung squamous cell carcinoma(192;0.0856)														---	---	---	---
ZMYM2	7750	broad.mit.edu	37	13	20625630	20625630	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20625630C>T	uc001umr.2	+	14	2648	c.2350C>T	c.(2350-2352)CGT>TGT	p.R784C	ZMYM2_uc001ums.2_Missense_Mutation_p.R784C|ZMYM2_uc001umt.2_Missense_Mutation_p.R784C|ZMYM2_uc010tco.1_RNA|ZMYM2_uc001umv.2_Missense_Mutation_p.R164C|ZMYM2_uc001umw.2_Missense_Mutation_p.R237C	NM_003453	NP_003444	Q9UBW7	ZMYM2_HUMAN	zinc finger protein 198	784					regulation of transcription, DNA-dependent|transcription, DNA-dependent	PML body	ubiquitin conjugating enzyme binding|zinc ion binding			lung(3)|ovary(2)|prostate(1)	6		all_cancers(29;8.65e-21)|all_epithelial(30;1.04e-18)|all_lung(29;6.75e-18)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;0.000148)|Epithelial(112;0.000249)|OV - Ovarian serous cystadenocarcinoma(117;0.00816)|Lung(94;0.0173)|LUSC - Lung squamous cell carcinoma(192;0.0856)														---	---	---	---
ZMYM2	7750	broad.mit.edu	37	13	20641139	20641139	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20641139T>C	uc001umr.2	+	21	3579	c.3281T>C	c.(3280-3282)GTA>GCA	p.V1094A	ZMYM2_uc001ums.2_Missense_Mutation_p.V1094A|ZMYM2_uc001umt.2_Missense_Mutation_p.V1094A|ZMYM2_uc001umv.2_Missense_Mutation_p.V474A|ZMYM2_uc001umw.2_Missense_Mutation_p.V547A	NM_003453	NP_003444	Q9UBW7	ZMYM2_HUMAN	zinc finger protein 198	1094					regulation of transcription, DNA-dependent|transcription, DNA-dependent	PML body	ubiquitin conjugating enzyme binding|zinc ion binding			lung(3)|ovary(2)|prostate(1)	6		all_cancers(29;8.65e-21)|all_epithelial(30;1.04e-18)|all_lung(29;6.75e-18)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;0.000148)|Epithelial(112;0.000249)|OV - Ovarian serous cystadenocarcinoma(117;0.00816)|Lung(94;0.0173)|LUSC - Lung squamous cell carcinoma(192;0.0856)														---	---	---	---
SPATA13	221178	broad.mit.edu	37	13	24858406	24858406	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24858406T>C	uc001upg.1	+	4	830	c.423T>C	c.(421-423)AAT>AAC	p.N141N	SPATA13_uc001upd.1_Silent_p.N766N|C1QTNF9_uc001upe.2_RNA|SPATA13_uc010tcy.1_Silent_p.N87N|SPATA13_uc010tcz.1_Silent_p.N87N|SPATA13_uc010tda.1_Silent_p.N85N|SPATA13_uc001uph.2_Silent_p.N63N|SPATA13_uc010tdb.1_Silent_p.N63N	NM_153023	NP_694568	Q96N96	SPT13_HUMAN	spermatogenesis associated 13	141	ABR (APC-binding region) domain.				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	24861032	24861032	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24861032C>T	uc001upg.1	+	6	1143	c.736C>T	c.(736-738)CGG>TGG	p.R246W	SPATA13_uc001upd.1_Missense_Mutation_p.R871W|C1QTNF9_uc001upe.2_RNA|SPATA13_uc010tcy.1_Missense_Mutation_p.R192W|SPATA13_uc010tcz.1_Intron|SPATA13_uc010tda.1_Missense_Mutation_p.R190W|SPATA13_uc001uph.2_Missense_Mutation_p.R168W|SPATA13_uc010tdb.1_Intron|SPATA13_uc009zzz.1_5'Flank	NM_153023	NP_694568	Q96N96	SPT13_HUMAN	spermatogenesis associated 13	246	DH.				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)														---	---	---	---
PAN3	255967	broad.mit.edu	37	13	28841313	28841313	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28841313G>A	uc001urz.2	+	10	1225	c.1217G>A	c.(1216-1218)CGT>CAT	p.R406H	PAN3_uc010tdo.1_Missense_Mutation_p.R552H|PAN3_uc001ury.2_Missense_Mutation_p.R240H|PAN3_uc001urx.2_Missense_Mutation_p.R352H	NM_175854	NP_787050	Q58A45	PAN3_HUMAN	PABP1-dependent poly A-specific ribonuclease	552	Protein kinase.|Interaction with PAN2.				nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening	centrosome|cytosol	ATP binding|protein kinase activity			ovary(1)	1	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)	Colorectal(13;0.000334)	all cancers(112;0.0102)|Epithelial(112;0.0803)|GBM - Glioblastoma multiforme(144;0.121)|OV - Ovarian serous cystadenocarcinoma(117;0.13)|Lung(94;0.174)														---	---	---	---
SLC7A1	6541	broad.mit.edu	37	13	30091734	30091734	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:30091734C>T	uc001uso.2	-	10	1873	c.1486G>A	c.(1486-1488)GTG>ATG	p.V496M		NM_003045	NP_003036	P30825	CTR1_HUMAN	solute carrier family 7 (cationic amino acid	496	Helical; (Potential).				cellular nitrogen compound metabolic process|ion transport	integral to plasma membrane	receptor activity				0		Lung SC(185;0.0257)|Breast(139;0.238)		all cancers(112;0.0148)|OV - Ovarian serous cystadenocarcinoma(117;0.0554)|Epithelial(112;0.0875)|GBM - Glioblastoma multiforme(144;0.179)	L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129)													---	---	---	---
USPL1	10208	broad.mit.edu	37	13	31205139	31205139	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31205139C>T	uc001utc.2	+	4	828	c.396C>T	c.(394-396)GAC>GAT	p.D132D	USPL1_uc001utb.2_Translation_Start_Site|USPL1_uc001utd.2_Intron	NM_005800	NP_005791	Q5W0Q7	USPL1_HUMAN	ubiquitin specific peptidase like 1	132					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)														---	---	---	---
SOHLH2	54937	broad.mit.edu	37	13	36776105	36776105	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:36776105C>T	uc001uvj.2	-	2	263	c.174G>A	c.(172-174)GCG>GCA	p.A58A	SOHLH2_uc010tei.1_Silent_p.A135A	NM_017826	NP_060296	Q9NX45	SOLH2_HUMAN	spermatogenesis and oogenesis specific basic	58					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	36888477	36888477	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:36888477C>T	uc001uvn.2	-	7	1640	c.1370G>A	c.(1369-1371)CGA>CAA	p.R457Q	SPG20_uc010ten.1_Missense_Mutation_p.R447Q|SPG20_uc001uvm.2_Missense_Mutation_p.R457Q|SPG20_uc001uvo.2_Missense_Mutation_p.R457Q|SPG20_uc001uvq.2_Missense_Mutation_p.R457Q	NM_001142296	NP_001135768	Q8N0X7	SPG20_HUMAN	spartin	457					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)														---	---	---	---
FAM48A	55578	broad.mit.edu	37	13	37598478	37598478	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37598478T>C	uc001uwg.2	-	18	1679	c.1431A>G	c.(1429-1431)TCA>TCG	p.S477S	FAM48A_uc010abt.2_Silent_p.S478S|FAM48A_uc001uwh.2_Silent_p.S478S|FAM48A_uc001uwi.2_Silent_p.S477S|FAM48A_uc001uwj.2_Silent_p.S478S|FAM48A_uc001uwk.2_Silent_p.S477S|FAM48A_uc010tes.1_Silent_p.S441S|FAM48A_uc001uwl.1_Silent_p.S477S|FAM48A_uc001uwd.2_5'Flank|FAM48A_uc001uwe.2_5'UTR|FAM48A_uc001uwf.2_Silent_p.S55S	NM_001014286	NP_001014308	Q8NEM7	FA48A_HUMAN	family with sequence similarity 48, member A	477					autophagy|gastrulation	SAGA-type complex	protein binding				0		Lung NSC(96;2.09e-06)|Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.0959)		all cancers(112;6.06e-07)|Epithelial(112;1.87e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00794)|BRCA - Breast invasive adenocarcinoma(63;0.0128)|GBM - Glioblastoma multiforme(144;0.0477)														---	---	---	---
POSTN	10631	broad.mit.edu	37	13	38161966	38161966	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38161966G>T	uc001uwo.3	-	5	717	c.599C>A	c.(598-600)CCT>CAT	p.P200H	POSTN_uc001uwp.3_Missense_Mutation_p.P200H|POSTN_uc001uwr.2_Missense_Mutation_p.P200H|POSTN_uc001uwq.2_Missense_Mutation_p.P200H|POSTN_uc010teu.1_Missense_Mutation_p.P200H|POSTN_uc010tev.1_Missense_Mutation_p.P200H|POSTN_uc010tew.1_Missense_Mutation_p.P200H|POSTN_uc010tex.1_Missense_Mutation_p.P115H	NM_006475	NP_006466	Q15063	POSTN_HUMAN	periostin, osteoblast specific factor isoform 1	200	FAS1 1.				cell adhesion|skeletal system development	proteinaceous extracellular matrix	heparin binding			ovary(2)	2		Lung NSC(96;2.09e-05)|Prostate(109;0.0513)|Breast(139;0.0538)|Lung SC(185;0.0743)		all cancers(112;2.48e-08)|Epithelial(112;2.78e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000853)|BRCA - Breast invasive adenocarcinoma(63;0.013)|GBM - Glioblastoma multiforme(144;0.0154)														---	---	---	---
C13orf23	80209	broad.mit.edu	37	13	39588012	39588012	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39588012G>A	uc001uwy.2	-	11	2250	c.1377C>T	c.(1375-1377)GCC>GCT	p.A459A	C13orf23_uc001uwz.2_Silent_p.A437A	NM_025138	NP_079414	Q86XN7	CM023_HUMAN	hypothetical protein LOC80209 isoform 1	459	Ser-rich.									ovary(2)|skin(2)|haematopoietic_and_lymphoid_tissue(1)	5		Lung NSC(96;6.01e-07)|Breast(139;0.00394)|Prostate(109;0.00676)|Lung SC(185;0.0548)|Hepatocellular(188;0.114)		all cancers(112;3.7e-08)|Epithelial(112;4.28e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00114)|BRCA - Breast invasive adenocarcinoma(63;0.00366)|GBM - Glioblastoma multiforme(144;0.0146)														---	---	---	---
COG6	57511	broad.mit.edu	37	13	40268797	40268797	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:40268797T>C	uc001uxh.2	+	12	1201	c.1101T>C	c.(1099-1101)GCT>GCC	p.A367A	COG6_uc001uxi.2_Silent_p.A315A|COG6_uc010acb.2_Silent_p.A367A	NM_020751	NP_065802	Q9Y2V7	COG6_HUMAN	component of oligomeric golgi complex 6 isoform	367					protein transport	Golgi membrane|Golgi transport complex				kidney(1)|skin(1)	2		Lung NSC(96;0.000124)|Breast(139;0.0199)|Prostate(109;0.0233)|Lung SC(185;0.0367)		all cancers(112;6.03e-09)|Epithelial(112;7e-07)|OV - Ovarian serous cystadenocarcinoma(117;0.00015)|BRCA - Breast invasive adenocarcinoma(63;0.00438)|GBM - Glioblastoma multiforme(144;0.0168)														---	---	---	---
ZC3H13	23091	broad.mit.edu	37	13	46549634	46549634	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46549634C>T	uc010tfw.1	-	11	2258	c.2252G>A	c.(2251-2253)CGA>CAA	p.R751Q	ZC3H13_uc001vas.1_Missense_Mutation_p.R751Q|ZC3H13_uc001vat.1_Missense_Mutation_p.R751Q	NM_015070	NP_055885	Q5T200	ZC3HD_HUMAN	zinc finger CCCH-type containing 13	751	Arg/Glu-rich.|Potential.						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)														---	---	---	---
RNASEH2B	79621	broad.mit.edu	37	13	51522213	51522213	+	Intron	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51522213T>C	uc001vfa.3	+						RNASEH2B_uc001vfb.3_Intron	NM_024570	NP_078846			ribonuclease H2, subunit B isoform 1						RNA catabolic process	nucleus|ribonuclease H2 complex					0		Acute lymphoblastic leukemia(7;1.03e-07)|Breast(56;0.00122)|Lung NSC(96;0.00143)|Prostate(109;0.0047)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;9e-08)														---	---	---	---
NEK5	341676	broad.mit.edu	37	13	52639603	52639603	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52639603G>C	uc001vge.2	-	22	2207	c.2067C>G	c.(2065-2067)AGC>AGG	p.S689R		NM_199289	NP_954983	Q6P3R8	NEK5_HUMAN	NIMA-related kinase 5	689							ATP binding|metal ion binding|protein serine/threonine kinase activity			upper_aerodigestive_tract(1)	1		Breast(56;0.00173)|Lung NSC(96;0.0168)|Prostate(109;0.0412)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;3.7e-08)														---	---	---	---
MYCBP2	23077	broad.mit.edu	37	13	77663139	77663139	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77663139G>A	uc001vkf.2	-	62	10530	c.10439C>T	c.(10438-10440)CCG>CTG	p.P3480L	MYCBP2_uc010aev.2_Missense_Mutation_p.P2884L|MYCBP2_uc001vke.2_Missense_Mutation_p.P100L	NM_015057	NP_055872	O75592	MYCB2_HUMAN	MYC binding protein 2	3480					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)														---	---	---	---
SOX21	11166	broad.mit.edu	37	13	95364019	95364019	+	Silent	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95364019C>A	uc001vma.2	-	1	371	c.285G>T	c.(283-285)CCG>CCT	p.P95P	uc001vmb.1_5'Flank	NM_007084	NP_009015	Q9Y651	SOX21_HUMAN	SRY-box 21	95					regulation of transcription from RNA polymerase II promoter|stem cell differentiation	nucleus	DNA binding|sequence-specific DNA binding RNA polymerase II transcription factor activity				0	all_neural(89;0.0646)|Medulloblastoma(90;0.163)																	---	---	---	---
UGGT2	55757	broad.mit.edu	37	13	96665657	96665657	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:96665657G>A	uc001vmt.2	-	5	734	c.564C>T	c.(562-564)GCC>GCT	p.A188A	UGGT2_uc010afo.2_RNA|UGGT2_uc001vmv.2_Silent_p.A188A|UGGT2_uc010afp.2_Silent_p.A188A	NM_020121	NP_064506	Q9NYU1	UGGG2_HUMAN	UDP-glucose ceramide glucosyltransferase-like 2	188					post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine	endoplasmic reticulum lumen|ER-Golgi intermediate compartment	UDP-glucose:glycoprotein glucosyltransferase activity			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
OXGR1	27199	broad.mit.edu	37	13	97639911	97639911	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:97639911A>G	uc001vmx.1	-	4	347	c.103T>C	c.(103-105)TAC>CAC	p.Y35H	OXGR1_uc010afr.1_Missense_Mutation_p.Y35H	NM_080818	NP_543008	Q96P68	OXGR1_HUMAN	oxoglutarate (alpha-ketoglutarate) receptor 1	35	Helical; Name=1; (Potential).					integral to membrane|plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			ovary(1)|skin(1)	2	all_neural(89;0.0982)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.186)															---	---	---	---
TMTC4	84899	broad.mit.edu	37	13	101315320	101315320	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101315320G>A	uc001vou.2	-	4	553	c.393C>T	c.(391-393)GGC>GGT	p.G131G	TMTC4_uc001vot.2_Silent_p.G150G|TMTC4_uc010tja.1_Intron	NM_001079669	NP_001073137	Q5T4D3	TMTC4_HUMAN	transmembrane and tetratricopeptide repeat	131	Helical; (Potential).					integral to membrane	binding			ovary(2)|breast(1)	3	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)																	---	---	---	---
NALCN	259232	broad.mit.edu	37	13	101910909	101910909	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101910909G>A	uc001vox.1	-	11	1340	c.1151C>T	c.(1150-1152)TCC>TTC	p.S384F	NALCN_uc001voy.2_Missense_Mutation_p.S99F|NALCN_uc001voz.2_Missense_Mutation_p.S384F|NALCN_uc001vpa.2_Missense_Mutation_p.S384F	NM_052867	NP_443099	Q8IZF0	NALCN_HUMAN	voltage gated channel like 1	384	Helical; Name=S1 of repeat II; (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)																	---	---	---	---
C13orf27	93081	broad.mit.edu	37	13	103418898	103418898	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103418898T>C	uc001vpo.2	-	6	715	c.537A>G	c.(535-537)CAA>CAG	p.Q179Q	C13orf27_uc001vpn.2_Silent_p.Q138Q|C13orf27_uc001vpp.2_Silent_p.Q138Q	NM_138779	NP_620134	Q5JUR7	CM027_HUMAN	hypothetical protein LOC93081	179											0	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)																	---	---	---	---
ARHGEF7	8874	broad.mit.edu	37	13	111944543	111944543	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111944543G>A	uc001vrs.2	+	20	2526	c.2276G>A	c.(2275-2277)CGC>CAC	p.R759H	ARHGEF7_uc001vrr.2_Missense_Mutation_p.R738H|ARHGEF7_uc001vrt.2_Missense_Mutation_p.R709H|ARHGEF7_uc001vrv.3_Intron|ARHGEF7_uc001vrw.3_Intron|ARHGEF7_uc001vrx.3_Intron|ARHGEF7_uc010tjo.1_Intron|ARHGEF7_uc010tjp.1_Missense_Mutation_p.R503H|ARHGEF7_uc001vry.1_Missense_Mutation_p.R175H	NM_001113511	NP_001106983	Q14155	ARHG7_HUMAN	PAK-interacting exchange factor beta isoform c	759					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)															---	---	---	---
F7	2155	broad.mit.edu	37	13	113771857	113771857	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113771857C>T	uc001vsv.2	+	8	803	c.752C>T	c.(751-753)GCG>GTG	p.A251V	F7_uc001vsw.2_Missense_Mutation_p.A229V|F7_uc010tjt.1_Missense_Mutation_p.A182V	NM_000131	NP_000122	P08709	FA7_HUMAN	coagulation factor VII isoform a precursor	251	Peptidase S1.		A -> P (in FA7D).|A -> T (in FA7D).		anti-apoptosis|blood coagulation, extrinsic pathway|peptidyl-glutamic acid carboxylation|positive regulation of leukocyte chemotaxis|positive regulation of platelet-derived growth factor receptor signaling pathway|positive regulation of positive chemotaxis|positive regulation of protein kinase B signaling cascade|post-translational protein modification|proteolysis	endoplasmic reticulum lumen|Golgi lumen|plasma membrane	calcium ion binding|glycoprotein binding|serine-type endopeptidase activity				0	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;0.0364)|all_epithelial(44;0.0393)|Lung NSC(25;0.128)|Breast(118;0.188)	all cancers(43;0.0737)|Epithelial(84;0.213)|BRCA - Breast invasive adenocarcinoma(86;0.218)		Coagulation Factor IX(DB00100)|Coagulation factor VIIa(DB00036)|Menadione(DB00170)													---	---	---	---
PCID2	55795	broad.mit.edu	37	13	113854825	113854825	+	Silent	SNP	G	A	A	rs3751414		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113854825G>A	uc010tju.1	-	2	123	c.42C>T	c.(40-42)TAC>TAT	p.Y14Y	PCID2_uc010tjv.1_Silent_p.Y14Y|PCID2_uc010tjw.1_Silent_p.Y14Y|PCID2_uc001vte.2_Translation_Start_Site|PCID2_uc001vtd.2_Translation_Start_Site|PCID2_uc001vtf.2_Translation_Start_Site|PCID2_uc001vtg.1_RNA	NM_001127203	NP_001120675	Q5JVF3	PCID2_HUMAN	PCI domain containing 2	14					negative regulation of apoptosis|negative regulation of cysteine-type endopeptidase activity|positive regulation of mitotic cell cycle spindle assembly checkpoint|positive regulation of transcription, DNA-dependent|regulation of mRNA stability|spleen development		protein binding				0	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_lung(25;0.216)|all_epithelial(44;0.234)	all cancers(43;0.104)															---	---	---	---
GAS6	2621	broad.mit.edu	37	13	114535359	114535359	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114535359G>A	uc001vud.2	-	10	1209	c.1056C>T	c.(1054-1056)GCC>GCT	p.A352A	GAS6_uc001vug.2_Silent_p.A53A|GAS6_uc001vuf.2_Silent_p.A79A	NM_000820	NP_000811	Q14393	GAS6_HUMAN	growth arrest-specific 6 isoform 1 precursor	395	Laminin G-like 1.				cell proliferation|leukocyte migration|peptidyl-glutamic acid carboxylation|platelet activation|platelet degranulation|positive regulation of ERK1 and ERK2 cascade|positive regulation of fibroblast proliferation|post-translational protein modification|proteolysis|regulation of growth	endoplasmic reticulum lumen|extracellular space|Golgi lumen|platelet alpha granule lumen	calcium ion binding|receptor agonist activity			central_nervous_system(4)	4	Lung NSC(43;0.00976)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0176)|all_epithelial(44;0.0104)|all_lung(25;0.0249)|Lung NSC(25;0.0908)|Breast(118;0.188)																---	---	---	---
TMEM55B	90809	broad.mit.edu	37	14	20928912	20928912	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20928912C>T	uc001vxl.2	-	2	388	c.235G>A	c.(235-237)GCC>ACC	p.A79T	TMEM55B_uc001vxk.2_Missense_Mutation_p.A86T	NM_144568	NP_653169	Q86T03	TM55B_HUMAN	transmembrane protein 55B isoform 2	79	Pro-rich.					integral to membrane|late endosome membrane|lysosomal membrane	hydrolase activity				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;0.0224)|READ - Rectum adenocarcinoma(17;0.193)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	22740304	22740304	+	Intron	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22740304C>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_Intron|uc010ajk.1_Intron|uc001wdg.1_Intron|uc010ajl.1_Intron|uc001wdj.2_Intron|uc010ajo.1_Intron|uc010ajp.1_Intron|uc001wdn.2_Missense_Mutation_p.R70C					SubName: Full=Alpha-chain C region; Flags: Fragment;																														---	---	---	---
SLC7A7	9056	broad.mit.edu	37	14	23243309	23243309	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23243309G>A	uc001wgr.3	-	9	1400	c.1262C>T	c.(1261-1263)CCG>CTG	p.P421L	SLC7A7_uc001wgs.3_Missense_Mutation_p.P421L|SLC7A7_uc001wgt.3_Missense_Mutation_p.P421L|SLC7A7_uc001wgu.3_Missense_Mutation_p.P421L|SLC7A7_uc001wgv.3_Missense_Mutation_p.P421L	NM_003982	NP_003973	Q9UM01	YLAT1_HUMAN	solute carrier family 7 member 7	421	Helical; (Potential).				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)														---	---	---	---
EFS	10278	broad.mit.edu	37	14	23829153	23829153	+	Silent	SNP	C	T	T	rs115947674	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23829153C>T	uc001wjo.2	-	4	1142	c.534G>A	c.(532-534)CCG>CCA	p.P178P	EFS_uc001wjp.2_Silent_p.P85P|EFS_uc010tnm.1_Silent_p.P85P	NM_005864	NP_005855	O43281	EFS_HUMAN	embryonal Fyn-associated substrate isoform 1	178	Pro-rich.				cell adhesion|intracellular signal transduction	cytoplasm	SH3 domain binding			large_intestine(1)	1	all_cancers(95;7.12e-06)			GBM - Glioblastoma multiforme(265;0.00649)														---	---	---	---
MYH7	4625	broad.mit.edu	37	14	23886745	23886745	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23886745T>C	uc001wjx.2	-	31	4426	c.4320A>G	c.(4318-4320)GCA>GCG	p.A1440A		NM_000257	NP_000248	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	1440	Potential.				adult heart development|muscle filament sliding|regulation of heart rate|ventricular cardiac muscle tissue morphogenesis	focal adhesion|muscle myosin complex|myosin filament|nucleus|sarcomere	actin binding|actin-dependent ATPase activity|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(3)|skin(1)	4	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)														---	---	---	---
AP1G2	8906	broad.mit.edu	37	14	24032638	24032638	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24032638G>A	uc001wkl.2	-	14	1698	c.1361C>T	c.(1360-1362)GCC>GTC	p.A454V	AP1G2_uc001wkj.2_Missense_Mutation_p.A73V|AP1G2_uc001wkk.3_Missense_Mutation_p.A382V|AP1G2_uc001wkn.2_Missense_Mutation_p.A73V|uc001wko.1_Intron|AP1G2_uc001wkp.1_RNA|AP1G2_uc010tnp.1_Missense_Mutation_p.A454V	NM_003917	NP_003908	O75843	AP1G2_HUMAN	adaptor-related protein complex 1, gamma 2	454					interspecies interaction between organisms|intracellular protein transport|vesicle-mediated transport	AP-1 adaptor complex|endosome membrane	protein binding|protein transporter activity			ovary(1)	1	all_cancers(95;0.000251)			GBM - Glioblastoma multiforme(265;0.00672)												OREG0022605	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
CPNE6	9362	broad.mit.edu	37	14	24542713	24542713	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24542713G>T	uc001wll.2	+	3	273	c.174G>T	c.(172-174)GAG>GAT	p.E58D	CPNE6_uc010tnv.1_Missense_Mutation_p.E113D|CPNE6_uc001wlm.2_5'UTR|CPNE6_uc001wln.2_5'Flank	NM_006032	NP_006023	O95741	CPNE6_HUMAN	copine 6	58	C2 1.				lipid metabolic process|nervous system development|synaptic transmission|vesicle-mediated transport		calcium ion binding|transporter activity			skin(2)|ovary(1)	3				GBM - Glioblastoma multiforme(265;0.0184)														---	---	---	---
CPNE6	9362	broad.mit.edu	37	14	24542860	24542860	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24542860C>T	uc001wll.2	+	3	420	c.321C>T	c.(319-321)CTC>CTT	p.L107L	CPNE6_uc010tnv.1_Silent_p.L162L|CPNE6_uc001wlm.2_5'UTR|CPNE6_uc001wln.2_5'Flank	NM_006032	NP_006023	O95741	CPNE6_HUMAN	copine 6	107	C2 1.				lipid metabolic process|nervous system development|synaptic transmission|vesicle-mediated transport		calcium ion binding|transporter activity			skin(2)|ovary(1)	3				GBM - Glioblastoma multiforme(265;0.0184)														---	---	---	---
RNF31	55072	broad.mit.edu	37	14	24621133	24621133	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24621133C>T	uc001wmn.1	+	11	2311	c.2062C>T	c.(2062-2064)CGG>TGG	p.R688W	RNF31_uc001wml.1_Missense_Mutation_p.R537W|RNF31_uc001wmm.1_RNA|RNF31_uc010alg.1_Missense_Mutation_p.R447W|RNF31_uc001wmo.1_Missense_Mutation_p.R155W|RNF31_uc001wmp.2_RNA	NM_017999	NP_060469	Q96EP0	RNF31_HUMAN	ring finger protein 31	688					CD40 signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|protein linear polyubiquitination|T cell receptor signaling pathway	CD40 receptor complex|internal side of plasma membrane|LUBAC complex	ubiquitin binding|ubiquitin-protein ligase activity|zinc ion binding			large_intestine(1)|ovary(1)	2				GBM - Glioblastoma multiforme(265;0.00861)														---	---	---	---
TGM1	7051	broad.mit.edu	37	14	24731001	24731001	+	Silent	SNP	G	A	A	rs142338588		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24731001G>A	uc001wod.2	-	3	532	c.408C>T	c.(406-408)TAC>TAT	p.Y136Y	TGM1_uc010tog.1_Intron	NM_000359	NP_000350	P22735	TGM1_HUMAN	transglutaminase 1	136					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)													---	---	---	---
NFATC4	4776	broad.mit.edu	37	14	24838782	24838782	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24838782G>A	uc001wpc.2	+	2	499	c.178G>A	c.(178-180)GGT>AGT	p.G60S	NFATC4_uc010tok.1_Missense_Mutation_p.G123S|NFATC4_uc010tol.1_Missense_Mutation_p.G123S|NFATC4_uc010alr.2_Missense_Mutation_p.G123S|NFATC4_uc010als.2_Missense_Mutation_p.G73S|NFATC4_uc010tom.1_Missense_Mutation_p.G73S|NFATC4_uc010ton.1_Missense_Mutation_p.G73S|NFATC4_uc010too.1_Missense_Mutation_p.G73S|NFATC4_uc010alt.2_Missense_Mutation_p.G92S|NFATC4_uc010top.1_Missense_Mutation_p.G92S|NFATC4_uc010toq.1_Missense_Mutation_p.G92S|NFATC4_uc010alu.2_Missense_Mutation_p.G60S|NFATC4_uc010tor.1_Missense_Mutation_p.G60S|NFATC4_uc010tos.1_5'UTR|NFATC4_uc010tot.1_Missense_Mutation_p.G48S|NFATC4_uc010tou.1_5'UTR|NFATC4_uc010tov.1_Missense_Mutation_p.G48S|NFATC4_uc010tow.1_5'UTR|NFATC4_uc010alv.2_Missense_Mutation_p.G48S|NFATC4_uc010tox.1_5'UTR	NM_004554	NP_004545	Q14934	NFAC4_HUMAN	nuclear factor of activated T-cells,	60	Pro-rich.				cell differentiation|inflammatory response|transcription from RNA polymerase II promoter	cytoplasm|intermediate filament cytoskeleton|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(1)|central_nervous_system(1)|skin(1)	3				GBM - Glioblastoma multiforme(265;0.018)														---	---	---	---
STRN3	29966	broad.mit.edu	37	14	31364745	31364745	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31364745T>C	uc001wqu.2	-	18	2482	c.2266A>G	c.(2266-2268)ACA>GCA	p.T756A	STRN3_uc001wqv.2_Missense_Mutation_p.T672A|STRN3_uc010tpj.1_RNA	NM_001083893	NP_001077362	Q13033	STRN3_HUMAN	nuclear autoantigen isoform 1	756	WD 5.				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	31588960	31588960	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31588960C>T	uc001wrc.1	-	29	5840	c.5351G>A	c.(5350-5352)CGT>CAT	p.R1784H	HECTD1_uc001wra.1_5'UTR|HECTD1_uc001wrb.1_5'UTR|HECTD1_uc001wrd.1_Missense_Mutation_p.R1252H	NM_015382	NP_056197	Q9ULT8	HECD1_HUMAN	HECT domain containing 1	1784					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)														---	---	---	---
SSTR1	6751	broad.mit.edu	37	14	38679606	38679606	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:38679606C>A	uc001wul.1	+	3	1629	c.1012C>A	c.(1012-1014)CTA>ATA	p.L338I	SSTR1_uc010amu.1_Intron	NM_001049	NP_001040	P30872	SSR1_HUMAN	somatostatin receptor 1	338	Cytoplasmic (Potential).				digestion|G-protein signaling, coupled to cyclic nucleotide second messenger|negative regulation of cell proliferation|response to nutrient	integral to plasma membrane	somatostatin receptor activity			central_nervous_system(3)|ovary(1)|lung(1)	5	Hepatocellular(127;0.213)|Esophageal squamous(585;0.22)		Lung(238;3.93e-06)|LUAD - Lung adenocarcinoma(48;2.62e-05)|Epithelial(34;0.187)	GBM - Glioblastoma multiforme(112;0.00444)	Octreotide(DB00104)													---	---	---	---
SSTR1	6751	broad.mit.edu	37	14	38679687	38679687	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:38679687G>A	uc001wul.1	+	3	1710	c.1093G>A	c.(1093-1095)GTG>ATG	p.V365M	SSTR1_uc010amu.1_Intron	NM_001049	NP_001040	P30872	SSR1_HUMAN	somatostatin receptor 1	365	Cytoplasmic (Potential).				digestion|G-protein signaling, coupled to cyclic nucleotide second messenger|negative regulation of cell proliferation|response to nutrient	integral to plasma membrane	somatostatin receptor activity			central_nervous_system(3)|ovary(1)|lung(1)	5	Hepatocellular(127;0.213)|Esophageal squamous(585;0.22)		Lung(238;3.93e-06)|LUAD - Lung adenocarcinoma(48;2.62e-05)|Epithelial(34;0.187)	GBM - Glioblastoma multiforme(112;0.00444)	Octreotide(DB00104)													---	---	---	---
SIP1	8487	broad.mit.edu	37	14	39601231	39601231	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39601231C>T	uc001wuq.2	+	8	725	c.703C>T	c.(703-705)CGG>TGG	p.R235W	SIP1_uc001wur.2_Missense_Mutation_p.R235W|SIP1_uc001wus.2_Missense_Mutation_p.R220W|SIP1_uc010amx.2_RNA	NM_003616	NP_003607	O14893	GEMI2_HUMAN	SMN-interacting protein 1 isoform alpha	235					ncRNA metabolic process|spliceosomal snRNP assembly|spliceosome assembly	Cajal body|cytosol|spliceosomal complex	protein binding				0	Hepatocellular(127;0.213)		Lung(238;0.00047)|LUAD - Lung adenocarcinoma(48;0.000565)	GBM - Glioblastoma multiforme(112;0.0121)														---	---	---	---
FKBP3	2287	broad.mit.edu	37	14	45603570	45603570	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45603570C>A	uc010tqf.1	-	1	163	c.90G>T	c.(88-90)CAG>CAT	p.Q30H	FANCM_uc001wwc.2_5'Flank|FANCM_uc001wwd.3_5'Flank|FANCM_uc010anf.2_5'Flank	NM_002013	NP_002004	Q00688	FKBP3_HUMAN	FK506 binding protein 3, 25kDa	30					protein folding	membrane|nucleus	FK506 binding|peptidyl-prolyl cis-trans isomerase activity|receptor activity				0																		---	---	---	---
NIN	51199	broad.mit.edu	37	14	51208344	51208344	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51208344C>A	uc001wym.2	-	25	5595	c.5404G>T	c.(5404-5406)GAA>TAA	p.E1802*	NIN_uc001wyi.2_Nonsense_Mutation_p.E1802*|NIN_uc001wyj.2_RNA|NIN_uc001wyk.2_Nonsense_Mutation_p.E1089*|NIN_uc010tqp.1_Nonsense_Mutation_p.E1808*|NIN_uc001wyo.2_Nonsense_Mutation_p.E1802*|NIN_uc001wyn.2_5'Flank	NM_182946	NP_891991	Q8N4C6	NIN_HUMAN	ninein isoform 5	1802	Potential.				centrosome localization	centrosome|microtubule	calcium ion binding|GTP binding|protein binding			skin(3)|ovary(1)|kidney(1)|central_nervous_system(1)	6	all_epithelial(31;0.00244)|Breast(41;0.127)							T	PDGFRB	MPD								---	---	---	---
PYGL	5836	broad.mit.edu	37	14	51375597	51375597	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51375597A>G	uc001wyu.2	-	18	2381	c.2254T>C	c.(2254-2256)TCT>CCT	p.S752P	PYGL_uc010tqq.1_Missense_Mutation_p.S718P|PYGL_uc001wyv.2_Missense_Mutation_p.S426P|PYGL_uc001wyt.2_5'Flank	NM_002863	NP_002854	P06737	PYGL_HUMAN	liver glycogen phosphorylase isoform 1	752					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	p.S752F(1)		skin(1)	1	all_epithelial(31;0.00825)|Breast(41;0.148)				Adenosine monophosphate(DB00131)|Pyridoxal Phosphate(DB00114)|Riboflavin(DB00140)													---	---	---	---
NID2	22795	broad.mit.edu	37	14	52534592	52534592	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52534592G>A	uc001wzo.2	-	2	752	c.518C>T	c.(517-519)GCG>GTG	p.A173V	NID2_uc010tqs.1_Missense_Mutation_p.A173V|NID2_uc010tqt.1_Missense_Mutation_p.A173V|NID2_uc001wzp.2_Missense_Mutation_p.A173V	NM_007361	NP_031387	Q14112	NID2_HUMAN	nidogen 2 precursor	173	NIDO.					basement membrane	calcium ion binding|collagen binding			pancreas(2)|breast(2)|ovary(1)|liver(1)|skin(1)	7	Breast(41;0.0639)|all_epithelial(31;0.123)																	---	---	---	---
NID2	22795	broad.mit.edu	37	14	52535601	52535601	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52535601G>A	uc001wzo.2	-	1	346	c.112C>T	c.(112-114)CCA>TCA	p.P38S	NID2_uc010tqs.1_Missense_Mutation_p.P38S|NID2_uc010tqt.1_Missense_Mutation_p.P38S|NID2_uc001wzp.2_Missense_Mutation_p.P38S	NM_007361	NP_031387	Q14112	NID2_HUMAN	nidogen 2 precursor	38						basement membrane	calcium ion binding|collagen binding			pancreas(2)|breast(2)|ovary(1)|liver(1)|skin(1)	7	Breast(41;0.0639)|all_epithelial(31;0.123)																	---	---	---	---
PTGDR	5729	broad.mit.edu	37	14	52735263	52735263	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52735263C>T	uc001wzq.2	+	1	833	c.731C>T	c.(730-732)GCC>GTC	p.A244V		NM_000953	NP_000944	Q13258	PD2R_HUMAN	prostaglandin D2 receptor	244	Cytoplasmic (Potential).					integral to membrane|plasma membrane	prostaglandin D receptor activity|protein binding			ovary(1)|lung(1)|central_nervous_system(1)|skin(1)	4	Breast(41;0.0639)|all_epithelial(31;0.0887)				Nedocromil(DB00716)													---	---	---	---
DDHD1	80821	broad.mit.edu	37	14	53619158	53619158	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53619158C>T	uc001xai.2	-	1	889	c.659G>A	c.(658-660)GGC>GAC	p.G220D	DDHD1_uc001xaj.2_Missense_Mutation_p.G220D|DDHD1_uc001xah.2_Missense_Mutation_p.G220D	NM_001160148	NP_001153620	Q8NEL9	DDHD1_HUMAN	DDHD domain containing 1 isoform c	220					lipid catabolic process	cytoplasm	hydrolase activity|metal ion binding			ovary(2)	2	Breast(41;0.037)																	---	---	---	---
KIAA0831	22863	broad.mit.edu	37	14	55848756	55848756	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55848756C>T	uc001xbx.1	-	6	837	c.801G>A	c.(799-801)TGG>TGA	p.W267*	FBXO34_uc001xbv.2_Intron|KIAA0831_uc001xbw.1_Nonsense_Mutation_p.W154*	NM_014924	NP_055739	Q6ZNE5	BAKOR_HUMAN	Barkor	267					autophagic vacuole assembly|positive regulation of autophagy	autophagic vacuole|endoplasmic reticulum|pre-autophagosomal structure membrane	protein binding				0																		---	---	---	---
EXOC5	10640	broad.mit.edu	37	14	57676280	57676280	+	Intron	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:57676280C>T	uc001xct.2	-						EXOC5_uc001xcs.2_Intron|EXOC5_uc010trg.1_Intron|EXOC5_uc010trh.1_Intron	NM_006544	NP_006535			SEC10 protein						exocytosis|post-Golgi vesicle-mediated transport|protein transport|vesicle docking	cytoplasm				ovary(2)|breast(1)	3																		---	---	---	---
C14orf37	145407	broad.mit.edu	37	14	58563560	58563560	+	Silent	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58563560G>T	uc001xdc.2	-	5	2082	c.1971C>A	c.(1969-1971)ACC>ACA	p.T657T	C14orf37_uc010tro.1_Silent_p.T695T|C14orf37_uc001xdd.2_Silent_p.T657T	NM_001001872	NP_001001872	Q86TY3	CN037_HUMAN	hypothetical protein LOC145407 precursor	657	Extracellular (Potential).					integral to membrane	binding				0																		---	---	---	---
DACT1	51339	broad.mit.edu	37	14	59108339	59108339	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:59108339G>T	uc001xdw.2	+	3	672	c.508G>T	c.(508-510)GGA>TGA	p.G170*	DACT1_uc010trv.1_Translation_Start_Site|DACT1_uc001xdx.2_Nonsense_Mutation_p.G170*|DACT1_uc010trw.1_Translation_Start_Site	NM_016651	NP_057735	Q9NYF0	DACT1_HUMAN	dapper 1 isoform 1	170					multicellular organismal development|Wnt receptor signaling pathway	cytoplasm|nucleus				large_intestine(2)|lung(2)|ovary(1)	5																		---	---	---	---
C14orf50	145376	broad.mit.edu	37	14	65053973	65053973	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65053973A>G	uc001xhl.1	+	10	869	c.773A>G	c.(772-774)GAG>GGG	p.E258G	C14orf50_uc001xhm.1_5'UTR	NM_172365	NP_758953	Q96LQ0	CN050_HUMAN	hypothetical protein LOC145376	258										skin(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.00382)|all cancers(60;0.00427)|BRCA - Breast invasive adenocarcinoma(234;0.0488)														---	---	---	---
FUT8	2530	broad.mit.edu	37	14	66082939	66082939	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:66082939G>A	uc001xin.2	+	5	1527	c.330G>A	c.(328-330)AAG>AAA	p.K110K	FUT8_uc001xio.2_Silent_p.K110K|FUT8_uc010tsp.1_5'UTR|FUT8_uc001xir.3_RNA|FUT8_uc001xip.2_Silent_p.K110K|FUT8_uc001xiq.2_5'UTR	NM_178155	NP_835368	Q9BYC5	FUT8_HUMAN	fucosyltransferase 8 isoform a	110	Lumenal (Potential).				in utero embryonic development|L-fucose catabolic process|N-glycan processing|oligosaccharide biosynthetic process|post-translational protein modification|protein glycosylation in Golgi|protein N-linked glycosylation via asparagine	Golgi cisterna membrane|integral to membrane	glycoprotein 6-alpha-L-fucosyltransferase activity|SH3 domain binding			ovary(1)	1				all cancers(60;0.00109)|OV - Ovarian serous cystadenocarcinoma(108;0.00242)|BRCA - Breast invasive adenocarcinoma(234;0.0114)														---	---	---	---
GPHN	10243	broad.mit.edu	37	14	67431987	67431987	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:67431987C>T	uc001xiy.2	+	8	1930	c.809C>T	c.(808-810)TCG>TTG	p.S270L	GPHN_uc001xiw.2_Missense_Mutation_p.S285L|GPHN_uc001xix.2_Missense_Mutation_p.S303L|GPHN_uc010tss.1_Missense_Mutation_p.S283L|GPHN_uc010tst.1_Missense_Mutation_p.S239L|GPHN_uc010tsu.1_Missense_Mutation_p.S193L	NM_001024218	NP_001019389	Q9NQX3	GEPH_HUMAN	gephyrin isoform 2	270	Interaction with GABARAP (By similarity).				Mo-molybdopterin cofactor biosynthetic process|water-soluble vitamin metabolic process	cell junction|cytoplasm|cytoskeleton|postsynaptic membrane	ATP binding|metal ion binding|nucleotidyltransferase activity			ovary(2)	2		all_cancers(7;0.0476)|all_hematologic(31;0.0116)		Epithelial(1;1.73e-08)|all cancers(60;3.15e-07)|OV - Ovarian serous cystadenocarcinoma(108;0.000275)|BRCA - Breast invasive adenocarcinoma(234;0.00323)|Colorectal(3;0.0938)|KIRC - Kidney renal clear cell carcinoma(182;0.184)				T	MLL	AL								---	---	---	---
GPHN	10243	broad.mit.edu	37	14	67576927	67576927	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:67576927A>G	uc001xiy.2	+	13	2386	c.1265A>G	c.(1264-1266)GAT>GGT	p.D422G	GPHN_uc001xix.2_Missense_Mutation_p.D455G|GPHN_uc010tss.1_Missense_Mutation_p.D468G|GPHN_uc010tst.1_Missense_Mutation_p.D391G|GPHN_uc010tsu.1_Missense_Mutation_p.D345G	NM_001024218	NP_001019389	Q9NQX3	GEPH_HUMAN	gephyrin isoform 2	422	MPT adenylyltransferase.				Mo-molybdopterin cofactor biosynthetic process|water-soluble vitamin metabolic process	cell junction|cytoplasm|cytoskeleton|postsynaptic membrane	ATP binding|metal ion binding|nucleotidyltransferase activity			ovary(2)	2		all_cancers(7;0.0476)|all_hematologic(31;0.0116)		Epithelial(1;1.73e-08)|all cancers(60;3.15e-07)|OV - Ovarian serous cystadenocarcinoma(108;0.000275)|BRCA - Breast invasive adenocarcinoma(234;0.00323)|Colorectal(3;0.0938)|KIRC - Kidney renal clear cell carcinoma(182;0.184)				T	MLL	AL								---	---	---	---
MAP3K9	4293	broad.mit.edu	37	14	71209080	71209080	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71209080T>C	uc001xmm.2	-	6	1555	c.1555A>G	c.(1555-1557)AGC>GGC	p.S519G	MAP3K9_uc010ttk.1_Missense_Mutation_p.S256G|MAP3K9_uc001xmk.2_Missense_Mutation_p.S213G|MAP3K9_uc001xml.2_Missense_Mutation_p.S519G	NM_033141	NP_149132	P80192	M3K9_HUMAN	mitogen-activated protein kinase kinase kinase	519				KLKDGNRISLPSDFQHKFTVQASPT -> AQPVLPFPHGHS RCPGGTGSSWGGQ (in Ref. 4).	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)														---	---	---	---
LTBP2	4053	broad.mit.edu	37	14	75022341	75022341	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75022341G>T	uc001xqa.2	-	4	1273	c.886C>A	c.(886-888)CGC>AGC	p.R296S		NM_000428	NP_000419	Q14767	LTBP2_HUMAN	latent transforming growth factor beta binding	296					protein secretion|protein targeting|transforming growth factor beta receptor signaling pathway	extracellular space|proteinaceous extracellular matrix	calcium ion binding|growth factor binding			liver(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(234;0.00219)|READ - Rectum adenocarcinoma(1;0.0649)														---	---	---	---
YLPM1	56252	broad.mit.edu	37	14	75277113	75277113	+	Silent	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75277113C>A	uc001xqj.3	+	9	5342	c.5218C>A	c.(5218-5220)CGA>AGA	p.R1740R	YLPM1_uc001xql.3_RNA|YLPM1_uc001xqm.1_Silent_p.R223R	NM_019589	NP_062535	P49750	YLPM1_HUMAN	YLP motif containing 1	1545	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)														---	---	---	---
VIPAR	63894	broad.mit.edu	37	14	77895366	77895366	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77895366G>A	uc001xtt.1	-	19	1677	c.1339C>T	c.(1339-1341)CAT>TAT	p.H447Y	VIPAR_uc001xtu.1_Missense_Mutation_p.H447Y|VIPAR_uc010tvj.1_Missense_Mutation_p.H398Y|VIPAR_uc001xtv.1_Missense_Mutation_p.H447Y	NM_022067	NP_071350	Q9H9C1	VIPAR_HUMAN	hypothetical protein LOC63894	447					endosome to lysosome transport|intracellular protein transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent	early endosome|late endosome|recycling endosome	protein binding			central_nervous_system(1)	1																		---	---	---	---
VIPAR	63894	broad.mit.edu	37	14	77900283	77900283	+	Intron	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77900283C>T	uc001xtt.1	-						VIPAR_uc001xtu.1_Intron|VIPAR_uc010tvj.1_Intron|VIPAR_uc001xtv.1_Intron	NM_022067	NP_071350			hypothetical protein LOC63894						endosome to lysosome transport|intracellular protein transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent	early endosome|late endosome|recycling endosome	protein binding			central_nervous_system(1)	1																		---	---	---	---
NRXN3	9369	broad.mit.edu	37	14	79933651	79933651	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:79933651G>A	uc001xun.2	+	13	2722	c.2231G>A	c.(2230-2232)CGC>CAC	p.R744H	NRXN3_uc001xum.1_RNA|NRXN3_uc001xup.2_RNA|NRXN3_uc001xuq.2_Missense_Mutation_p.R112H|NRXN3_uc010asw.2_Missense_Mutation_p.R112H|NRXN3_uc001xur.3_Missense_Mutation_p.R112H	NM_004796	NP_004787	Q9Y4C0	NRX3A_HUMAN	neurexin 3 isoform 1 precursor	1117	Extracellular (Potential).|Laminin G-like 6.				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)														---	---	---	---
SMEK1	55671	broad.mit.edu	37	14	91942843	91942843	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91942843G>A	uc001xzn.2	-	6	1841	c.1019C>T	c.(1018-1020)GCG>GTG	p.A340V	SMEK1_uc001xzm.2_Missense_Mutation_p.A340V|SMEK1_uc001xzo.2_Missense_Mutation_p.A340V|SMEK1_uc010atz.2_Missense_Mutation_p.A101V|SMEK1_uc001xzp.1_RNA|SMEK1_uc001xzq.1_Missense_Mutation_p.A216V	NM_032560	NP_115949	Q6IN85	P4R3A_HUMAN	SMEK homolog 1, suppressor of mek1	340						microtubule organizing center|nucleus	protein binding				0		all_cancers(154;0.0691)|all_epithelial(191;0.219)		COAD - Colon adenocarcinoma(157;0.221)														---	---	---	---
GOLGA5	9950	broad.mit.edu	37	14	93299632	93299632	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93299632G>A	uc001yaz.1	+	10	2067	c.1885G>A	c.(1885-1887)GCC>ACC	p.A629T	GOLGA5_uc001yba.1_Missense_Mutation_p.A26T	NM_005113	NP_005104	Q8TBA6	GOGA5_HUMAN	Golgi autoantigen, golgin subfamily a, 5	629	Cytoplasmic (Potential).|Potential.				Golgi organization	cis-Golgi network|integral to membrane	ATP binding|protein homodimerization activity|protein tyrosine kinase activity|Rab GTPase binding			ovary(2)|lung(1)	3		all_cancers(154;0.0934)		COAD - Colon adenocarcinoma(157;0.222)				T	RET	papillary thyroid								---	---	---	---
OTUB2	78990	broad.mit.edu	37	14	94510971	94510971	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94510971G>A	uc001yci.2	+	5	503	c.343G>A	c.(343-345)GTG>ATG	p.V115M		NM_023112	NP_075601	Q96DC9	OTUB2_HUMAN	OTU domain, ubiquitin aldehyde binding 2	115	OTU.				cellular amino acid metabolic process|protein K48-linked deubiquitination|protein K63-linked deubiquitination		omega peptidase activity|protein binding|ubiquitin-specific protease activity				0		all_cancers(154;0.12)		Epithelial(152;0.124)|all cancers(159;0.21)|COAD - Colon adenocarcinoma(157;0.215)														---	---	---	---
SERPINA4	5267	broad.mit.edu	37	14	95029814	95029814	+	5'UTR	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95029814C>T	uc001ydk.2	+	2					SERPINA4_uc010avd.2_Nonsense_Mutation_p.Q36*|SERPINA4_uc001ydl.2_5'UTR	NM_006215	NP_006206			serine (or cysteine) proteinase inhibitor, clade						regulation of proteolysis	extracellular space	serine-type endopeptidase inhibitor activity			ovary(3)|skin(1)	4				COAD - Colon adenocarcinoma(157;0.211)														---	---	---	---
VRK1	7443	broad.mit.edu	37	14	97326912	97326912	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:97326912T>C	uc001yft.2	+	11	1014	c.908T>C	c.(907-909)ATG>ACG	p.M303T		NM_003384	NP_003375	Q99986	VRK1_HUMAN	vaccinia related kinase 1	303	Protein kinase.					cytoplasm|nucleolus	ATP binding|protein binding|protein serine/threonine kinase activity			large_intestine(1)|stomach(1)	2		Melanoma(154;0.155)		COAD - Colon adenocarcinoma(157;0.234)														---	---	---	---
EVL	51466	broad.mit.edu	37	14	100551127	100551127	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100551127A>G	uc001ygt.2	+	2	348	c.109A>G	c.(109-111)AAC>GAC	p.N37D	EVL_uc001ygv.2_Missense_Mutation_p.N43D|EVL_uc001ygu.2_Missense_Mutation_p.N39D|EVL_uc010avu.2_5'UTR	NM_016337	NP_057421	Q9UI08	EVL_HUMAN	Enah/Vasp-like	37	WH1.				actin polymerization or depolymerization|axon guidance|cell surface receptor linked signaling pathway|organ morphogenesis	cytoskeleton|cytosol|focal adhesion|lamellipodium	actin binding|profilin binding|SH3 domain binding			large_intestine(2)|ovary(1)	3		Melanoma(154;0.152)																---	---	---	---
DYNC1H1	1778	broad.mit.edu	37	14	102471206	102471206	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102471206G>A	uc001yks.2	+	25	5321	c.5157G>A	c.(5155-5157)GAG>GAA	p.E1719E		NM_001376	NP_001367	Q14204	DYHC1_HUMAN	cytoplasmic dynein 1 heavy chain 1	1719	Stem (By similarity).				cytoplasmic mRNA processing body assembly|G2/M transition of mitotic cell cycle|microtubule-based movement|mitotic spindle organization|stress granule assembly|transport	centrosome|cytoplasmic dynein complex|cytosol|Golgi apparatus|microtubule	ATP binding|ATPase activity, coupled|microtubule motor activity|protein binding			ovary(7)|central_nervous_system(2)|pancreas(1)	10																		---	---	---	---
DYNC1H1	1778	broad.mit.edu	37	14	102494049	102494049	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102494049G>A	uc001yks.2	+	47	9306	c.9142G>A	c.(9142-9144)GAG>AAG	p.E3048K		NM_001376	NP_001367	Q14204	DYHC1_HUMAN	cytoplasmic dynein 1 heavy chain 1	3048	AAA 4 (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																		---	---	---	---
TECPR2	9895	broad.mit.edu	37	14	102843129	102843129	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102843129C>T	uc001ylw.1	+	2	219	c.71C>T	c.(70-72)CCG>CTG	p.P24L	TECPR2_uc010txw.1_Missense_Mutation_p.P24L|TECPR2_uc010awl.2_Missense_Mutation_p.P24L|TECPR2_uc010txx.1_Nonsense_Mutation_p.R4*	NM_014844	NP_055659	O15040	TCPR2_HUMAN	tectonin beta-propeller repeat containing 2	24							protein binding			lung(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
EIF5	1983	broad.mit.edu	37	14	103806054	103806054	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103806054C>T	uc001ymq.2	+	10	1507	c.985C>T	c.(985-987)CTT>TTT	p.L329F	EIF5_uc001ymr.2_Missense_Mutation_p.L329F|EIF5_uc001yms.2_Missense_Mutation_p.L329F|EIF5_uc001ymt.2_Missense_Mutation_p.L329F|EIF5_uc001ymu.2_Missense_Mutation_p.L329F	NM_001969	NP_001960	P55010	IF5_HUMAN	eukaryotic translation initiation factor 5	329	W2.				regulation of translational initiation|RNA metabolic process	cytosol	GTP binding|GTPase activity|translation initiation factor activity			pancreas(1)|breast(1)|skin(1)	3		Melanoma(154;0.155)	Epithelial(46;0.182)															---	---	---	---
TRMT61A	115708	broad.mit.edu	37	14	104000996	104000996	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104000996G>T	uc001yng.2	+	4	827	c.708G>T	c.(706-708)CAG>CAT	p.Q236H	TRMT61A_uc010aws.2_Missense_Mutation_p.G21C	NM_152307	NP_689520	Q96FX7	TRM61_HUMAN	tRNA(m1A58)-methyltransferase subunit TRM61	236						nucleus	protein binding|tRNA (adenine-N1-)-methyltransferase activity				0																		---	---	---	---
AHNAK2	113146	broad.mit.edu	37	14	105409290	105409290	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105409290G>A	uc010axc.1	-	7	12618	c.12498C>T	c.(12496-12498)GAC>GAT	p.D4166D	AHNAK2_uc001ypx.2_Silent_p.D4066D	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	4166						nucleus				ovary(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)															---	---	---	---
AHNAK2	113146	broad.mit.edu	37	14	105415997	105415997	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105415997C>T	uc010axc.1	-	7	5911	c.5791G>A	c.(5791-5793)GCC>ACC	p.A1931T	AHNAK2_uc001ypx.2_Missense_Mutation_p.A1831T	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1931						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)															---	---	---	---
ADAM6	8755	broad.mit.edu	37	14	106994115	106994115	+	RNA	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106994115A>G	uc010tyt.1	-	187		c.8332T>C								Parts of antibodies, mostly variable regions.												0																		---	---	---	---
CYFIP1	23191	broad.mit.edu	37	15	22955256	22955256	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22955256C>T	uc001yus.2	+	15	1754	c.1650C>T	c.(1648-1650)CGC>CGT	p.R550R	CYFIP1_uc001yut.2_Silent_p.R550R|CYFIP1_uc010aya.1_Silent_p.R578R|CYFIP1_uc001yuu.2_5'Flank	NM_014608	NP_055423	Q7L576	CYFP1_HUMAN	cytoplasmic FMR1 interacting protein 1 isoform	550					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)														---	---	---	---
MKRN3	7681	broad.mit.edu	37	15	23811639	23811639	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23811639T>C	uc001ywh.3	+	1	1186	c.710T>C	c.(709-711)GTG>GCG	p.V237A	MKRN3_uc001ywi.2_Intron|MKRN3_uc010ayi.1_Missense_Mutation_p.V237A	NM_005664	NP_005655	Q13064	MKRN3_HUMAN	makorin ring finger protein 3	237						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)														---	---	---	---
MAGEL2	54551	broad.mit.edu	37	15	23889460	23889460	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23889460G>A	uc001ywj.3	-	1	1716	c.1621C>T	c.(1621-1623)CGG>TGG	p.R541W		NM_019066	NP_061939			MAGE-like protein 2												0		all_cancers(20;1.78e-24)|all_epithelial(15;7.75e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000625)|Colorectal(260;0.14)		all cancers(64;1.84e-06)|Epithelial(43;1.2e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00177)														---	---	---	---
SNRPN	6638	broad.mit.edu	37	15	25222053	25222053	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25222053A>G	uc001ywp.1	+	10	1187	c.297A>G	c.(295-297)GGA>GGG	p.G99G	SNRPN_uc001ywq.1_Silent_p.G99G|SNRPN_uc001ywr.1_Silent_p.G99G|SNRPN_uc001yws.1_Silent_p.G99G|SNRPN_uc001ywt.1_Silent_p.G99G|SNRPN_uc001ywv.1_Silent_p.G102G|SNRPN_uc001yww.1_Silent_p.G99G|SNRPN_uc001ywx.1_Silent_p.G99G|SNRPN_uc001ywz.1_Intron|PAR-SN_uc001yxa.1_Intron|SNRPN_uc001ywy.1_3'UTR	NM_022807	NP_073718	P63162	RSMN_HUMAN	small nuclear ribonucleoprotein polypeptide N	99					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				---	---	---	---
HERC2	8924	broad.mit.edu	37	15	28357109	28357109	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28357109G>A	uc001zbj.2	-	93	14411	c.14305C>T	c.(14305-14307)CCC>TCC	p.P4769S	HERC2_uc001zbi.2_Missense_Mutation_p.P458S	NM_004667	NP_004658	O95714	HERC2_HUMAN	hect domain and RLD 2	4769	HECT.				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	28366563	28366563	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28366563G>A	uc001zbj.2	-	86	13307	c.13201C>T	c.(13201-13203)CGG>TGG	p.R4401W		NM_004667	NP_004658	O95714	HERC2_HUMAN	hect domain and RLD 2	4401					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	28538035	28538035	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28538035T>C	uc001zbj.2	-	4	427	c.321A>G	c.(319-321)CCA>CCG	p.P107P	HERC2_uc001zbl.1_5'UTR	NM_004667	NP_004658	O95714	HERC2_HUMAN	hect domain and RLD 2	107					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)														---	---	---	---
FMN1	342184	broad.mit.edu	37	15	33192305	33192305	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33192305C>T	uc001zhf.3	-	10	2860	c.2860G>A	c.(2860-2862)GTG>ATG	p.V954M		NM_001103184	NP_001096654	Q68DA7	FMN1_HUMAN	formin 1	1177	FH2.				actin cytoskeleton organization	actin cytoskeleton|adherens junction|cytoplasm|nucleus	actin binding			ovary(1)	1		all_lung(180;1.14e-07)		all cancers(64;3.05e-15)|Epithelial(43;1.67e-10)|GBM - Glioblastoma multiforme(186;4.95e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0262)														---	---	---	---
PGBD4	161779	broad.mit.edu	37	15	34396276	34396276	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34396276C>T	uc001zho.2	+	1	2003	c.1544C>T	c.(1543-1545)ACA>ATA	p.T515I	C15orf24_uc001zhm.2_5'Flank|C15orf24_uc001zhn.2_5'Flank	NM_152595	NP_689808	Q96DM1	PGBD4_HUMAN	piggyBac transposable element derived 4	515											0		all_lung(180;1.76e-08)		all cancers(64;1.22e-17)|GBM - Glioblastoma multiforme(113;1.78e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0242)														---	---	---	---
SPRED1	161742	broad.mit.edu	37	15	38641674	38641674	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38641674G>A	uc001zka.3	+	6	969	c.634G>A	c.(634-636)GTA>ATA	p.V212I		NM_152594	NP_689807	Q7Z699	SPRE1_HUMAN	sprouty-related protein 1 with EVH-1 domain	212					inactivation of MAPK activity|multicellular organismal development	caveola|nucleus	stem cell factor receptor binding			ovary(2)|lung(2)|skin(1)	5		all_cancers(109;4.88e-13)|all_epithelial(112;1.83e-11)|Lung NSC(122;2.21e-09)|all_lung(180;4.64e-08)|Melanoma(134;0.091)		GBM - Glioblastoma multiforme(113;2.41e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0244)										Legius_syndrome				---	---	---	---
BAHD1	22893	broad.mit.edu	37	15	40758302	40758302	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40758302C>T	uc001zlu.2	+	7	2387	c.2316C>T	c.(2314-2316)CAC>CAT	p.H772H	BAHD1_uc001zlt.2_Silent_p.H771H|BAHD1_uc010bbp.1_Silent_p.H768H|BAHD1_uc001zlv.2_Silent_p.H769H	NM_014952	NP_055767	Q8TBE0	BAHD1_HUMAN	bromo adjacent homology domain containing 1	772	BAH.				heterochromatin formation|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromatin silencing complex|chromosome	chromatin binding|DNA binding|protein binding				0		all_cancers(109;8.28e-19)|all_epithelial(112;2.64e-15)|Lung NSC(122;5.14e-11)|all_lung(180;1.27e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;3.46e-06)|BRCA - Breast invasive adenocarcinoma(123;0.08)														---	---	---	---
RAD51	5888	broad.mit.edu	37	15	41021004	41021004	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41021004C>T	uc001zmi.3	+	7	925	c.626C>T	c.(625-627)GCC>GTC	p.A209V	RAD51_uc010bbw.2_Missense_Mutation_p.A209V|RAD51_uc010bbx.2_Missense_Mutation_p.A210V|RAD51_uc001zmk.3_RNA|RAD51_uc001zml.3_Missense_Mutation_p.A210V	NM_002875	NP_002866	Q06609	RAD51_HUMAN	RAD51 homolog protein isoform 1	209	Interaction with PALB2.				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					---	---	---	---
RPAP1	26015	broad.mit.edu	37	15	41820101	41820101	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41820101G>A	uc001zod.2	-	11	1509	c.1385C>T	c.(1384-1386)GCC>GTC	p.A462V		NM_015540	NP_056355	Q9BWH6	RPAP1_HUMAN	RNA polymerase II associated protein 1	462						nucleus	DNA binding|DNA-directed RNA polymerase activity			large_intestine(1)	1		all_cancers(109;6.59e-20)|all_epithelial(112;7.67e-17)|Lung NSC(122;5.34e-11)|all_lung(180;4.17e-10)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		OV - Ovarian serous cystadenocarcinoma(18;2.84e-17)|GBM - Glioblastoma multiforme(113;1.68e-06)|Colorectal(105;0.0163)|BRCA - Breast invasive adenocarcinoma(123;0.117)														---	---	---	---
ZFP106	64397	broad.mit.edu	37	15	42743354	42743354	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42743354C>T	uc001zpw.2	-	2	1382	c.1047G>A	c.(1045-1047)TGG>TGA	p.W349*	ZFP106_uc001zpu.2_5'Flank|ZFP106_uc001zpv.2_Intron|ZFP106_uc001zpx.2_Intron|ZFP106_uc010udh.1_Nonsense_Mutation_p.W132*|ZFP106_uc001zpy.1_Nonsense_Mutation_p.W372*	NM_022473	NP_071918	Q9H2Y7	ZF106_HUMAN	zinc finger protein 106 homolog	349						nucleolus	zinc ion binding			central_nervous_system(2)|ovary(1)	3		all_cancers(109;1.63e-12)|all_epithelial(112;3.97e-11)|Lung NSC(122;2.04e-07)|all_lung(180;8.31e-07)|Melanoma(134;0.091)		GBM - Glioblastoma multiforme(94;8.6e-07)														---	---	---	---
TTBK2	146057	broad.mit.edu	37	15	43093562	43093562	+	Intron	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43093562C>T	uc001zqo.2	-						TTBK2_uc010bcy.2_Intron|TTBK2_uc001zqp.2_Intron|TTBK2_uc010bcz.1_Intron	NM_173500	NP_775771			tau tubulin kinase 2						cell death		ATP binding|protein serine/threonine kinase activity			ovary(2)|lung(2)|stomach(1)|pancreas(1)|skin(1)	7		all_cancers(109;6.11e-16)|all_epithelial(112;5.5e-14)|Lung NSC(122;1.76e-08)|all_lung(180;6.04e-08)|Melanoma(134;0.0179)|Colorectal(260;0.216)		GBM - Glioblastoma multiforme(94;3.23e-07)														---	---	---	---
EPB42	2038	broad.mit.edu	37	15	43513034	43513034	+	5'UTR	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43513034C>T	uc001zra.3	-	1					EPB42_uc001zrb.3_5'UTR|EPB42_uc010udm.1_5'UTR	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)														---	---	---	---
TGM5	9333	broad.mit.edu	37	15	43533132	43533132	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43533132C>T	uc001zrd.1	-	7	927	c.919G>A	c.(919-921)GAT>AAT	p.D307N	TGM5_uc001zrc.1_5'Flank|TGM5_uc001zre.1_Missense_Mutation_p.D225N	NM_201631	NP_963925	O43548	TGM5_HUMAN	transglutaminase 5 isoform 1	307					epidermis development|peptide cross-linking	cytoplasm	acyltransferase activity|metal ion binding|protein-glutamine gamma-glutamyltransferase activity			central_nervous_system(1)	1		all_cancers(109;1.37e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.216)		GBM - Glioblastoma multiforme(94;4e-07)	L-Glutamine(DB00130)													---	---	---	---
TUBGCP4	27229	broad.mit.edu	37	15	43677988	43677988	+	Splice_Site	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43677988G>A	uc001zro.2	+	8	964	c.724_splice	c.e8-1	p.R242_splice	TUBGCP4_uc001zrn.2_Splice_Site_p.R242_splice|TUBGCP4_uc010bdh.2_Splice_Site	NM_014444	NP_055259			tubulin, gamma complex associated protein 4						G2/M transition of mitotic cell cycle|microtubule nucleation|protein complex assembly	centrosome|cytosol|gamma-tubulin ring complex|microtubule|spindle pole	structural constituent of cytoskeleton			ovary(3)	3		all_cancers(109;1.27e-10)|all_epithelial(112;4.82e-09)|Lung NSC(122;1.72e-06)|all_lung(180;1.59e-05)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;3.53e-07)														---	---	---	---
TP53BP1	7158	broad.mit.edu	37	15	43707815	43707815	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43707815C>T	uc001zrs.2	-	23	5199	c.5051G>A	c.(5050-5052)CGC>CAC	p.R1684H	TP53BP1_uc010udp.1_Missense_Mutation_p.R1684H|TP53BP1_uc001zrq.3_Missense_Mutation_p.R1689H|TP53BP1_uc001zrr.3_Missense_Mutation_p.R1689H|TP53BP1_uc010udq.1_Missense_Mutation_p.R1689H|TP53BP1_uc001zrp.2_Missense_Mutation_p.R101H	NM_005657	NP_005648	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1 isoform 3	1684					double-strand break repair via homologous recombination|positive regulation of transcription from RNA polymerase II promoter	condensed chromosome kinetochore|cytoplasm|nucleoplasm	p53 binding|RNA polymerase II activating transcription factor binding|RNA polymerase II transcription cofactor activity			ovary(2)|skin(2)|large_intestine(1)|pancreas(1)|kidney(1)	7		all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;1.59e-06)									Direct_reversal_of_damage|Other_conserved_DNA_damage_response_genes					---	---	---	---
SPG11	80208	broad.mit.edu	37	15	44951445	44951445	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44951445A>G	uc001ztx.2	-	3	530	c.499T>C	c.(499-501)TTC>CTC	p.F167L	SPG11_uc010ueh.1_Missense_Mutation_p.F167L|SPG11_uc010uei.1_Missense_Mutation_p.F167L|SPG11_uc001zua.1_Missense_Mutation_p.F167L	NM_025137	NP_079413	Q96JI7	SPTCS_HUMAN	spatacsin isoform 1	167	Extracellular (Potential).				cell death	cytosol|integral to membrane|nucleus	protein binding			ovary(4)|skin(1)	5		all_cancers(109;1.29e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;1.34e-07)|all_lung(180;1.21e-06)|Melanoma(134;0.0122)		all cancers(107;2.93e-22)|GBM - Glioblastoma multiforme(94;1.55e-06)|COAD - Colon adenocarcinoma(120;0.0432)|Colorectal(105;0.0484)|Lung(196;0.104)|LUSC - Lung squamous cell carcinoma(244;0.214)														---	---	---	---
DUOX2	50506	broad.mit.edu	37	15	45387642	45387642	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45387642C>T	uc010bea.2	-	31	4435	c.4232G>A	c.(4231-4233)TGT>TAT	p.C1411Y	DUOX2_uc001zun.2_Missense_Mutation_p.C1411Y	NM_014080	NP_054799	Q9NRD8	DUOX2_HUMAN	dual oxidase 2 precursor	1411	Cytoplasmic (Potential).				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)														---	---	---	---
SLC28A2	9153	broad.mit.edu	37	15	45556197	45556197	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45556197G>A	uc001zva.2	+	6	630	c.565G>A	c.(565-567)GCC>ACC	p.A189T		NM_004212	NP_004203	O43868	S28A2_HUMAN	solute carrier family 28 (sodium-coupled	189	Helical; (Potential).				nucleobase, nucleoside and nucleotide metabolic process	integral to plasma membrane|membrane fraction	nucleoside binding|nucleoside:sodium symporter activity|purine nucleoside transmembrane transporter activity			ovary(4)	4		all_cancers(109;8.53e-07)|all_epithelial(112;1.39e-05)|Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;3.77e-16)|GBM - Glioblastoma multiforme(94;2.71e-06)														---	---	---	---
HDC	3067	broad.mit.edu	37	15	50534934	50534934	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50534934C>T	uc001zxz.2	-	12	1618	c.1512G>A	c.(1510-1512)ACG>ACA	p.T504T	HDC_uc001zxy.2_Silent_p.T247T|HDC_uc010uff.1_Silent_p.T471T	NM_002112	NP_002103	P19113	DCHS_HUMAN	histidine decarboxylase	504					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)													---	---	---	---
TRPM7	54822	broad.mit.edu	37	15	50878623	50878623	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50878623A>G	uc001zyt.3	-	28	4716	c.4452T>C	c.(4450-4452)TGT>TGC	p.C1484C	TRPM7_uc010bew.1_Silent_p.C1484C	NM_017672	NP_060142	Q96QT4	TRPM7_HUMAN	transient receptor potential cation channel,	1484	Cytoplasmic (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)														---	---	---	---
UNC13C	440279	broad.mit.edu	37	15	54590004	54590004	+	Intron	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:54590004A>G	uc002ack.2	+						UNC13C_uc002acl.2_Intron	NM_001080534	NP_001074003			unc-13 homolog C						exocytosis|intracellular signal transduction	cell junction|cytoplasm|presynaptic membrane	metal ion binding			ovary(5)|pancreas(2)	7				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)														---	---	---	---
VPS13C	54832	broad.mit.edu	37	15	62147068	62147068	+	Splice_Site	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62147068A>G	uc002agz.2	-	84	11234	c.11160_splice	c.e84+1	p.E3720_splice	VPS13C_uc002aha.2_Splice_Site_p.E3677_splice	NM_020821	NP_065872			vacuolar protein sorting 13C protein isoform 2A						protein localization					ovary(2)	2																		---	---	---	---
VPS13C	54832	broad.mit.edu	37	15	62170797	62170797	+	Intron	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62170797A>G	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																		---	---	---	---
TLN2	83660	broad.mit.edu	37	15	63063176	63063176	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63063176C>T	uc002alb.3	+	39	5210	c.5210C>T	c.(5209-5211)GCA>GTA	p.A1737V	TLN2_uc002alc.3_Missense_Mutation_p.A130V|TLN2_uc002ald.2_Missense_Mutation_p.A130V	NM_015059	NP_055874	Q9Y4G6	TLN2_HUMAN	talin 2	1737					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																		---	---	---	---
USP3	9960	broad.mit.edu	37	15	63824853	63824853	+	Silent	SNP	G	A	A	rs148908419		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63824853G>A	uc002amf.2	+	2	228	c.99G>A	c.(97-99)CGG>CGA	p.R33R	USP3_uc010uii.1_RNA|USP3_uc002amg.2_5'UTR|USP3_uc002amh.2_Silent_p.R11R|USP3_uc010uij.1_Silent_p.R33R|USP3_uc010uik.1_Intron|USP3_uc010bgs.2_Silent_p.R16R	NM_006537	NP_006528	Q9Y6I4	UBP3_HUMAN	ubiquitin thiolesterase 3	33	UBP-type.				DNA repair|histone deubiquitination|mitotic cell cycle|regulation of protein stability|ubiquitin-dependent protein catabolic process	nuclear chromatin	histone binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			lung(1)	1				GBM - Glioblastoma multiforme(80;0.0187)														---	---	---	---
USP3	9960	broad.mit.edu	37	15	63881145	63881145	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63881145T>C	uc002amf.2	+	14	1461	c.1332T>C	c.(1330-1332)CCT>CCC	p.P444P	USP3_uc002amg.2_Silent_p.P359P|USP3_uc002amh.2_Silent_p.P422P|USP3_uc010uij.1_Silent_p.P400P|USP3_uc010uik.1_Silent_p.P195P|USP3_uc010bgs.2_Silent_p.P427P|USP3_uc002ami.2_Silent_p.P275P|uc002amj.2_RNA|uc002amk.2_RNA|uc002aml.2_RNA	NM_006537	NP_006528	Q9Y6I4	UBP3_HUMAN	ubiquitin thiolesterase 3	444					DNA repair|histone deubiquitination|mitotic cell cycle|regulation of protein stability|ubiquitin-dependent protein catabolic process	nuclear chromatin	histone binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			lung(1)	1				GBM - Glioblastoma multiforme(80;0.0187)														---	---	---	---
HERC1	8925	broad.mit.edu	37	15	63904654	63904654	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63904654C>A	uc002amp.2	-	77	14344	c.14196G>T	c.(14194-14196)GAG>GAT	p.E4732D	HERC1_uc002amo.2_5'Flank	NM_003922	NP_003913	Q15751	HERC1_HUMAN	hect domain and RCC1-like domain 1	4732	HECT.				protein modification process|transport	cytosol|Golgi apparatus|membrane	acid-amino acid ligase activity|ARF guanyl-nucleotide exchange factor activity			ovary(6)|breast(6)|lung(5)|central_nervous_system(2)	19																		---	---	---	---
HERC1	8925	broad.mit.edu	37	15	64067377	64067377	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64067377C>T	uc002amp.2	-	2	594	c.446G>A	c.(445-447)CGC>CAC	p.R149H	HERC1_uc010uil.1_Missense_Mutation_p.R149H|HERC1_uc010bgt.1_Missense_Mutation_p.R149H|HERC1_uc002amq.1_Missense_Mutation_p.R149H	NM_003922	NP_003913	Q15751	HERC1_HUMAN	hect domain and RCC1-like domain 1	149					protein modification process|transport	cytosol|Golgi apparatus|membrane	acid-amino acid ligase activity|ARF guanyl-nucleotide exchange factor activity			ovary(6)|breast(6)|lung(5)|central_nervous_system(2)	19																		---	---	---	---
SLC24A1	9187	broad.mit.edu	37	15	65945038	65945038	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65945038G>A	uc010ujf.1	+	9	3229	c.2942G>A	c.(2941-2943)GGC>GAC	p.G981D	SLC24A1_uc010ujd.1_3'UTR|SLC24A1_uc010uje.1_Missense_Mutation_p.G963D|SLC24A1_uc010ujg.1_Missense_Mutation_p.G951D|SLC24A1_uc010ujh.1_Missense_Mutation_p.G963D|SLC24A1_uc010uji.1_Missense_Mutation_p.G308D	NM_004727	NP_004718	O60721	NCKX1_HUMAN	solute carrier family 24	981	Helical; (Potential).|Alpha-2.				response to light intensity|visual perception	integral to plasma membrane|membrane fraction|outer membrane	calcium, potassium:sodium antiporter activity|protein binding|symporter activity				0																		---	---	---	---
ITGA11	22801	broad.mit.edu	37	15	68661610	68661610	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:68661610G>A	uc002ari.2	-	3	264	c.177C>T	c.(175-177)GGC>GGT	p.G59G	ITGA11_uc010bib.2_Silent_p.G59G	NM_001004439	NP_001004439	Q9UKX5	ITA11_HUMAN	integrin, alpha 11 precursor	59	FG-GAP 1.|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)													---	---	---	---
PTPN9	5780	broad.mit.edu	37	15	75782616	75782616	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75782616C>T	uc002bal.2	-	8	1503	c.995G>A	c.(994-996)CGT>CAT	p.R332H		NM_002833	NP_002824	P43378	PTN9_HUMAN	protein tyrosine phosphatase, non-receptor type	332	Tyrosine-protein phosphatase.					cytoplasmic part	non-membrane spanning protein tyrosine phosphatase activity|protein binding			lung(1)|skin(1)	2																		---	---	---	---
ODF3L1	161753	broad.mit.edu	37	15	76019571	76019571	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76019571C>A	uc002bax.1	+	4	737	c.515C>A	c.(514-516)CCT>CAT	p.P172H		NM_175881	NP_787077	Q8IXM7	OD3L1_HUMAN	outer dense fiber of sperm tails 3-like 1	172											0																		---	---	---	---
SGK269	79834	broad.mit.edu	37	15	77425402	77425402	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77425402G>A	uc002bcm.2	-	5	4330	c.4022C>T	c.(4021-4023)GCG>GTG	p.A1341V		NM_024776	NP_079052	Q9H792	PEAK1_HUMAN	NKF3 kinase family member	1341	Protein kinase.				cell migration|protein autophosphorylation|substrate adhesion-dependent cell spreading	actin cytoskeleton|cytoplasm|focal adhesion	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding				0				STAD - Stomach adenocarcinoma(199;0.124)														---	---	---	---
CIB2	10518	broad.mit.edu	37	15	78398176	78398176	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78398176G>A	uc002bdb.1	-	5	768	c.447C>T	c.(445-447)TGC>TGT	p.C149C	CIB2_uc002bdc.1_Silent_p.C106C|CIB2_uc010ums.1_Silent_p.C149C	NM_006383	NP_006374	O75838	CIB2_HUMAN	DNA-dependent protein kinase catalytic	149	EF-hand 3.						calcium ion binding				0																		---	---	---	---
AGPHD1	123688	broad.mit.edu	37	15	78807371	78807371	+	Silent	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78807371C>A	uc010unc.1	+	3	512	c.399C>A	c.(397-399)CCC>CCA	p.P133P	AGPHD1_uc002bdt.2_Silent_p.P133P|AGPHD1_uc010ble.2_Silent_p.P133P	NM_001013619	NP_001013641	A2RU49	AGPD1_HUMAN	aminoglycoside phosphotransferase domain	133						cytoplasm	kinase activity				0																		---	---	---	---
ARNT2	9915	broad.mit.edu	37	15	80872883	80872883	+	Missense_Mutation	SNP	C	T	T	rs147344883		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:80872883C>T	uc002bfr.2	+	16	1911	c.1745C>T	c.(1744-1746)CCG>CTG	p.P582L	ARNT2_uc010unm.1_Missense_Mutation_p.P571L|ARNT2_uc002bfs.2_Missense_Mutation_p.P571L	NM_014862	NP_055677	Q9HBZ2	ARNT2_HUMAN	aryl hydrocarbon receptor nuclear translocator	582					central nervous system development|in utero embryonic development|response to hypoxia		aryl hydrocarbon receptor binding|DNA binding|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|signal transducer activity	p.P582Q(1)		central_nervous_system(3)|ovary(1)|pancreas(1)	5			BRCA - Breast invasive adenocarcinoma(143;0.134)															---	---	---	---
IL16	3603	broad.mit.edu	37	15	81575086	81575086	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81575086C>T	uc002bgh.3	+	9	1564	c.1188C>T	c.(1186-1188)GAC>GAT	p.D396D	IL16_uc002bgc.2_RNA|IL16_uc010blq.1_Silent_p.D396D|IL16_uc002bge.3_RNA|IL16_uc010unp.1_Silent_p.D438D|IL16_uc002bgg.2_Silent_p.D396D|IL16_uc002bgi.1_Translation_Start_Site	NM_172217	NP_757366	Q14005	IL16_HUMAN	interleukin 16 isoform 2	396	PDZ 2.|Interaction with GRIN2A.				immune response|interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|extracellular space|nucleus|plasma membrane	cytokine activity			ovary(2)|lung(1)|skin(1)	4																		---	---	---	---
FSD2	123722	broad.mit.edu	37	15	83451613	83451613	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83451613A>G	uc002bjd.2	-	4	1067	c.900T>C	c.(898-900)GAT>GAC	p.D300D	FSD2_uc010uol.1_Silent_p.D300D|FSD2_uc010uom.1_Silent_p.D300D	NM_001007122	NP_001007123	A1L4K1	FSD2_HUMAN	fibronectin type III and SPRY domain containing	300	Potential.									central_nervous_system(1)	1																		---	---	---	---
ZNF592	9640	broad.mit.edu	37	15	85327240	85327240	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85327240C>G	uc002bld.2	+	4	1670	c.1334C>G	c.(1333-1335)GCC>GGC	p.A445G	ZNF592_uc010upb.1_RNA	NM_014630	NP_055445	Q92610	ZN592_HUMAN	zinc finger protein 592	445					cell death|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)|skin(2)	6			BRCA - Breast invasive adenocarcinoma(143;0.0587)															---	---	---	---
ABHD2	11057	broad.mit.edu	37	15	89738497	89738497	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89738497G>T	uc002bnj.2	+	16	2038	c.1121G>T	c.(1120-1122)GGG>GTG	p.G374V	ABHD2_uc002bnk.2_Missense_Mutation_p.G374V	NM_007011	NP_008942	P08910	ABHD2_HUMAN	alpha/beta hydrolase domain containing protein	374						integral to membrane	carboxylesterase activity			ovary(1)|lung(1)	2	Lung NSC(78;0.0472)|all_lung(78;0.089)																	---	---	---	---
C15orf42	90381	broad.mit.edu	37	15	90167247	90167247	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90167247C>T	uc002boe.2	+	20	3706	c.3706C>T	c.(3706-3708)CCC>TCC	p.P1236S	C15orf42_uc010upv.1_RNA	NM_152259	NP_689472	Q7Z2Z1	TICRR_HUMAN	leucine-rich repeat kinase 1	1236	Pro-rich.				cell cycle|DNA repair|DNA replication|formation of translation preinitiation complex|G2/M transition checkpoint|mitotic cell cycle DNA replication checkpoint|regulation of DNA-dependent DNA replication initiation|response to ionizing radiation	nucleus	chromatin binding|protein binding			ovary(4)|central_nervous_system(2)|skin(1)	7	Lung NSC(78;0.0237)|all_lung(78;0.0478)		BRCA - Breast invasive adenocarcinoma(143;0.128)															---	---	---	---
BLM	641	broad.mit.edu	37	15	91295078	91295078	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91295078A>G	uc002bpr.2	+	4	958	c.861A>G	c.(859-861)CCA>CCG	p.P287P	BLM_uc010uqh.1_Silent_p.P287P|BLM_uc010uqi.1_5'UTR|BLM_uc010bnx.2_Silent_p.P287P	NM_000057	NP_000048	P54132	BLM_HUMAN	Bloom syndrome protein	287					double-strand break repair via homologous recombination|G2 phase of mitotic cell cycle|G2/M transition DNA damage checkpoint|negative regulation of cell division|positive regulation of transcription, DNA-dependent|protein oligomerization|regulation of cyclin-dependent protein kinase activity|replication fork processing|replication fork protection|response to X-ray	cytoplasm|lateral element|nuclear matrix|nucleolus|PML body	ATP binding|bubble DNA binding|DNA strand annealing activity|four-way junction helicase activity|G-quadruplex DNA binding|p53 binding			ovary(3)|skin(2)|breast(1)	6	Lung NSC(78;0.0875)|all_lung(78;0.109)		Lung(145;0.189)					Mis|N|F			leukemia|lymphoma|skin squamous cell |other cancers		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Bloom_syndrome				---	---	---	---
ADAMTS17	170691	broad.mit.edu	37	15	100821558	100821558	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:100821558C>T	uc002bvv.1	-	4	744	c.665G>A	c.(664-666)CGG>CAG	p.R222Q	ADAMTS17_uc002bvx.1_5'UTR	NM_139057	NP_620688	Q8TE56	ATS17_HUMAN	ADAM metallopeptidase with thrombospondin type 1	222					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)														---	---	---	---
ASB7	140460	broad.mit.edu	37	15	101170100	101170100	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101170100A>G	uc002bwk.2	+	5	1439	c.670A>G	c.(670-672)AGG>GGG	p.R224G	ASB7_uc002bwj.2_Missense_Mutation_p.R224G	NM_198243	NP_937886	Q9H672	ASB7_HUMAN	ankyrin repeat and SOCS box-containing protein 7	224	ANK 7.				intracellular signal transduction					skin(1)	1	Lung NSC(78;0.00121)|all_lung(78;0.00152)|Melanoma(26;0.00852)		OV - Ovarian serous cystadenocarcinoma(32;0.00168)|LUSC - Lung squamous cell carcinoma(107;0.0766)|Lung(145;0.103)															---	---	---	---
LRRK1	79705	broad.mit.edu	37	15	101528988	101528988	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101528988C>T	uc002bwr.2	+	5	902	c.583C>T	c.(583-585)CGC>TGC	p.R195C	LRRK1_uc010usb.1_RNA|LRRK1_uc010usc.1_RNA|LRRK1_uc002bwq.1_Missense_Mutation_p.R195C	NM_024652	NP_078928	Q38SD2	LRRK1_HUMAN	leucine-rich repeat kinase 1	195	ANK 4.				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)															---	---	---	---
RHBDF1	64285	broad.mit.edu	37	16	113713	113713	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:113713G>A	uc002cfl.3	-	7	482	c.334C>T	c.(334-336)CGC>TGC	p.R112C	RHBDF1_uc010uty.1_Missense_Mutation_p.R135C|RHBDF1_uc010utz.1_Missense_Mutation_p.R112C|RHBDF1_uc010bqo.1_RNA	NM_022450	NP_071895	Q96CC6	RHDF1_HUMAN	rhomboid family 1	112	Cytoplasmic (Potential).				cell migration|cell proliferation|negative regulation of protein secretion|protein transport|proteolysis|regulation of epidermal growth factor receptor signaling pathway|regulation of proteasomal protein catabolic process	endoplasmic reticulum membrane|Golgi membrane|integral to membrane	growth factor binding|serine-type endopeptidase activity			ovary(1)|pancreas(1)	2		all_cancers(16;2.56e-05)|all_epithelial(16;0.000116)|Hepatocellular(780;0.0068)|Lung NSC(18;0.0795)|all_lung(18;0.159)																---	---	---	---
CACNA1H	8912	broad.mit.edu	37	16	1250513	1250513	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1250513C>T	uc002cks.2	+	7	1309	c.1061C>T	c.(1060-1062)CCC>CTC	p.P354L	CACNA1H_uc002ckt.2_Missense_Mutation_p.P354L	NM_021098	NP_066921	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type,	354	Extracellular (Potential).|I.				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)													---	---	---	---
CACNA1H	8912	broad.mit.edu	37	16	1262117	1262117	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1262117C>T	uc002cks.2	+	25	4986	c.4738C>T	c.(4738-4740)CGC>TGC	p.R1580C	CACNA1H_uc002ckt.2_Missense_Mutation_p.R1580C|CACNA1H_uc002cku.2_Missense_Mutation_p.R286C|CACNA1H_uc010brj.2_Missense_Mutation_p.R286C|CACNA1H_uc002ckv.2_Missense_Mutation_p.R286C	NM_021098	NP_066921	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type,	1580	Cytoplasmic (Potential).				aldosterone biosynthetic process|axon guidance|cellular response to hormone stimulus|cellular response to potassium ion|cortisol biosynthetic process|muscle contraction|myoblast fusion|positive regulation of acrosome reaction|regulation of heart contraction	voltage-gated calcium channel complex	low voltage-gated calcium channel activity			breast(2)	2		Hepatocellular(780;0.00369)			Flunarizine(DB04841)|Mibefradil(DB01388)													---	---	---	---
CLCN7	1186	broad.mit.edu	37	16	1503825	1503825	+	Intron	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1503825T>C	uc002clv.2	-						CLCN7_uc002clw.2_Intron	NM_001287	NP_001278			chloride channel 7 isoform a							integral to membrane|lysosomal membrane	antiporter activity|ATP binding|voltage-gated chloride channel activity			central_nervous_system(2)|ovary(1)|skin(1)	4		Hepatocellular(780;0.0893)																---	---	---	---
CASKIN1	57524	broad.mit.edu	37	16	2239020	2239020	+	Intron	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2239020G>T	uc010bsg.1	-							NM_020764	NP_065815			CASK interacting protein 1						signal transduction	cytoplasm				skin(2)	2																		---	---	---	---
E4F1	1877	broad.mit.edu	37	16	2282576	2282576	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2282576G>A	uc002cpm.2	+	5	777	c.729G>A	c.(727-729)ACG>ACA	p.T243T	E4F1_uc010bsi.2_Silent_p.T243T|E4F1_uc010bsj.2_Silent_p.T243T	NM_004424	NP_004415	Q66K89	E4F1_HUMAN	p120E4F	243	Mediates dimerization, DNA-binding, transcription repression of CCNA2 and interaction with HMGA2.				cell division|cell proliferation|interspecies interaction between organisms|mitosis|regulation of growth	cytoplasm|nucleoplasm	DNA binding|ligase activity|protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity|zinc ion binding			ovary(1)	1																		---	---	---	---
ABCA3	21	broad.mit.edu	37	16	2333210	2333210	+	Missense_Mutation	SNP	C	T	T	rs149871856		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2333210C>T	uc002cpy.1	-	26	4724	c.4012G>A	c.(4012-4014)GCC>ACC	p.A1338T	ABCA3_uc010bsk.1_Missense_Mutation_p.A1280T	NM_001089	NP_001080	Q99758	ABCA3_HUMAN	ATP-binding cassette, sub-family A member 3	1338					response to drug	integral to membrane|lamellar body|membrane fraction|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			breast(5)|ovary(5)|central_nervous_system(3)|upper_aerodigestive_tract(1)|lung(1)|skin(1)	16		Ovarian(90;0.17)																---	---	---	---
PRSS27	83886	broad.mit.edu	37	16	2764112	2764112	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2764112C>T	uc002crf.2	-	4	853	c.462G>A	c.(460-462)ACG>ACA	p.T154T	PRSS27_uc002cre.2_Silent_p.T118T|PRSS27_uc002crg.2_Silent_p.T52T|PRSS27_uc010bst.1_Silent_p.T52T	NM_031948	NP_114154	Q9BQR3	PRS27_HUMAN	marapsin precursor	154	Peptidase S1.				proteolysis	extracellular region	serine-type endopeptidase activity			ovary(1)	1																		---	---	---	---
SRRM2	23524	broad.mit.edu	37	16	2812472	2812472	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2812472G>A	uc002crk.2	+	11	2492	c.1943G>A	c.(1942-1944)CGC>CAC	p.R648H	SRRM2_uc002crj.1_Missense_Mutation_p.R552H|SRRM2_uc002crl.1_Missense_Mutation_p.R648H|SRRM2_uc010bsu.1_Missense_Mutation_p.R552H	NM_016333	NP_057417	Q9UQ35	SRRM2_HUMAN	splicing coactivator subunit SRm300	648	Arg-rich.|Ser-rich.					Cajal body|catalytic step 2 spliceosome|nuclear speck	C2H2 zinc finger domain binding|protein N-terminus binding|RNA binding			ovary(1)|pancreas(1)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
C16orf90	646174	broad.mit.edu	37	16	3544554	3544554	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3544554G>A	uc002cvi.2	-	2	370	c.370C>T	c.(370-372)CGA>TGA	p.R124*		NM_001080524	NP_001073993	A8MZG2	CP090_HUMAN	hypothetical protein LOC646174	114											0																		---	---	---	---
BTBD12	84464	broad.mit.edu	37	16	3632513	3632513	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3632513G>A	uc002cvp.2	-	15	5962	c.5335C>T	c.(5335-5337)CGG>TGG	p.R1779W		NM_032444	NP_115820	Q8IY92	SLX4_HUMAN	BTB (POZ) domain containing 12	1779	Interaction with PLK1 and TERF2-TERF2IP.|Interaction with SLX1.				DNA double-strand break processing involved in repair via single-strand annealing|double-strand break repair via homologous recombination|nucleotide-excision repair	Slx1-Slx4 complex	enzyme activator activity|protein binding				0													Direct_reversal_of_damage|Homologous_recombination	Fanconi_Anemia				---	---	---	---
CREBBP	1387	broad.mit.edu	37	16	3900561	3900561	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3900561C>T	uc002cvv.2	-	2	739	c.535G>A	c.(535-537)GCT>ACT	p.A179T	CREBBP_uc002cvw.2_Missense_Mutation_p.A179T	NM_004380	NP_004371	Q92793	CBP_HUMAN	CREB binding protein isoform a	179					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				---	---	---	---
ADCY9	115	broad.mit.edu	37	16	4016953	4016953	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4016953G>A	uc002cvx.2	-	11	3424	c.2885C>T	c.(2884-2886)CCG>CTG	p.P962L		NM_001116	NP_001107	O60503	ADCY9_HUMAN	adenylate cyclase 9	962	Extracellular (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding			ovary(4)|large_intestine(1)|central_nervous_system(1)	6																		---	---	---	---
VASN	114990	broad.mit.edu	37	16	4432050	4432050	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4432050G>A	uc002cwj.1	+	2	1327	c.1172G>A	c.(1171-1173)AGC>AAC	p.S391N	CORO7_uc002cwe.2_Intron|CORO7_uc002cwf.2_Intron|CORO7_uc002cwg.3_Intron|CORO7_uc002cwh.3_Intron|CORO7_uc010uxh.1_Intron|CORO7_uc010uxi.1_Intron|CORO7_uc002cwi.1_Intron|CORO7_uc010uxj.1_Intron|CORO7_uc010btp.1_Intron	NM_138440	NP_612449	Q6EMK4	VASN_HUMAN	slit-like 2 precursor	391	Extracellular (Potential).					extracellular region|integral to membrane					0																		---	---	---	---
GRIN2A	2903	broad.mit.edu	37	16	9857426	9857426	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9857426G>A	uc002czo.3	-	13	4523	c.3975C>T	c.(3973-3975)TAC>TAT	p.Y1325Y	GRIN2A_uc010uym.1_Silent_p.Y1325Y|GRIN2A_uc010uyn.1_Intron|GRIN2A_uc002czr.3_Intron	NM_001134407	NP_001127879	Q12879	NMDE1_HUMAN	N-methyl-D-aspartate receptor subunit 2A isoform	1325	Cytoplasmic (Potential).				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)													---	---	---	---
TEKT5	146279	broad.mit.edu	37	16	10788514	10788514	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10788514G>A	uc002czz.1	-	1	289	c.217C>T	c.(217-219)CGG>TGG	p.R73W		NM_144674	NP_653275	Q96M29	TEKT5_HUMAN	tektin 5	73					microtubule cytoskeleton organization	cilium axoneme|flagellar axoneme|microtubule				ovary(2)	2																		---	---	---	---
CIITA	4261	broad.mit.edu	37	16	11000846	11000846	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11000846C>T	uc002dai.3	+	11	1630	c.1497C>T	c.(1495-1497)GAC>GAT	p.D499D	CIITA_uc002daj.3_Silent_p.D500D|CIITA_uc002dak.3_Intron|CIITA_uc002dag.2_Silent_p.D499D|CIITA_uc002dah.2_Silent_p.D451D|CIITA_uc010bup.1_Intron	NM_000246	NP_000237	P33076	C2TA_HUMAN	class II transactivator	499	NACHT.				interferon-gamma-mediated signaling pathway|negative regulation of transcription from RNA polymerase II promoter|positive regulation of MHC class I biosynthetic process|positive regulation of transcription from RNA polymerase II promoter|response to antibiotic|transcription, DNA-dependent	nucleus	activating transcription factor binding|ATP binding|protein C-terminus binding|protein complex binding|transcription coactivator activity|transcription regulatory region DNA binding			central_nervous_system(1)	1								T	FLJ27352|CD274|CD273|RALGDS|RUNDC2A|C16orf75	PMBL|Hodgkin Lymphona|								---	---	---	---
CIITA	4261	broad.mit.edu	37	16	11012293	11012293	+	Intron	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11012293G>A	uc002dai.3	+						CIITA_uc002daj.3_Intron|CIITA_uc002dak.3_Intron	NM_000246	NP_000237			class II transactivator						interferon-gamma-mediated signaling pathway|negative regulation of transcription from RNA polymerase II promoter|positive regulation of MHC class I biosynthetic process|positive regulation of transcription from RNA polymerase II promoter|response to antibiotic|transcription, DNA-dependent	nucleus	activating transcription factor binding|ATP binding|protein C-terminus binding|protein complex binding|transcription coactivator activity|transcription regulatory region DNA binding			central_nervous_system(1)	1								T	FLJ27352|CD274|CD273|RALGDS|RUNDC2A|C16orf75	PMBL|Hodgkin Lymphona|						OREG0023606	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
PDXDC1	23042	broad.mit.edu	37	16	15112747	15112747	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15112747C>T	uc002dda.3	+	12	1238	c.1014C>T	c.(1012-1014)GCC>GCT	p.A338A	PDXDC1_uc010uzl.1_Silent_p.A323A|PDXDC1_uc010uzm.1_Silent_p.A247A|PDXDC1_uc002dcz.2_Silent_p.A315A|PDXDC1_uc002ddb.3_Silent_p.A311A|PDXDC1_uc010uzn.1_Silent_p.A310A|PDXDC1_uc002ddc.2_Silent_p.A338A	NM_015027	NP_055842	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain	338					carboxylic acid metabolic process		carboxy-lyase activity|protein binding|pyridoxal phosphate binding			skin(1)	1					Pyridoxal Phosphate(DB00114)													---	---	---	---
TMC5	79838	broad.mit.edu	37	16	19451526	19451526	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19451526T>G	uc002dgc.3	+	3	915	c.166T>G	c.(166-168)TCT>GCT	p.S56A	TMC5_uc010vaq.1_Missense_Mutation_p.S56A|TMC5_uc002dgb.3_Missense_Mutation_p.S56A|TMC5_uc010var.1_Missense_Mutation_p.S56A	NM_001105248	NP_001098718	Q6UXY8	TMC5_HUMAN	transmembrane channel-like 5 isoform a	56	Extracellular (Potential).					integral to membrane				skin(1)	1																		---	---	---	---
TMC5	79838	broad.mit.edu	37	16	19498632	19498632	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19498632G>A	uc002dgc.3	+	17	3306	c.2557G>A	c.(2557-2559)GCC>ACC	p.A853T	TMC5_uc010vaq.1_Missense_Mutation_p.A801T|TMC5_uc002dgb.3_Missense_Mutation_p.A853T|TMC5_uc010var.1_Missense_Mutation_p.A853T|TMC5_uc002dgd.1_Missense_Mutation_p.A607T|TMC5_uc002dge.3_Missense_Mutation_p.A607T|TMC5_uc002dgf.3_Missense_Mutation_p.A536T|TMC5_uc002dgg.3_Missense_Mutation_p.A494T	NM_001105248	NP_001098718	Q6UXY8	TMC5_HUMAN	transmembrane channel-like 5 isoform a	853	Helical; (Potential).					integral to membrane				skin(1)	1																		---	---	---	---
GPR139	124274	broad.mit.edu	37	16	20043576	20043576	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20043576G>A	uc002dgu.1	-	2	705	c.543C>T	c.(541-543)CAC>CAT	p.H181H	GPR139_uc010vaw.1_Silent_p.H88H	NM_001002911	NP_001002911	Q6DWJ6	GP139_HUMAN	G protein-coupled receptor 139	181	Extracellular (Potential).					integral to membrane|plasma membrane				ovary(2)	2																		---	---	---	---
OTOA	146183	broad.mit.edu	37	16	21739665	21739665	+	Missense_Mutation	SNP	C	T	T	rs145160241		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21739665C>T	uc002djh.2	+	19	2121	c.2120C>T	c.(2119-2121)GCG>GTG	p.A707V	uc002diq.3_Intron|OTOA_uc010vbj.1_Missense_Mutation_p.A628V|OTOA_uc002dji.2_Missense_Mutation_p.A383V|OTOA_uc010vbk.1_Missense_Mutation_p.A355V	NM_144672	NP_653273	Q7RTW8	OTOAN_HUMAN	otoancorin isoform 1	721					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)														---	---	---	---
VWA3A	146177	broad.mit.edu	37	16	22163922	22163922	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22163922C>T	uc010vbq.1	+	31	3468	c.3372C>T	c.(3370-3372)CAC>CAT	p.H1124H	VWA3A_uc010bxd.2_RNA|VWA3A_uc002dkg.3_Silent_p.H202H|VWA3A_uc010bxe.1_Silent_p.H226H	NM_173615	NP_775886	A6NCI4	VWA3A_HUMAN	von Willebrand factor A domain containing 3A	1124	VWFA 2.					extracellular region				skin(1)	1				GBM - Glioblastoma multiforme(48;0.0439)														---	---	---	---
SCNN1B	6338	broad.mit.edu	37	16	23382745	23382745	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23382745G>A	uc002dln.2	+	6	1182	c.1006G>A	c.(1006-1008)GCC>ACC	p.A336T		NM_000336	NP_000327	P51168	SCNNB_HUMAN	sodium channel, nonvoltage-gated 1, beta	336	Extracellular (By similarity).		A -> P.		excretion|sensory perception of taste	apical plasma membrane	ligand-gated sodium channel activity|WW domain binding			ovary(3)|breast(2)|large_intestine(1)|pancreas(1)	7				GBM - Glioblastoma multiforme(48;0.0465)	Amiloride(DB00594)|Triamterene(DB00384)													---	---	---	---
GGA2	23062	broad.mit.edu	37	16	23494294	23494294	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23494294G>T	uc002dlq.2	-	9	906	c.830C>A	c.(829-831)CCC>CAC	p.P277H	GGA2_uc010bxo.1_RNA	NM_015044	NP_055859	Q9UJY4	GGA2_HUMAN	ADP-ribosylation factor binding protein 2	277	GAT.				intracellular protein transport|vesicle-mediated transport	clathrin adaptor complex|clathrin-coated vesicle|endosome membrane|trans-Golgi network	ADP-ribosylation factor binding			ovary(1)|central_nervous_system(1)	2				GBM - Glioblastoma multiforme(48;0.0386)														---	---	---	---
ARHGAP17	55114	broad.mit.edu	37	16	24946893	24946893	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24946893C>T	uc002dnb.2	-	18	1885	c.1792G>A	c.(1792-1794)GCA>ACA	p.A598T	ARHGAP17_uc002dmy.2_Missense_Mutation_p.A43T|ARHGAP17_uc002dmz.2_Missense_Mutation_p.A122T|ARHGAP17_uc002dna.2_Missense_Mutation_p.A325T|ARHGAP17_uc002dnc.2_Missense_Mutation_p.A520T|ARHGAP17_uc010vcf.1_Missense_Mutation_p.A341T	NM_001006634	NP_001006635	Q68EM7	RHG17_HUMAN	nadrin isoform 1	598	Pro-rich.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|tight junction	GTPase activator activity|SH3 domain binding				0				GBM - Glioblastoma multiforme(48;0.0407)														---	---	---	---
GTF3C1	2975	broad.mit.edu	37	16	27481632	27481632	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27481632G>A	uc002dov.1	-	31	4651	c.4611C>T	c.(4609-4611)GAC>GAT	p.D1537D	GTF3C1_uc002dou.2_Silent_p.D1537D	NM_001520	NP_001511	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide	1537						transcription factor TFIIIC complex	DNA binding|protein binding			ovary(2)|pancreas(1)|breast(1)|skin(1)	5																		---	---	---	---
KIAA0556	23247	broad.mit.edu	37	16	27585252	27585252	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27585252G>A	uc002dow.2	+	2	62	c.38G>A	c.(37-39)TGG>TAG	p.W13*		NM_015202	NP_056017	O60303	K0556_HUMAN	hypothetical protein LOC23247	13										ovary(4)|large_intestine(2)|upper_aerodigestive_tract(1)|skin(1)	8																		---	---	---	---
CORO1A	11151	broad.mit.edu	37	16	30199821	30199821	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30199821G>A	uc002dww.2	+	10	1327	c.1205G>A	c.(1204-1206)CGG>CAG	p.R402Q	uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|CORO1A_uc010bzq.2_Missense_Mutation_p.R402Q|CORO1A_uc010bzr.2_Intron|CORO1A_uc002dwx.2_Missense_Mutation_p.R296Q|CORO1A_uc002dwy.1_3'UTR|LOC606724_uc002dwz.1_5'Flank	NM_007074	NP_009005	P31146	COR1A_HUMAN	coronin, actin binding protein, 1A	402					cell-substrate adhesion|innate immune response|leukocyte chemotaxis|negative regulation of actin nucleation|phagolysosome assembly|positive chemotaxis|regulation of cell shape|uropod organization	actin filament|cortical actin cytoskeleton|lamellipodium|phagocytic cup|phagocytic vesicle membrane	actin filament binding|phosphatidylinositol 3-kinase binding|protein C-terminus binding|protein homodimerization activity				0																		---	---	---	---
PRSS36	146547	broad.mit.edu	37	16	31154679	31154679	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31154679C>T	uc002ebd.2	-	8	1143	c.1084G>A	c.(1084-1086)GCC>ACC	p.A362T	PRSS36_uc010vff.1_Missense_Mutation_p.A137T|PRSS36_uc010vfg.1_Missense_Mutation_p.A362T|PRSS36_uc010vfh.1_Missense_Mutation_p.A362T	NM_173502	NP_775773	Q5K4E3	POLS2_HUMAN	protease, serine, 36 precursor	362	Peptidase S1 2.				proteolysis	cytoplasm|proteinaceous extracellular matrix	serine-type endopeptidase activity			ovary(1)	1																		---	---	---	---
ITGAX	3687	broad.mit.edu	37	16	31371370	31371370	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31371370G>A	uc002ebu.1	+	7	758	c.691G>A	c.(691-693)GCC>ACC	p.A231T	ITGAX_uc002ebt.2_Missense_Mutation_p.A231T|ITGAX_uc010vfk.1_5'Flank	NM_000887	NP_000878	P20702	ITAX_HUMAN	integrin alpha X precursor	231	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																		---	---	---	---
ABCC12	94160	broad.mit.edu	37	16	48155695	48155695	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48155695C>T	uc002efc.1	-	11	1990	c.1644G>A	c.(1642-1644)CAG>CAA	p.Q548Q	ABCC12_uc002eey.1_RNA|ABCC12_uc002eez.1_RNA|ABCC12_uc002efa.1_RNA|ABCC12_uc002efb.1_RNA|ABCC12_uc002efd.1_RNA|ABCC12_uc002efe.1_Silent_p.Q548Q	NM_033226	NP_150229	Q96J65	MRP9_HUMAN	ATP-binding cassette protein C12	548	ABC transporter 1.					integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(2)|skin(1)	3		all_cancers(37;0.0474)|all_lung(18;0.047)																---	---	---	---
TOX3	27324	broad.mit.edu	37	16	52473718	52473718	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:52473718C>T	uc002egw.2	-	7	1321	c.1150G>A	c.(1150-1152)GCT>ACT	p.A384T	TOX3_uc010vgt.1_Missense_Mutation_p.A379T|TOX3_uc010vgu.1_Missense_Mutation_p.A384T	NM_001080430	NP_001073899	O15405	TOX3_HUMAN	TOX high mobility group box family member 3	384					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																		---	---	---	---
IRX3	79191	broad.mit.edu	37	16	54317634	54317634	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54317634G>A	uc002eht.1	-	4	1886	c.1470C>T	c.(1468-1470)GAC>GAT	p.D490D		NM_024336	NP_077312	P78415	IRX3_HUMAN	iroquois homeobox 3	490					multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
MMP2	4313	broad.mit.edu	37	16	55518003	55518003	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55518003C>T	uc002ehz.3	+	3	767	c.456C>T	c.(454-456)AGC>AGT	p.S152S	MMP2_uc010vhd.1_Silent_p.S76S|MMP2_uc010ccc.2_Silent_p.S102S	NM_004530	NP_004521	P08253	MMP2_HUMAN	matrix metalloproteinase 2 isoform a	152	Collagenase-like 1.				angiogenesis|collagen catabolic process|proteolysis	extracellular space|membrane|nucleus|proteinaceous extracellular matrix	metalloendopeptidase activity|protein binding|zinc ion binding			large_intestine(3)|ovary(3)|lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)	11		Renal(780;0.00183)|Breast(268;0.00354)|Hepatocellular(780;0.00826)|all_neural(199;0.0189)		UCEC - Uterine corpus endometrioid carcinoma (183;0.0185)|all cancers(182;7.16e-45)|Epithelial(162;5.26e-37)|GBM - Glioblastoma multiforme(240;9e-08)|Kidney(780;0.00227)|BRCA - Breast invasive adenocarcinoma(181;0.00786)	Marimastat(DB00786)|Sulindac(DB00605)													---	---	---	---
CES1	1066	broad.mit.edu	37	16	55862670	55862670	+	Intron	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55862670G>A	uc002eim.2	-						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)													---	---	---	---
CDH11	1009	broad.mit.edu	37	16	64984769	64984769	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:64984769C>T	uc002eoi.2	-	12	2229	c.1795G>A	c.(1795-1797)GGG>AGG	p.G599R	CDH11_uc010cdn.2_RNA|CDH11_uc002eoj.2_Missense_Mutation_p.G599R|CDH11_uc010vin.1_Missense_Mutation_p.G473R	NM_001797	NP_001788	P55287	CAD11_HUMAN	cadherin 11, type 2 preproprotein	599	Cadherin 5.|Extracellular (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion|ossification|skeletal system development	integral to membrane|plasma membrane	calcium ion binding|protein binding			lung(10)|ovary(3)|skin(1)	14		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)				T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)			---	---	---	---
CDH16	1014	broad.mit.edu	37	16	66947046	66947046	+	Missense_Mutation	SNP	G	A	A	rs79541908		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66947046G>A	uc002eql.2	-	9	1115	c.1042C>T	c.(1042-1044)CTC>TTC	p.L348F	CDH16_uc010cdy.2_Missense_Mutation_p.L348F|CDH16_uc002eqm.2_Missense_Mutation_p.L251F	NM_004062	NP_004053	O75309	CAD16_HUMAN	cadherin 16 precursor	348	Extracellular (Potential).|Cadherin 4.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)|upper_aerodigestive_tract(1)	3		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0877)|Epithelial(162;0.203)														---	---	---	---
AGRP	181	broad.mit.edu	37	16	67516943	67516943	+	Silent	SNP	A	C	C	rs77812484		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67516943A>C	uc002etg.1	-	3	501	c.201T>G	c.(199-201)GCT>GCG	p.A67A	ATP6V0D1_uc002ete.1_5'Flank|ATP6V0D1_uc010vjo.1_5'Flank	NM_001138	NP_001129	O00253	AGRP_HUMAN	agouti related protein homolog isoform 1	67					hormone-mediated signaling pathway|neuropeptide signaling pathway|regulation of feeding behavior	extracellular space|Golgi lumen	neuropeptide hormone activity				0		Acute lymphoblastic leukemia(13;0.00263)|all_hematologic(13;0.0274)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0717)|Epithelial(162;0.16)														---	---	---	---
FAM65A	79567	broad.mit.edu	37	16	67573627	67573627	+	Intron	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67573627G>A	uc010vjp.1	+						FAM65A_uc010cei.1_Intron|FAM65A_uc002eth.2_Intron|FAM65A_uc010cej.2_Intron|FAM65A_uc002eti.1_Intron|FAM65A_uc010vjq.1_Intron|FAM65A_uc002etj.1_Intron|FAM65A_uc002etk.2_Intron	NM_024519	NP_078795			hypothetical protein LOC79567							cytoplasm	binding			ovary(2)|central_nervous_system(1)	3		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0474)|Epithelial(162;0.117)														---	---	---	---
ACD	65057	broad.mit.edu	37	16	67691889	67691889	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67691889C>A	uc002etq.3	-	10	1801	c.1464G>T	c.(1462-1464)TGG>TGT	p.W488C	ACD_uc002etp.3_Missense_Mutation_p.W485C|ACD_uc002etr.3_Missense_Mutation_p.W485C|ACD_uc010vjt.1_3'UTR|PARD6A_uc002ets.2_5'Flank|PARD6A_uc002ett.2_5'Flank	NM_001082486	NP_001075955	Q96AP0	ACD_HUMAN	adrenocortical dysplasia homolog isoform 1	488					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)														---	---	---	---
TSNAXIP1	55815	broad.mit.edu	37	16	67860079	67860079	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67860079G>A	uc002euj.2	+	10	1401	c.1007G>A	c.(1006-1008)CGC>CAC	p.R336H	TSNAXIP1_uc010cep.2_3'UTR|TSNAXIP1_uc010vjz.1_Missense_Mutation_p.R213H|TSNAXIP1_uc002euf.3_Missense_Mutation_p.R69H|TSNAXIP1_uc010vka.1_Missense_Mutation_p.R390H|TSNAXIP1_uc010vkb.1_Missense_Mutation_p.R321H|TSNAXIP1_uc002eug.3_Missense_Mutation_p.R44H|TSNAXIP1_uc002euh.3_Missense_Mutation_p.R44H|TSNAXIP1_uc002eui.3_Missense_Mutation_p.R44H|TSNAXIP1_uc002euk.2_Missense_Mutation_p.R69H	NM_018430	NP_060900	Q2TAA8	TXIP1_HUMAN	translin-associated factor X interacting protein	336					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)														---	---	---	---
DPEP2	64174	broad.mit.edu	37	16	68026860	68026860	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68026860C>T	uc010cey.2	-	1	420	c.256G>A	c.(256-258)GTG>ATG	p.V86M	DPEP2_uc002evd.3_Missense_Mutation_p.V86M|DPEP2_uc002eve.2_Missense_Mutation_p.V86M|DPEP2_uc002evf.2_RNA|DPEP2_uc002evg.2_Missense_Mutation_p.V86M	NM_022355	NP_071750	Q9H4A9	DPEP2_HUMAN	dipeptidase 2 precursor	86					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)														---	---	---	---
HAS3	3038	broad.mit.edu	37	16	69143549	69143549	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69143549G>A	uc010cfh.2	+	2	475	c.251G>A	c.(250-252)CGG>CAG	p.R84Q	HAS3_uc002ewk.2_Missense_Mutation_p.R84Q|HAS3_uc010vlk.1_Missense_Mutation_p.R84Q|HAS3_uc002ewl.2_Missense_Mutation_p.R84Q	NM_005329	NP_005320	O00219	HAS3_HUMAN	hyaluronan synthase 3 isoform a	84	Cytoplasmic (Potential).				carbohydrate metabolic process	integral to plasma membrane	hyaluronan synthase activity				0		Ovarian(137;0.101)		OV - Ovarian serous cystadenocarcinoma(108;0.0694)														---	---	---	---
WWP2	11060	broad.mit.edu	37	16	69964118	69964118	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69964118C>T	uc002exu.1	+	14	1491	c.1402C>T	c.(1402-1404)CGC>TGC	p.R468C	WWP2_uc002exv.1_Missense_Mutation_p.R468C|WWP2_uc010vlm.1_Missense_Mutation_p.R352C|WWP2_uc010vln.1_Missense_Mutation_p.R86C|WWP2_uc002exw.1_Missense_Mutation_p.R29C|uc002exx.1_5'Flank|MIR140_hsa-mir-140|MI0000456_5'Flank	NM_007014	NP_008945	O00308	WWP2_HUMAN	WW domain containing E3 ubiquitin protein ligase	468	WW 4.				entry of virus into host cell|negative regulation of protein transport|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transporter activity|proteasomal ubiquitin-dependent protein catabolic process|protein K63-linked ubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus|ubiquitin ligase complex	RNA polymerase II transcription factor binding|ubiquitin-protein ligase activity			lung(3)|ovary(1)|breast(1)|skin(1)	6																OREG0023910	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
COG4	25839	broad.mit.edu	37	16	70557297	70557297	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70557297G>A	uc002ezc.2	-	1	161	c.150C>T	c.(148-150)TAC>TAT	p.Y50Y	COG4_uc010cfu.2_RNA|COG4_uc002ezd.2_Silent_p.Y50Y|COG4_uc002eze.2_Translation_Start_Site|SF3B3_uc002ezf.2_5'Flank	NM_015386	NP_056201	Q9H9E3	COG4_HUMAN	component of oligomeric golgi complex 4	46	Interacts with SCFD1.				Golgi organization|Golgi vesicle prefusion complex stabilization|protein transport|retrograde vesicle-mediated transport, Golgi to ER	Golgi membrane|Golgi transport complex	protein binding				0		Ovarian(137;0.0694)																---	---	---	---
ZFHX3	463	broad.mit.edu	37	16	72828552	72828552	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72828552C>T	uc002fck.2	-	9	8702	c.8029G>A	c.(8029-8031)GAG>AAG	p.E2677K	ZFHX3_uc002fcl.2_Missense_Mutation_p.E1763K	NM_006885	NP_008816	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3 isoform A	2677	Homeobox 3.				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)																---	---	---	---
GLG1	2734	broad.mit.edu	37	16	74496466	74496466	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74496466C>T	uc002fcy.3	-	21	2904	c.2854G>A	c.(2854-2856)GGT>AGT	p.G952S	GLG1_uc002fcx.2_Missense_Mutation_p.G952S|GLG1_uc002fcw.3_Missense_Mutation_p.G941S|GLG1_uc002fcz.3_Missense_Mutation_p.G369S	NM_001145667	NP_001139139	Q92896	GSLG1_HUMAN	golgi apparatus protein 1 isoform 3	952	Cys-rich GLG1 14.|Extracellular (Potential).					Golgi membrane|integral to membrane	receptor binding			ovary(1)|breast(1)	2																		---	---	---	---
MLKL	197259	broad.mit.edu	37	16	74729299	74729299	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74729299C>T	uc002fdb.2	-	2	798	c.357G>A	c.(355-357)GAG>GAA	p.E119E	MLKL_uc002fdc.2_Silent_p.E119E	NM_152649	NP_689862	Q8NB16	MLKL_HUMAN	mixed lineage kinase domain-like isoform 1	119							ATP binding|protein binding|protein kinase activity			stomach(2)	2																		---	---	---	---
KARS	3735	broad.mit.edu	37	16	75663449	75663449	+	Intron	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75663449G>T	uc002feq.2	-						KARS_uc002fer.2_Intron|KARS_uc002fes.2_Intron	NM_005548	NP_005539			lysyl-tRNA synthetase isoform 2						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)													---	---	---	---
CNTNAP4	85445	broad.mit.edu	37	16	76587778	76587778	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:76587778T>C	uc002feu.1	+	25	4092	c.3707T>C	c.(3706-3708)ATC>ACC	p.I1236T	CNTNAP4_uc002fev.1_Missense_Mutation_p.I1100T|CNTNAP4_uc010chb.1_Missense_Mutation_p.I1163T|CNTNAP4_uc002fex.1_Missense_Mutation_p.I1239T	NM_033401	NP_207837	Q9C0A0	CNTP4_HUMAN	cell recognition protein CASPR4 isoform 1	1236	Extracellular (Potential).				cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(1)|pancreas(1)	2																		---	---	---	---
ADAMTS18	170692	broad.mit.edu	37	16	77356319	77356319	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77356319A>T	uc002ffc.3	-	14	2496	c.2077T>A	c.(2077-2079)TTT>ATT	p.F693I	ADAMTS18_uc010chc.1_Missense_Mutation_p.F281I|ADAMTS18_uc002ffe.1_Missense_Mutation_p.F389I	NM_199355	NP_955387	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1	693	Cys-rich.				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																		---	---	---	---
BCMO1	53630	broad.mit.edu	37	16	81320986	81320986	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81320986G>A	uc002fgn.1	+	10	1607	c.1389G>A	c.(1387-1389)GCG>GCA	p.A463A	BCMO1_uc010vnp.1_Silent_p.A394A	NM_017429	NP_059125	Q9HAY6	BCDO1_HUMAN	beta-carotene 15,15'-monooxygenase	463					retinoid metabolic process|steroid metabolic process	cytosol	beta-carotene 15,15'-monooxygenase activity|metal ion binding|monooxygenase activity				0																		---	---	---	---
CDH13	1012	broad.mit.edu	37	16	83065685	83065685	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:83065685C>T	uc002fgx.2	+	3	348	c.228C>T	c.(226-228)AAC>AAT	p.N76N	CDH13_uc010chh.2_Silent_p.N76N|CDH13_uc010vns.1_Silent_p.N123N|CDH13_uc010vnt.1_Intron|CDH13_uc010vnu.1_Silent_p.N76N	NM_001257	NP_001248	P55290	CAD13_HUMAN	cadherin 13 preproprotein	76					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)														---	---	---	---
ZC3H18	124245	broad.mit.edu	37	16	88694379	88694379	+	Missense_Mutation	SNP	C	T	T	rs139646372	byFrequency	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88694379C>T	uc002fky.2	+	15	2521	c.2321C>T	c.(2320-2322)TCG>TTG	p.S774L	ZC3H18_uc010voz.1_Missense_Mutation_p.S798L|ZC3H18_uc010chw.2_Intron|ZC3H18_uc002fkz.2_Missense_Mutation_p.S44L	NM_144604	NP_653205	Q86VM9	ZCH18_HUMAN	zinc finger CCCH-type containing 18	774						nucleus	nucleic acid binding|zinc ion binding			skin(1)	1				BRCA - Breast invasive adenocarcinoma(80;0.0542)														---	---	---	---
APRT	353	broad.mit.edu	37	16	88876887	88876887	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88876887G>A	uc002flv.2	-	3	300	c.265C>T	c.(265-267)CGG>TGG	p.R89W	APRT_uc002flw.2_Missense_Mutation_p.R89W	NM_000485	NP_000476	P07741	APT_HUMAN	adenine phosphoribosyltransferase isoform a	89					purine ribonucleoside salvage	cytosol|nucleus	adenine phosphoribosyltransferase activity|AMP binding|protein binding				0				BRCA - Breast invasive adenocarcinoma(80;0.0477)	Adenine(DB00173)|Adenosine monophosphate(DB00131)													---	---	---	---
SPG7	6687	broad.mit.edu	37	16	89614458	89614458	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89614458C>T	uc002fnj.2	+	12	1621	c.1600C>T	c.(1600-1602)CGG>TGG	p.R534W	SPG7_uc002fnk.1_RNA|SPG7_uc002fnl.2_5'Flank	NM_003119	NP_003110	Q9UQ90	SPG7_HUMAN	spastic paraplegia 7 isoform 1	534	Mitochondrial matrix (Potential).				cell death|nervous system development|protein catabolic process|proteolysis	integral to membrane|mitochondrial membrane	ATP binding|metalloendopeptidase activity|nucleoside-triphosphatase activity|unfolded protein binding|zinc ion binding				0		all_hematologic(23;0.00824)|Colorectal(91;0.102)		all cancers(4;1.39e-07)|OV - Ovarian serous cystadenocarcinoma(4;5.64e-06)|BRCA - Breast invasive adenocarcinoma(80;0.015)														---	---	---	---
CENPBD1	92806	broad.mit.edu	37	16	90038269	90038269	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:90038269G>A	uc002fpr.2	-	1	674	c.62C>T	c.(61-63)GCG>GTG	p.A21V	AFG3L1_uc002fps.1_5'Flank|AFG3L1_uc002fpt.1_5'Flank|AFG3L1_uc002fpu.1_5'Flank|AFG3L1_uc002fpv.1_5'Flank|AFG3L1_uc002fpw.1_5'Flank|AFG3L1_uc002fpx.1_5'Flank	NM_145039	NP_659476	B2RD01	CENP1_HUMAN	CENPB DNA-binding domains containing 1	21	HTH psq-type.				regulation of transcription, DNA-dependent	chromosome, centromeric region|nucleus	DNA binding				0																		---	---	---	---
NXN	64359	broad.mit.edu	37	17	725610	725610	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:725610C>T	uc002fsa.2	-	4	792	c.700G>A	c.(700-702)GTT>ATT	p.V234I	NXN_uc002fsb.1_Missense_Mutation_p.V121I|NXN_uc010vqd.1_5'UTR|NXN_uc002frz.2_5'UTR|NXN_uc010vqe.1_Missense_Mutation_p.V126I	NM_022463	NP_071908	Q6DKJ4	NXN_HUMAN	nucleoredoxin	234	Thioredoxin.				cell differentiation|cell redox homeostasis|multicellular organismal development|Wnt receptor signaling pathway	cytosol|nucleus	protein-disulfide reductase activity			ovary(2)|breast(1)|pancreas(1)	4				UCEC - Uterine corpus endometrioid carcinoma (25;0.0237)														---	---	---	---
SLC43A2	124935	broad.mit.edu	37	17	1520058	1520058	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1520058C>T	uc002fsv.2	-	3	255	c.166G>A	c.(166-168)GTC>ATC	p.V56I	SLC43A2_uc002fsu.2_Missense_Mutation_p.V56I|SLC43A2_uc002fsw.2_Missense_Mutation_p.V56I|SLC43A2_uc002fsx.2_Missense_Mutation_p.V56I	NM_152346	NP_689559	Q8N370	LAT4_HUMAN	solute carrier family 43, member 2	56					cellular nitrogen compound metabolic process|ion transport	integral to membrane|plasma membrane					0				UCEC - Uterine corpus endometrioid carcinoma (25;0.0883)														---	---	---	---
WDR81	124997	broad.mit.edu	37	17	1640830	1640830	+	Missense_Mutation	SNP	G	A	A	rs139156426		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1640830G>A	uc002fti.2	+	10	2257	c.1996G>A	c.(1996-1998)GTC>ATC	p.V666I	WDR81_uc002fth.2_Missense_Mutation_p.V842I|WDR81_uc010vqp.1_Missense_Mutation_p.V690I|WDR81_uc002ftj.2_Missense_Mutation_p.V1893I|WDR81_uc010vqq.1_Missense_Mutation_p.V524I	NM_001163811	NP_001157283	Q562E7	WDR81_HUMAN	WD repeat domain 81 isoform 4	666										skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)														---	---	---	---
SERPINF1	5176	broad.mit.edu	37	17	1679914	1679914	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1679914G>A	uc002ftl.2	+	7	1032	c.875G>A	c.(874-876)AGC>AAC	p.S292N	SERPINF1_uc010cjw.2_Missense_Mutation_p.S105N	NM_002615	NP_002606	P36955	PEDF_HUMAN	serine (or cysteine) proteinase inhibitor, clade	292					cell proliferation|negative regulation of angiogenesis|positive regulation of neurogenesis|regulation of proteolysis	extracellular space|melanosome	serine-type endopeptidase inhibitor activity			ovary(1)	1																		---	---	---	---
ITGAE	3682	broad.mit.edu	37	17	3655092	3655092	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3655092G>A	uc002fwo.3	-	15	1844	c.1745C>T	c.(1744-1746)GCG>GTG	p.A582V		NM_002208	NP_002199	P38570	ITAE_HUMAN	integrin, alpha E precursor	582	FG-GAP 6.|Extracellular (Potential).				cell adhesion|integrin-mediated signaling pathway	integrin complex	receptor activity			large_intestine(2)|breast(1)|pancreas(1)	4				UCEC - Uterine corpus endometrioid carcinoma (3;0.0813)														---	---	---	---
MYBBP1A	10514	broad.mit.edu	37	17	4446359	4446359	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4446359T>G	uc002fyb.3	-	20	2803	c.2741A>C	c.(2740-2742)CAG>CCG	p.Q914P	MYBBP1A_uc002fxz.3_Missense_Mutation_p.Q914P|MYBBP1A_uc002fya.3_5'Flank|MYBBP1A_uc010vsa.1_5'UTR	NM_014520	NP_055335	Q9BQG0	MBB1A_HUMAN	MYB binding protein 1a isoform 2	914					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																		---	---	---	---
MYBBP1A	10514	broad.mit.edu	37	17	4448439	4448439	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4448439C>T	uc002fyb.3	-	17	2254	c.2192G>A	c.(2191-2193)AGC>AAC	p.S731N	MYBBP1A_uc002fxz.3_Missense_Mutation_p.S731N|MYBBP1A_uc002fya.3_5'Flank|MYBBP1A_uc010vsa.1_5'Flank	NM_014520	NP_055335	Q9BQG0	MBB1A_HUMAN	MYB binding protein 1a isoform 2	731	Glu-rich.				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																		---	---	---	---
PELP1	27043	broad.mit.edu	37	17	4594694	4594694	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4594694C>T	uc002fyi.3	-	2	519	c.293G>A	c.(292-294)CGT>CAT	p.R98H	PELP1_uc010vsf.1_5'UTR	NM_014389	NP_055204	Q8IZL8	PELP1_HUMAN	proline, glutamic acid and leucine rich protein	98					transcription, DNA-dependent	cytoplasm|MLL1 complex	protein binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
TM4SF5	9032	broad.mit.edu	37	17	4685809	4685809	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4685809G>A	uc002fyw.1	+	3	301	c.270G>A	c.(268-270)TCG>TCA	p.S90S		NM_003963	NP_003954	O14894	T4S5_HUMAN	transmembrane 4 superfamily member 5	90	Cytoplasmic (Potential).					integral to plasma membrane				ovary(1)	1																		---	---	---	---
C17orf107	100130311	broad.mit.edu	37	17	4804924	4804924	+	3'UTR	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4804924C>T	uc002fzl.3	+	3					CHRNE_uc002fzk.1_Intron	NM_001145536	NP_001139008			hypothetical protein LOC100130311												0																		---	---	---	---
RNF167	26001	broad.mit.edu	37	17	4848022	4848022	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4848022G>A	uc002fzq.2	+	11	1180	c.764G>A	c.(763-765)CGC>CAC	p.R255H	RNF167_uc002fzr.2_Missense_Mutation_p.R255H|RNF167_uc002fzs.2_Missense_Mutation_p.R255H|RNF167_uc002fzt.2_Missense_Mutation_p.R255H|RNF167_uc002fzu.2_Missense_Mutation_p.R254H|RNF167_uc002fzv.2_Missense_Mutation_p.R220H|RNF167_uc002fzx.2_Missense_Mutation_p.R219H|RNF167_uc002fzy.2_Missense_Mutation_p.R54H	NM_015528	NP_056343	Q9H6Y7	RN167_HUMAN	ring finger protein 167 precursor	255	RING-type; atypical.				negative regulation of cell cycle|protein polyubiquitination	cytoplasm|endomembrane system|integral to membrane	protein binding|ubiquitin-protein ligase activity|zinc ion binding				0																		---	---	---	---
BCL6B	255877	broad.mit.edu	37	17	6927588	6927588	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6927588C>T	uc002geg.2	+	3	423	c.366C>T	c.(364-366)CAC>CAT	p.H122H	BCL6B_uc010clt.1_Silent_p.H122H	NM_181844	NP_862827	Q8N143	BCL6B_HUMAN	B-cell CLL/lymphoma 6, member B (zinc finger	122						nucleus	zinc ion binding			skin(1)	1																		---	---	---	---
EIF5A	1984	broad.mit.edu	37	17	7211859	7211859	+	Intron	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7211859A>G	uc010vtv.1	+						EIF5A_uc002gfr.2_Intron|EIF5A_uc010vtu.1_Intron|EIF5A_uc002gft.2_Intron|EIF5A_uc002gfu.2_5'UTR	NM_001970	NP_001961			eukaryotic translation initiation factor 5A						induction of apoptosis|mRNA export from nucleus|peptidyl-lysine modification to hypusine|positive regulation of cell proliferation|positive regulation of translational elongation|positive regulation of translational termination|post-translational protein modification|protein export from nucleus|translational frameshifting|transmembrane transport	annulate lamellae|cytosol|endoplasmic reticulum membrane|nuclear pore	protein N-terminus binding|ribosome binding|translation elongation factor activity|U6 snRNA binding				0																		---	---	---	---
ACAP1	9744	broad.mit.edu	37	17	7252342	7252342	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7252342G>A	uc002ggd.2	+	18	1913	c.1707G>A	c.(1705-1707)CTG>CTA	p.L569L	KCTD11_uc002gge.3_5'Flank	NM_014716	NP_055531	Q15027	ACAP1_HUMAN	centaurin beta1	569	Required for interaction with GULP1.				intracellular signal transduction|lipid metabolic process|protein transport|regulation of ARF GTPase activity		ARF GTPase activator activity|phospholipase C activity|protein binding|zinc ion binding			breast(2)|large_intestine(1)	3																		---	---	---	---
C17orf74	201243	broad.mit.edu	37	17	7329690	7329690	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7329690G>A	uc002ggw.2	+	3	453	c.380G>A	c.(379-381)CGC>CAC	p.R127H	FGF11_uc010vtw.1_Intron	NM_175734	NP_783861	Q0P670	CQ074_HUMAN	hypothetical protein LOC201243	127	Arg-rich.					integral to membrane					0		Prostate(122;0.157)																---	---	---	---
ZBTB4	57659	broad.mit.edu	37	17	7369348	7369348	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7369348C>T	uc002ghc.3	-	3	1023	c.773G>A	c.(772-774)CGA>CAA	p.R258Q	ZBTB4_uc002ghd.3_Missense_Mutation_p.R258Q	NM_001128833	NP_001122305	Q9P1Z0	ZBTB4_HUMAN	zinc finger and BTB domain containing 4	258					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(2)|ovary(1)|central_nervous_system(1)	4		Colorectal(1115;3.46e-05)|Myeloproliferative disorder(207;0.0255)		COAD - Colon adenocarcinoma(228;4.1e-06)|READ - Rectum adenocarcinoma(115;0.0642)														---	---	---	---
KDM6B	23135	broad.mit.edu	37	17	7750871	7750871	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7750871C>T	uc002giw.1	+	11	1641	c.1265C>T	c.(1264-1266)GCT>GTT	p.A422V	KDM6B_uc002gix.2_5'UTR	NM_001080424	NP_001073893	O15054	KDM6B_HUMAN	lysine (K)-specific demethylase 6B	422	Pro-rich.				inflammatory response	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			central_nervous_system(1)|pancreas(1)	2																		---	---	---	---
ALOXE3	59344	broad.mit.edu	37	17	7999976	7999976	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7999976G>T	uc010cnr.2	-	16	2475	c.2105C>A	c.(2104-2106)CCT>CAT	p.P702H	ALOXE3_uc002gka.2_Missense_Mutation_p.P858H|ALOXE3_uc010vuo.1_Missense_Mutation_p.P834H	NM_021628	NP_067641	Q9BYJ1	LOXE3_HUMAN	arachidonate lipoxygenase 3 isoform 2	702	Lipoxygenase.				leukotriene biosynthetic process		iron ion binding|lipoxygenase activity			skin(3)|lung(1)|central_nervous_system(1)	5																		---	---	---	---
PFAS	5198	broad.mit.edu	37	17	8158378	8158378	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8158378C>T	uc002gkr.2	+	4	453	c.312C>T	c.(310-312)ATC>ATT	p.I104I	PFAS_uc010vuv.1_5'UTR	NM_012393	NP_036525	O15067	PUR4_HUMAN	phosphoribosylformylglycinamidine synthase	104					'de novo' IMP biosynthetic process|glutamine metabolic process|purine base metabolic process	cytosol	ATP binding|phosphoribosylformylglycinamidine synthase activity|protein binding			ovary(2)|central_nervous_system(2)|pancreas(1)	5					L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)													---	---	---	---
KRBA2	124751	broad.mit.edu	37	17	8272949	8272949	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8272949C>T	uc002glf.1	-	2	988	c.982G>A	c.(982-984)GTT>ATT	p.V328I	KRBA2_uc002glg.1_Missense_Mutation_p.V245I	NM_213597	NP_998762	Q6ZNG9	KRBA2_HUMAN	KRAB-A domain containing 2	328	Integrase catalytic.				DNA integration|regulation of transcription, DNA-dependent	intracellular	DNA binding				0																		---	---	---	---
MYH10	4628	broad.mit.edu	37	17	8396161	8396161	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8396161G>A	uc002gll.2	-	31	4394	c.4298C>T	c.(4297-4299)ACG>ATG	p.T1433M	MYH10_uc002glm.2_Missense_Mutation_p.T1464M|MYH10_uc010cnx.2_Missense_Mutation_p.T1442M	NM_005964	NP_005955	P35580	MYH10_HUMAN	myosin, heavy polypeptide 10, non-muscle	1433	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																		---	---	---	---
USP43	124739	broad.mit.edu	37	17	9615374	9615374	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9615374T>G	uc010cod.2	+	14	2260	c.2260T>G	c.(2260-2262)TCT>GCT	p.S754A	USP43_uc002gma.3_Missense_Mutation_p.S443A|USP43_uc010vva.1_Missense_Mutation_p.S749A|USP43_uc010coe.2_Missense_Mutation_p.S551A|USP43_uc002gmc.3_Missense_Mutation_p.S266A	NM_153210	NP_694942	Q70EL4	UBP43_HUMAN	ubiquitin specific protease 43	754					ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(2)|lung(1)|breast(1)|central_nervous_system(1)	5																		---	---	---	---
DHRS7C	201140	broad.mit.edu	37	17	9674812	9674812	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9674812T>C	uc010vvb.1	-	6	932	c.932A>G	c.(931-933)GAG>GGG	p.E311G	DHRS7C_uc010cof.2_Missense_Mutation_p.E310G	NM_001105571	NP_001099041	A6NNS2	DRS7C_HUMAN	dehydrogenase/reductase (SDR family) member 7C	311						extracellular region	binding|oxidoreductase activity				0																		---	---	---	---
MYH13	8735	broad.mit.edu	37	17	10231407	10231407	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10231407G>T	uc002gmk.1	-	22	2557	c.2467C>A	c.(2467-2469)CGC>AGC	p.R823S		NM_003802	NP_003793	Q9UKX3	MYH13_HUMAN	myosin, heavy polypeptide 13, skeletal muscle	823					muscle contraction	muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(4)|skin(2)	6																OREG0024177	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
DNAH9	1770	broad.mit.edu	37	17	11757668	11757668	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11757668C>T	uc002gne.2	+	50	9924	c.9856C>T	c.(9856-9858)CGC>TGC	p.R3286C	DNAH9_uc010coo.2_Missense_Mutation_p.R2580C	NM_001372	NP_001363	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9 isoform 2	3286	Stalk (By similarity).|Potential.				cell projection organization|cellular component movement|microtubule-based movement|spermatogenesis	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			skin(10)|ovary(4)|breast(3)|central_nervous_system(2)|pancreas(1)	20		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)														---	---	---	---
DNAH9	1770	broad.mit.edu	37	17	11778363	11778363	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11778363G>A	uc002gne.2	+	53	10408	c.10340G>A	c.(10339-10341)CGC>CAC	p.R3447H	DNAH9_uc010coo.2_Missense_Mutation_p.R2741H	NM_001372	NP_001363	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9 isoform 2	3447	AAA 5 (By similarity).				cell projection organization|cellular component movement|microtubule-based movement|spermatogenesis	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			skin(10)|ovary(4)|breast(3)|central_nervous_system(2)|pancreas(1)	20		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)														---	---	---	---
DNAH9	1770	broad.mit.edu	37	17	11806149	11806149	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11806149G>T	uc002gne.2	+	60	11588	c.11520G>T	c.(11518-11520)CAG>CAT	p.Q3840H	DNAH9_uc010coo.2_Missense_Mutation_p.Q3134H|DNAH9_uc002gnf.2_Missense_Mutation_p.Q152H|DNAH9_uc010vvh.1_Missense_Mutation_p.Q193H	NM_001372	NP_001363	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9 isoform 2	3840					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)														---	---	---	---
MYOCD	93649	broad.mit.edu	37	17	12661453	12661453	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:12661453T>C	uc002gnn.2	+	11	2409	c.2110T>C	c.(2110-2112)TCC>CCC	p.S704P	MYOCD_uc002gno.2_Missense_Mutation_p.S752P|MYOCD_uc002gnp.1_Missense_Mutation_p.S656P|MYOCD_uc002gnq.2_Intron	NM_153604	NP_705832	Q8IZQ8	MYCD_HUMAN	myocardin isoform 2	704					cardiac muscle cell differentiation|negative regulation of cell proliferation|negative regulation of cyclin-dependent protein kinase activity|positive regulation of smooth muscle cell differentiation|positive regulation of smooth muscle contraction|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation|regulation of histone acetylation|smooth muscle cell differentiation	nucleus	nucleic acid binding|RNA polymerase II transcription factor binding transcription factor activity|transcription factor binding			central_nervous_system(2)|skin(2)|ovary(1)	5				UCEC - Uterine corpus endometrioid carcinoma (92;0.0969)														---	---	---	---
MPRIP	23164	broad.mit.edu	37	17	17075070	17075070	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17075070G>A	uc002gqu.1	+	16	2258	c.2202G>A	c.(2200-2202)ACG>ACA	p.T734T	MPRIP_uc002gqv.1_Silent_p.T734T|MPRIP_uc002gqw.1_Silent_p.T489T|MPRIP_uc002gqx.1_Silent_p.T963T|MPRIP_uc002gqy.1_Silent_p.T963T|MPRIP_uc010cpl.1_5'Flank|MPRIP_uc010cpm.1_5'Flank	NM_201274	NP_958431	Q6WCQ1	MPRIP_HUMAN	myosin phosphatase-Rho interacting protein	734	Interaction with RHOA.|Potential.					cytoplasm|cytoskeleton	actin binding				0																		---	---	---	---
RAI1	10743	broad.mit.edu	37	17	17698482	17698482	+	Silent	SNP	C	T	T	rs149807469		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17698482C>T	uc002grm.2	+	3	2689	c.2220C>T	c.(2218-2220)AGC>AGT	p.S740S	RAI1_uc002grn.1_Silent_p.S740S	NM_030665	NP_109590	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	740						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	17720322	17720322	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17720322C>T	uc002gru.1	-	9	1929	c.1735G>A	c.(1735-1737)GCC>ACC	p.A579T	SREBF1_uc002grp.1_Missense_Mutation_p.A198T|SREBF1_uc002grq.1_Missense_Mutation_p.A98T|SREBF1_uc002grr.1_Missense_Mutation_p.A325T|SREBF1_uc002grs.1_Missense_Mutation_p.A555T|SREBF1_uc002grt.1_Missense_Mutation_p.A609T	NM_004176	NP_004167	P36956	SRBP1_HUMAN	sterol regulatory element binding transcription	579	Cytoplasmic (Potential).				cellular response to starvation|cholesterol metabolic process|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter	endoplasmic reticulum|endoplasmic reticulum membrane|ER to Golgi transport vesicle membrane|Golgi membrane|integral to membrane|nuclear envelope|nucleus	protein binding|protein binding|sequence-specific DNA binding transcription factor activity|sterol response element binding			skin(1)	1																		---	---	---	---
TOM1L2	146691	broad.mit.edu	37	17	17766046	17766046	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17766046T>C	uc002grz.3	-	11	1358	c.1201A>G	c.(1201-1203)ACG>GCG	p.T401A	TOM1L2_uc002gry.3_Missense_Mutation_p.T351A|TOM1L2_uc010vwy.1_Missense_Mutation_p.T348A|TOM1L2_uc010cpr.2_Missense_Mutation_p.T356A|TOM1L2_uc010vwz.1_Missense_Mutation_p.T253A|TOM1L2_uc010vxa.1_Missense_Mutation_p.T303A|TOM1L2_uc002grv.3_Missense_Mutation_p.T134A	NM_001082968	NP_001076437	Q6ZVM7	TM1L2_HUMAN	target of myb1-like 2 isoform 3	401					intracellular protein transport	intracellular					0	all_neural(463;0.228)																	---	---	---	---
SLC5A10	125206	broad.mit.edu	37	17	18874437	18874437	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18874437A>T	uc002guu.1	+	8	793	c.752A>T	c.(751-753)CAC>CTC	p.H251L	SLC5A10_uc002gur.1_Missense_Mutation_p.H168L|SLC5A10_uc002gut.1_Missense_Mutation_p.H251L|SLC5A10_uc002guv.1_Missense_Mutation_p.H224L|SLC5A10_uc010vyl.1_Missense_Mutation_p.H251L|FAM83G_uc002guw.2_3'UTR	NM_001042450	NP_001035915	A0PJK1	SC5AA_HUMAN	solute carrier family 5 (sodium/glucose	251	Extracellular (Potential).				sodium ion transport|transmembrane transport	integral to membrane	transporter activity			ovary(1)	1																		---	---	---	---
EPN2	22905	broad.mit.edu	37	17	19213313	19213313	+	Intron	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19213313C>A	uc002gvd.3	+						EPN2_uc010cql.1_Intron|EPN2_uc002gve.3_Intron|EPN2_uc002gvf.3_Intron|EPN2_uc010vyo.1_Intron|EPN2_uc002gvg.1_Intron|EPN2_uc010vyp.1_Intron|EPN2_uc010vyq.1_Intron|EPN2_uc002gvh.1_Intron	NM_014964	NP_055779			epsin 2 isoform b						endocytosis		lipid binding			skin(1)	1	all_cancers(12;3.11e-05)|all_epithelial(12;0.00121)|Hepatocellular(7;0.00345)|Breast(13;0.143)																	---	---	---	---
ALDH3A2	224	broad.mit.edu	37	17	19568354	19568354	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19568354G>T	uc002gwb.1	+	8	1422	c.1201G>T	c.(1201-1203)GGA>TGA	p.G401*	ALDH3A2_uc002gwa.1_Nonsense_Mutation_p.G401*|ALDH3A2_uc010cqr.1_Nonsense_Mutation_p.G208*|ALDH3A2_uc002gwc.1_Nonsense_Mutation_p.G401*|ALDH3A2_uc002gwd.1_Nonsense_Mutation_p.G208*	NM_000382	NP_000373	P51648	AL3A2_HUMAN	aldehyde dehydrogenase 3A2 isoform 2	401	Cytoplasmic.				cellular aldehyde metabolic process|central nervous system development|epidermis development|lipid metabolic process|peripheral nervous system development	endoplasmic reticulum membrane|integral to membrane	3-chloroallyl aldehyde dehydrogenase activity|aldehyde dehydrogenase (NAD) activity|aldehyde dehydrogenase			ovary(2)	2	all_cancers(12;1.39e-05)|all_epithelial(12;0.00158)|Breast(13;0.245)				NADH(DB00157)													---	---	---	---
MAP2K3	5606	broad.mit.edu	37	17	21201726	21201726	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21201726A>G	uc002gys.2	+	2	316	c.51A>G	c.(49-51)GGA>GGG	p.G17G	MAP2K3_uc002gyt.2_5'UTR|MAP2K3_uc002gyu.2_5'UTR	NM_145109	NP_659731	P46734	MP2K3_HUMAN	mitogen-activated protein kinase kinase 3	17					activation of MAPK activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of transcription, DNA-dependent|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				0				COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553)														---	---	---	---
KIAA0100	9703	broad.mit.edu	37	17	26943183	26943183	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26943183C>T	uc002hbu.2	-	37	6420	c.6321G>A	c.(6319-6321)GAG>GAA	p.E2107E	SGK494_uc010waq.1_5'Flank|SGK494_uc010war.1_5'Flank|SGK494_uc002hbr.1_5'Flank|uc002hbs.1_Intron|KIAA0100_uc002hbt.2_Silent_p.E436E	NM_014680	NP_055495	Q14667	K0100_HUMAN	hypothetical protein LOC9703 precursor	2107						extracellular region				ovary(2)|breast(1)|skin(1)	4	Lung NSC(42;0.00431)																	---	---	---	---
RAB34	83871	broad.mit.edu	37	17	27042914	27042914	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27042914C>T	uc002hce.2	-	4	842	c.218G>A	c.(217-219)TGC>TAC	p.C73Y	RAB34_uc002hcg.2_Missense_Mutation_p.C73Y|RAB34_uc002hcf.2_Missense_Mutation_p.C74Y|RAB34_uc010was.1_Missense_Mutation_p.C130Y|RAB34_uc010wat.1_Missense_Mutation_p.C130Y|RAB34_uc002hch.2_Missense_Mutation_p.C73Y|RAB34_uc010wau.1_Missense_Mutation_p.C51Y|RAB34_uc010wav.1_Missense_Mutation_p.C131Y	NM_031934	NP_114140	Q9BZG1	RAB34_HUMAN	Ras-related protein RAB34 isoform 1	73					protein transport|small GTPase mediated signal transduction	Golgi apparatus	GTP binding				0	Lung NSC(42;0.00431)																	---	---	---	---
PHF12	57649	broad.mit.edu	37	17	27251130	27251130	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27251130G>A	uc002hdg.1	-	4	1042	c.512C>T	c.(511-513)GCC>GTC	p.A171V	PHF12_uc010wbb.1_Missense_Mutation_p.A153V|PHF12_uc002hdi.1_Missense_Mutation_p.A167V|PHF12_uc002hdj.1_Missense_Mutation_p.A171V|PHF12_uc010crw.1_Intron|uc002hdl.2_5'Flank|PHF12_uc002hdh.1_5'UTR	NM_001033561	NP_001028733	Q96QT6	PHF12_HUMAN	PHD finger protein 12 isoform 1	171	Interaction with SIN3A.				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)															---	---	---	---
ANKRD13B	124930	broad.mit.edu	37	17	27936364	27936364	+	Intron	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27936364C>T	uc002hei.2	+						ANKRD13B_uc002heh.2_Intron|ANKRD13B_uc002hej.2_Intron	NM_152345	NP_689558			ankyrin repeat domain 13B												0																		---	---	---	---
SSH2	85464	broad.mit.edu	37	17	28003848	28003848	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28003848G>A	uc002heo.1	-	7	523	c.523C>T	c.(523-525)CAG>TAG	p.Q175*	SSH2_uc010wbh.1_Nonsense_Mutation_p.Q202*|SSH2_uc002hep.1_Nonsense_Mutation_p.Q175*|SSH2_uc002heq.2_Nonsense_Mutation_p.Q182*|SSH2_uc002her.2_Nonsense_Mutation_p.Q175*|SSH2_uc010csc.1_Nonsense_Mutation_p.Q175*	NM_033389	NP_203747	Q76I76	SSH2_HUMAN	slingshot 2	175					actin cytoskeleton organization|regulation of actin polymerization or depolymerization|regulation of axonogenesis|regulation of lamellipodium assembly	cytoplasm|cytoskeleton	actin binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			skin(2)	2																		---	---	---	---
BLMH	642	broad.mit.edu	37	17	28599573	28599573	+	Intron	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28599573A>G	uc002hez.1	-						BLMH_uc010wbn.1_Intron	NM_000386	NP_000377			bleomycin hydrolase						proteolysis	cytoplasm|nucleus	aminopeptidase activity|carboxypeptidase activity|cysteine-type endopeptidase activity|protein binding			ovary(1)	1																		---	---	---	---
RDM1	201299	broad.mit.edu	37	17	34257080	34257080	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34257080C>A	uc002hkh.2	-	2	325	c.276G>T	c.(274-276)AAG>AAT	p.K92N	RDM1_uc010cty.2_RNA|RDM1_uc010ctz.2_Missense_Mutation_p.K69N|RDM1_uc010cua.2_Missense_Mutation_p.K69N|RDM1_uc002hkg.3_Missense_Mutation_p.K69N|RDM1_uc010cub.2_RNA|RDM1_uc010cud.2_Missense_Mutation_p.K92N|RDM1_uc010cuf.2_RNA|RDM1_uc010cue.2_Intron|RDM1_uc010cug.2_RNA|RDM1_uc010cuc.2_Missense_Mutation_p.K92N|RDM1_uc010wco.1_Missense_Mutation_p.K69N|RDM1_uc010wcp.1_Missense_Mutation_p.K69N|RDM1_uc002hki.2_Missense_Mutation_p.K92N	NM_145654	NP_663629	Q8NG50	RDM1_HUMAN	RAD52 motif 1 isoform 1	92	RRM.|Necessary for nuclear and nucleolar localization.|Necessary for nuclear localization and for nucleolar accumulation in response to heat shock.				DNA recombination|DNA repair	Cajal body|cytoplasm|nucleolus|PML body	DNA binding|nucleotide binding|RNA binding			ovary(1)	1		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)									Direct_reversal_of_damage|Other_identified_genes_with_known_or_suspected_DNA_repair_function					---	---	---	---
GPR179	440435	broad.mit.edu	37	17	36483525	36483525	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36483525C>T	uc002hpz.2	-	11	5948	c.5927G>A	c.(5926-5928)CGC>CAC	p.R1976H		NM_001004334	NP_001004334	Q6PRD1	GP179_HUMAN	GPR158-like 1 precursor	1976	Cytoplasmic (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(3)	3	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)																---	---	---	---
PIP4K2B	8396	broad.mit.edu	37	17	36933950	36933950	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36933950C>A	uc002hqs.2	-	7	1278	c.797G>T	c.(796-798)CGG>CTG	p.R266L	PIP4K2B_uc010wdt.1_Missense_Mutation_p.R266L|PIP4K2B_uc010wdu.1_Missense_Mutation_p.R202L	NM_003559	NP_003550	P78356	PI42B_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type	266	PIPK.				cell surface receptor linked signaling pathway	endoplasmic reticulum membrane|plasma membrane	1-phosphatidylinositol-4-phosphate 5-kinase activity|1-phosphatidylinositol-5-phosphate 4-kinase activity|ATP binding|receptor signaling protein activity			ovary(1)	1																		---	---	---	---
CDK12	51755	broad.mit.edu	37	17	37673788	37673788	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37673788G>A	uc010cvv.2	+	10	3528	c.2942G>A	c.(2941-2943)CGT>CAT	p.R981H	CDK12_uc010wef.1_Missense_Mutation_p.R980H|CDK12_uc002hrw.3_Missense_Mutation_p.R981H	NM_016507	NP_057591	Q9NYV4	CDK12_HUMAN	Cdc2-related kinase, arginine/serine-rich	981	Protein kinase.				mRNA processing|phosphorylation of RNA polymerase II C-terminal domain|protein autophosphorylation|regulation of MAP kinase activity|RNA splicing	nuclear cyclin-dependent protein kinase holoenzyme complex|nuclear speck|nucleolus	ATP binding|cyclin-dependent protein kinase activity|protein binding|RNA polymerase II carboxy-terminal domain kinase activity			ovary(10)|lung(4)|breast(2)|skin(2)|large_intestine(1)	19															TCGA Ovarian(9;0.13)			---	---	---	---
ZPBP2	124626	broad.mit.edu	37	17	38024801	38024801	+	Splice_Site	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38024801G>A	uc002hte.2	+	2	206	c.53_splice	c.e2-1	p.V18_splice	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)															---	---	---	---
KRT28	162605	broad.mit.edu	37	17	38955915	38955915	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38955915G>A	uc002hvh.1	-	1	297	c.231C>T	c.(229-231)AGC>AGT	p.S77S		NM_181535	NP_853513	Q7Z3Y7	K1C28_HUMAN	keratin 25D	77	Gly-rich.|Head.					cytoplasm|intermediate filament	structural molecule activity			ovary(1)	1		Breast(137;0.000301)																---	---	---	---
KRT38	8687	broad.mit.edu	37	17	39593778	39593778	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39593778C>T	uc002hwq.1	-	7	1680	c.1257G>A	c.(1255-1257)CCG>CCA	p.P419P		NM_006771	NP_006762	O76015	KRT38_HUMAN	keratin 38	419	Tail.					intermediate filament	structural molecule activity			skin(2)	2		Breast(137;0.000496)																---	---	---	---
JUP	3728	broad.mit.edu	37	17	39680724	39680724	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39680724G>A	uc010wfs.1	-	7	1226	c.1218C>T	c.(1216-1218)ACC>ACT	p.T406T	KRT15_uc002hxb.1_5'Flank|uc002hxc.1_5'Flank|KRT19_uc002hxd.3_Silent_p.T243T	NM_021991	NP_068831	P14923	PLAK_HUMAN	junction plakoglobin	Error:Variant_position_missing_in_P14923_after_alignment					adherens junction organization|atrioventricular valve morphogenesis|cell migration|cell morphogenesis|cellular response to indole-3-methanol|cytoskeletal anchoring at plasma membrane|detection of mechanical stimulus|ectoderm development|endothelial cell-cell adhesion|gastrulation|morphogenesis of embryonic epithelium|negative regulation of heart induction by canonical Wnt receptor signaling pathway|negative regulation of Wnt receptor signaling pathway involved in heart development|nervous system development|oocyte development|positive regulation of protein import into nucleus|positive regulation of sequence-specific DNA binding transcription factor activity|skin development	actin cytoskeleton|Axin-APC-beta-catenin-GSK3B complex|basolateral plasma membrane|catenin complex|desmosome|fascia adherens|gamma-catenin-TCF7L2 complex|internal side of plasma membrane|nucleus|protein-DNA complex|Z disc|zonula adherens	alpha-catenin binding|cadherin binding|protein homodimerization activity|protein kinase binding|protein phosphatase binding|RPTP-like protein binding|specific RNA polymerase II transcription factor activity|transcription coactivator activity			ovary(2)|lung(2)|breast(1)	5		Breast(137;0.000162)	BRCA - Breast invasive adenocarcinoma(4;0.233)	BRCA - Breast invasive adenocarcinoma(366;0.15)														---	---	---	---
HAP1	9001	broad.mit.edu	37	17	39881413	39881413	+	Intron	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39881413G>A	uc002hxm.1	-						JUP_uc010wfs.1_Intron|HAP1_uc002hxn.1_Intron|HAP1_uc002hxo.1_Intron|HAP1_uc002hxp.1_Intron	NM_177977	NP_817084			huntingtin-associated protein 1 isoform 2						brain development|protein localization|synaptic transmission	actin cytoskeleton	protein binding			ovary(2)	2		Breast(137;0.000162)	BRCA - Breast invasive adenocarcinoma(4;0.0677)															---	---	---	---
PSMC3IP	29893	broad.mit.edu	37	17	40729286	40729286	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40729286T>C	uc002iai.2	-	3	213	c.170A>G	c.(169-171)CAA>CGA	p.Q57R	PSMC3IP_uc002iaj.2_5'UTR|PSMC3IP_uc002iak.2_Missense_Mutation_p.Q57R|PSMC3IP_uc010wgn.1_5'UTR|PSMC3IP_uc010wgo.1_RNA|PSMC3IP_uc010wgp.1_RNA	NM_016556	NP_057640	Q9P2W1	HOP2_HUMAN	PSMC3 interacting protein isoform 2	57					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)														---	---	---	---
TUBG2	27175	broad.mit.edu	37	17	40818663	40818663	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40818663C>T	uc010wgr.1	+	11	1457	c.1201C>T	c.(1201-1203)CGG>TGG	p.R401W	TUBG2_uc002iaq.2_3'UTR|TUBG2_uc002iar.2_Missense_Mutation_p.R248W|TUBG2_uc002ias.2_Missense_Mutation_p.R243W|TUBG2_uc002iap.2_Missense_Mutation_p.R248W	NM_016437	NP_057521	Q9NRH3	TBG2_HUMAN	tubulin, gamma 2	401					G2/M transition of mitotic cell cycle|microtubule-based process|protein polymerization	cytosol	GTP binding|GTPase activity|structural molecule activity			ovary(1)	1		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.141)														---	---	---	---
DHX8	1659	broad.mit.edu	37	17	41570275	41570275	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41570275C>T	uc002idu.1	+	6	803	c.730C>T	c.(730-732)CGG>TGG	p.R244W	DHX8_uc010wif.1_Missense_Mutation_p.R153W|DHX8_uc010wig.1_Missense_Mutation_p.R244W	NM_004941	NP_004932	Q14562	DHX8_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 8	244						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)														---	---	---	---
MPP3	4356	broad.mit.edu	37	17	41879176	41879176	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41879176C>T	uc002iei.3	-	20	1817	c.1651G>A	c.(1651-1653)GCC>ACC	p.A551T	MPP3_uc002ieh.2_Missense_Mutation_p.A576T|MPP3_uc002iej.2_RNA	NM_001932	NP_001923	Q13368	MPP3_HUMAN	palmitoylated membrane protein 3	551	Guanylate kinase-like.				signal transduction	cell surface|integral to plasma membrane	guanylate kinase activity			large_intestine(1)|skin(1)	2		Breast(137;0.00394)		BRCA - Breast invasive adenocarcinoma(366;0.119)														---	---	---	---
HDAC5	10014	broad.mit.edu	37	17	42156018	42156018	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42156018C>T	uc002ifd.1	-	26	3390	c.3179G>A	c.(3178-3180)TGT>TAT	p.C1060Y	HDAC5_uc002ife.1_Missense_Mutation_p.C1060Y|HDAC5_uc002iff.1_Missense_Mutation_p.C1061Y|HDAC5_uc010czp.1_Missense_Mutation_p.C975Y	NM_005474	NP_005465	Q9UQL6	HDAC5_HUMAN	histone deacetylase 5 isoform 1	1060					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)														---	---	---	---
RUNDC3A	10900	broad.mit.edu	37	17	42390862	42390862	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42390862G>A	uc002igl.3	+	4	723	c.449G>A	c.(448-450)CGG>CAG	p.R150Q	RUNDC3A_uc002igi.2_Missense_Mutation_p.R150Q|RUNDC3A_uc002igj.2_Missense_Mutation_p.R145Q|RUNDC3A_uc002igk.2_Missense_Mutation_p.R146Q	NM_001144825	NP_001138297	Q59EK9	RUN3A_HUMAN	RUN domain containing 3A isoform 1	150	Interaction with RAP2A (By similarity).|RUN.				small GTPase mediated signal transduction		small GTPase regulator activity				0		Prostate(33;0.0233)		BRCA - Breast invasive adenocarcinoma(366;0.189)														---	---	---	---
KIAA1267	284058	broad.mit.edu	37	17	44116010	44116010	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44116010G>A	uc002ikb.2	-	9	2520	c.2435C>T	c.(2434-2436)GCA>GTA	p.A812V	KIAA1267_uc002ikc.2_Missense_Mutation_p.A812V|KIAA1267_uc002ikd.2_Missense_Mutation_p.A812V|KIAA1267_uc010dav.2_Missense_Mutation_p.A812V|KIAA1267_uc010wkb.1_Missense_Mutation_p.A143V|KIAA1267_uc010wkc.1_Missense_Mutation_p.A80V	NM_015443	NP_056258	Q7Z3B3	K1267_HUMAN	hypothetical protein LOC284058	812						MLL1 complex	protein binding			skin(2)	2		Melanoma(429;0.211)																---	---	---	---
NFE2L1	4779	broad.mit.edu	37	17	46136299	46136299	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46136299G>A	uc002imz.3	+	6	2266	c.1615G>A	c.(1615-1617)GAG>AAG	p.E539K	NFE2L1_uc002ina.3_Missense_Mutation_p.E509K|NFE2L1_uc002inb.3_Missense_Mutation_p.E509K|NFE2L1_uc010wle.1_Missense_Mutation_p.E351K|NFE2L1_uc010wlf.1_Missense_Mutation_p.E383K	NM_003204	NP_003195	Q14494	NF2L1_HUMAN	nuclear factor erythroid 2-like 1	539					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																		---	---	---	---
B4GALNT2	124872	broad.mit.edu	37	17	47236420	47236420	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47236420G>T	uc002ion.2	+	6	759	c.700G>T	c.(700-702)GGG>TGG	p.G234W	B4GALNT2_uc010wlt.1_Missense_Mutation_p.G148W|B4GALNT2_uc010wlu.1_Missense_Mutation_p.G174W	NM_153446	NP_703147	Q8NHY0	B4GN2_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 2	234	Lumenal (Potential).				lipid glycosylation|negative regulation of cell-cell adhesion|UDP-N-acetylgalactosamine metabolic process	integral to Golgi membrane	acetylgalactosaminyltransferase activity			large_intestine(1)|ovary(1)	2			all cancers(6;0.000316)															---	---	---	---
SCPEP1	59342	broad.mit.edu	37	17	55083545	55083545	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55083545C>T	uc002iuv.3	+	13	1361	c.1308C>T	c.(1306-1308)GAC>GAT	p.D436D	SCPEP1_uc010dcl.2_RNA|SCPEP1_uc010wnk.1_Silent_p.D386D	NM_021626	NP_067639	Q9HB40	RISC_HUMAN	serine carboxypeptidase 1 precursor	436					proteolysis	extracellular region	serine-type carboxypeptidase activity			skin(1)	1	Breast(9;2.86e-08)																	---	---	---	---
RNF43	54894	broad.mit.edu	37	17	56437605	56437605	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56437605C>T	uc002iwf.2	-	7	2813	c.857G>A	c.(856-858)CGG>CAG	p.R286Q	RNF43_uc010wnv.1_Missense_Mutation_p.R245Q|RNF43_uc002iwh.3_Missense_Mutation_p.R286Q|RNF43_uc002iwg.3_Missense_Mutation_p.R286Q|RNF43_uc010dcw.2_Missense_Mutation_p.R159Q	NM_017763	NP_060233	Q68DV7	RNF43_HUMAN	ring finger protein 43 precursor	286	RING-type; atypical.|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)																	---	---	---	---
CLTC	1213	broad.mit.edu	37	17	57744280	57744280	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57744280T>C	uc002ixq.1	+	13	2513	c.2070T>C	c.(2068-2070)CAT>CAC	p.H690H	CLTC_uc002ixp.2_Silent_p.H690H|CLTC_uc002ixr.1_Silent_p.H694H	NM_004859	NP_004850	Q00610	CLH1_HUMAN	clathrin heavy chain 1	690	Heavy chain arm.|Proximal segment.				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	57771129	57771129	+	Silent	SNP	C	A	A	rs148633723		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57771129C>A	uc002ixq.1	+	32	5387	c.4944C>A	c.(4942-4944)GCC>GCA	p.A1648A	CLTC_uc002ixr.1_Silent_p.A1652A	NM_004859	NP_004850	Q00610	CLH1_HUMAN	clathrin heavy chain 1	1648	Heavy chain arm.|Proximal segment.|Trimerization (By similarity).				axon guidance|epidermal growth factor receptor signaling pathway|intracellular protein transport|mitosis|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|post-Golgi vesicle-mediated transport|receptor internalization|transferrin transport	clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|cytosol|melanosome|spindle	protein binding|structural molecule activity		CLTC/ALK(44)|CLTC/TFE3(2)	haematopoietic_and_lymphoid_tissue(33)|soft_tissue(11)|kidney(2)|ovary(1)|breast(1)	48	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)							T	ALK|TFE3	ALCL|renal 								---	---	---	---
RPS6KB1	6198	broad.mit.edu	37	17	58003953	58003953	+	Intron	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58003953C>T	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)															---	---	---	---
HEATR6	63897	broad.mit.edu	37	17	58134524	58134524	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58134524C>T	uc002iyk.1	-	12	1981	c.1964G>A	c.(1963-1965)CGA>CAA	p.R655Q	HEATR6_uc010ddk.1_Missense_Mutation_p.R194Q|HEATR6_uc010wos.1_Missense_Mutation_p.R487Q	NM_022070	NP_071353	Q6AI08	HEAT6_HUMAN	HEAT repeat containing 6	655							binding			ovary(1)|skin(1)	2	all_cancers(5;2.25e-13)|Breast(5;4.84e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		BRCA - Breast invasive adenocarcinoma(1;5.93e-19)|Epithelial(12;7.59e-12)|all cancers(12;1.26e-10)															---	---	---	---
HEATR6	63897	broad.mit.edu	37	17	58147131	58147131	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58147131C>T	uc002iyk.1	-	7	897	c.880G>A	c.(880-882)GAT>AAT	p.D294N	HEATR6_uc010wos.1_Missense_Mutation_p.D126N	NM_022070	NP_071353	Q6AI08	HEAT6_HUMAN	HEAT repeat containing 6	294							binding			ovary(1)|skin(1)	2	all_cancers(5;2.25e-13)|Breast(5;4.84e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		BRCA - Breast invasive adenocarcinoma(1;5.93e-19)|Epithelial(12;7.59e-12)|all cancers(12;1.26e-10)															---	---	---	---
TANC2	26115	broad.mit.edu	37	17	61497887	61497887	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61497887G>A	uc002jal.3	+	25	4567	c.4544G>A	c.(4543-4545)CGT>CAT	p.R1515H	TANC2_uc010wpe.1_3'UTR|TANC2_uc002jao.3_Missense_Mutation_p.R626H	NM_025185	NP_079461	Q9HCD6	TANC2_HUMAN	tetratricopeptide repeat, ankyrin repeat and	1515							binding			ovary(2)	2																		---	---	---	---
TANC2	26115	broad.mit.edu	37	17	61497916	61497916	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61497916G>T	uc002jal.3	+	25	4596	c.4573G>T	c.(4573-4575)GGC>TGC	p.G1525C	TANC2_uc010wpe.1_3'UTR|TANC2_uc002jao.3_Missense_Mutation_p.G636C	NM_025185	NP_079461	Q9HCD6	TANC2_HUMAN	tetratricopeptide repeat, ankyrin repeat and	1525							binding			ovary(2)	2																		---	---	---	---
FTSJ3	117246	broad.mit.edu	37	17	61898993	61898993	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61898993G>A	uc002jbz.2	-	15	1685	c.1607C>T	c.(1606-1608)GCT>GTT	p.A536V	FTSJ3_uc002jca.2_Missense_Mutation_p.A536V	NM_017647	NP_060117	Q8IY81	RRMJ3_HUMAN	FtsJ homolog 3	536					RNA methylation|rRNA processing	nucleolus	methyltransferase activity|nucleic acid binding			ovary(1)	1																		---	---	---	---
SMARCD2	6603	broad.mit.edu	37	17	61912092	61912092	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61912092C>T	uc010deb.1	-	6	1109	c.792G>A	c.(790-792)CTG>CTA	p.L264L	SMARCD2_uc010wpt.1_Silent_p.L216L|SMARCD2_uc010dea.1_Silent_p.L189L|SMARCD2_uc010dec.1_Silent_p.L243L	NM_001098426	NP_001091896	Q92925	SMRD2_HUMAN	SWI/SNF-related matrix-associated	264					chromatin modification|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	SWI/SNF complex	protein binding|transcription coactivator activity				0																OREG0024642	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
SCN4A	6329	broad.mit.edu	37	17	62020407	62020407	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62020407T>C	uc002jds.1	-	23	4144	c.4067A>G	c.(4066-4068)GAC>GGC	p.D1356G		NM_000334	NP_000325	P35499	SCN4A_HUMAN	voltage-gated sodium channel type 4 alpha	1356	Helical; Name=S1 of repeat IV; (Potential).|IV.				muscle contraction	voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(1)|pancreas(1)|skin(1)	3					Lamotrigine(DB00555)													---	---	---	---
LRRC37A3	374819	broad.mit.edu	37	17	62852005	62852005	+	Missense_Mutation	SNP	G	C	C	rs140806799	by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62852005G>C	uc002jey.2	-	13	5343	c.4812C>G	c.(4810-4812)ATC>ATG	p.I1604M	LRRC37A3_uc010wqg.1_Missense_Mutation_p.I722M|LRRC37A3_uc002jex.1_Missense_Mutation_p.I581M|LRRC37A3_uc010wqf.1_Missense_Mutation_p.I642M	NM_199340	NP_955372	O60309	L37A3_HUMAN	leucine rich repeat containing 37, member A3	1604	Cytoplasmic (Potential).					integral to membrane					0																		---	---	---	---
CACNG5	27091	broad.mit.edu	37	17	64880822	64880822	+	Intron	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64880822C>T	uc010wqi.1	+						CACNG5_uc002jfr.2_Missense_Mutation_p.T205I|CACNG5_uc010wqj.1_Intron	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)															---	---	---	---
ARSG	22901	broad.mit.edu	37	17	66303763	66303763	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66303763C>T	uc002jhc.2	+	2	925	c.129C>T	c.(127-129)GCC>GCT	p.A43A	ARSG_uc002jhb.1_Intron	NM_014960	NP_055775	Q96EG1	ARSG_HUMAN	Arylsulfatase G precursor	43					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)															---	---	---	---
ABCA8	10351	broad.mit.edu	37	17	66937011	66937011	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66937011G>A	uc002jhp.2	-	3	368	c.189C>T	c.(187-189)GAC>GAT	p.D63D	ABCA8_uc002jhq.2_Silent_p.D63D|ABCA8_uc010wqq.1_Silent_p.D63D|ABCA8_uc010wqr.1_Silent_p.D2D|ABCA8_uc002jhr.2_Silent_p.D63D|ABCA8_uc002jhs.2_Silent_p.D63D|ABCA8_uc002jht.2_Silent_p.D63D	NM_007168	NP_009099	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A member 8	63						integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(2)|skin(1)	3	Breast(10;4.56e-13)																	---	---	---	---
ABCA9	10350	broad.mit.edu	37	17	66982353	66982353	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66982353G>A	uc002jhu.2	-	32	4303	c.4160C>T	c.(4159-4161)GCT>GTT	p.A1387V	ABCA9_uc010dez.2_Missense_Mutation_p.A1349V	NM_080283	NP_525022	Q8IUA7	ABCA9_HUMAN	ATP-binding cassette, sub-family A, member 9	1387	ABC transporter 2.				transport	integral to membrane	ATP binding|ATPase activity			ovary(4)|upper_aerodigestive_tract(1)|central_nervous_system(1)	6	Breast(10;1.47e-12)																	---	---	---	---
ABCA9	10350	broad.mit.edu	37	17	67016664	67016664	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67016664A>G	uc002jhu.2	-	19	2608	c.2465T>C	c.(2464-2466)CTG>CCG	p.L822P	ABCA9_uc010dez.2_Missense_Mutation_p.L822P	NM_080283	NP_525022	Q8IUA7	ABCA9_HUMAN	ATP-binding cassette, sub-family A, member 9	822					transport	integral to membrane	ATP binding|ATPase activity			ovary(4)|upper_aerodigestive_tract(1)|central_nervous_system(1)	6	Breast(10;1.47e-12)																	---	---	---	---
ABCA9	10350	broad.mit.edu	37	17	67039677	67039677	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67039677G>A	uc002jhu.2	-	6	896	c.753C>T	c.(751-753)TAC>TAT	p.Y251Y	ABCA9_uc010dez.2_Silent_p.Y251Y|ABCA9_uc002jhv.2_Silent_p.Y251Y	NM_080283	NP_525022	Q8IUA7	ABCA9_HUMAN	ATP-binding cassette, sub-family A, member 9	251					transport	integral to membrane	ATP binding|ATPase activity			ovary(4)|upper_aerodigestive_tract(1)|central_nervous_system(1)	6	Breast(10;1.47e-12)																	---	---	---	---
ABCA6	23460	broad.mit.edu	37	17	67110969	67110969	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67110969G>A	uc002jhw.1	-	13	1891	c.1716C>T	c.(1714-1716)ACC>ACT	p.T572T	ABCA6_uc002jhx.1_Silent_p.T25T	NM_080284	NP_525023	Q8N139	ABCA6_HUMAN	ATP-binding cassette, sub-family A, member 6	572	ABC transporter 1.				transport	integral to membrane	ATP binding|ATPase activity			upper_aerodigestive_tract(2)|large_intestine(2)|ovary(2)|skin(1)	7	Breast(10;5.65e-12)																	---	---	---	---
ABCA10	10349	broad.mit.edu	37	17	67170767	67170767	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67170767C>A	uc010dfa.1	-	25	3908	c.3029G>T	c.(3028-3030)TGG>TTG	p.W1010L	ABCA10_uc010wqs.1_Intron|ABCA10_uc010wqt.1_RNA	NM_080282	NP_525021	Q8WWZ4	ABCAA_HUMAN	ATP-binding cassette, sub-family A, member 10	1010					transport	integral to membrane	ATP binding|ATPase activity			ovary(2)|central_nervous_system(1)|skin(1)	4	Breast(10;6.95e-12)																	---	---	---	---
CDC42EP4	23580	broad.mit.edu	37	17	71282053	71282053	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71282053G>T	uc002jjn.2	-	2	734	c.587C>A	c.(586-588)GCC>GAC	p.A196D	CDC42EP4_uc002jjo.2_Missense_Mutation_p.A196D|CDC42EP4_uc002jjp.1_Missense_Mutation_p.A126D	NM_012121	NP_036253	Q9H3Q1	BORG4_HUMAN	Cdc42 effector protein 4	196					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)															---	---	---	---
MRPS7	51081	broad.mit.edu	37	17	73259534	73259534	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73259534C>A	uc002jnm.3	+	4	686	c.453C>A	c.(451-453)AAC>AAA	p.N151K	GGA3_uc002jni.1_5'Flank|GGA3_uc002jnj.1_5'Flank|GGA3_uc010wrw.1_5'Flank|GGA3_uc002jnk.1_5'Flank|GGA3_uc010wrx.1_5'Flank|GGA3_uc010wry.1_5'Flank|GGA3_uc010wrz.1_5'Flank|MRPS7_uc002jnl.2_Missense_Mutation_p.N151K|MRPS7_uc002jnn.3_Missense_Mutation_p.N180K	NM_015971	NP_057055	Q9Y2R9	RT07_HUMAN	mitochondrial ribosomal protein S7 precursor	151					translation	cytosolic small ribosomal subunit|mitochondrion	protein binding|RNA binding|structural constituent of ribosome			central_nervous_system(1)	1	all_cancers(13;1.25e-07)|all_epithelial(9;2.63e-08)|Breast(9;1.06e-07)		all cancers(21;3.02e-07)|Epithelial(20;2.92e-06)															---	---	---	---
FBF1	85302	broad.mit.edu	37	17	73908365	73908365	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73908365T>C	uc002jqc.2	-	28	3500	c.3226A>G	c.(3226-3228)ACC>GCC	p.T1076A	FBF1_uc002jqa.1_RNA|FBF1_uc010wsp.1_Missense_Mutation_p.T1067A|MRPL38_uc002jpz.1_5'Flank|FBF1_uc002jqb.2_RNA|FBF1_uc010dgr.1_Missense_Mutation_p.T386A	NM_001080542	NP_001074011	Q8TES7	FBF1_HUMAN	Fas (TNFRSF6) binding factor 1	1076											0																		---	---	---	---
QRICH2	84074	broad.mit.edu	37	17	74288203	74288203	+	Missense_Mutation	SNP	G	A	A	rs148029652		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74288203G>A	uc002jrd.1	-	4	2287	c.2107C>T	c.(2107-2109)CGT>TGT	p.R703C	QRICH2_uc010wsz.1_Missense_Mutation_p.R629C|QRICH2_uc010dgw.1_Intron	NM_032134	NP_115510	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	703	Gln-rich.						protein binding			ovary(1)|pancreas(1)|lung(1)|central_nervous_system(1)|skin(1)	5																		---	---	---	---
RHBDF2	79651	broad.mit.edu	37	17	74470845	74470845	+	Silent	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74470845G>T	uc002jrq.1	-	11	1649	c.1356C>A	c.(1354-1356)ATC>ATA	p.I452I	RHBDF2_uc002jrp.1_Silent_p.I423I|RHBDF2_uc002jrr.1_Silent_p.I304I|RHBDF2_uc010wtf.1_Silent_p.I423I	NM_024599	NP_078875	Q6PJF5	RHDF2_HUMAN	rhomboid, veinlet-like 6 isoform 1	452	Lumenal (Potential).				negative regulation of protein secretion|protein transport|proteolysis	endoplasmic reticulum membrane|integral to membrane	growth factor binding|serine-type endopeptidase activity				0																		---	---	---	---
CYGB	114757	broad.mit.edu	37	17	74527577	74527577	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74527577C>T	uc002jru.1	-	2	498	c.340G>A	c.(340-342)GCC>ACC	p.A114T	CYGB_uc002jrv.1_Missense_Mutation_p.A49T|PRCD_uc002jrw.1_Intron	NM_134268	NP_599030	Q8WWM9	CYGB_HUMAN	cytoglobin	114	Globin.				response to oxidative stress	cytoplasm	heme binding|oxygen binding|oxygen transporter activity|peroxidase activity				0																		---	---	---	---
SEC14L1	6397	broad.mit.edu	37	17	75212636	75212636	+	3'UTR	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75212636G>A	uc002jto.2	+	17					SEC14L1_uc010dhc.2_Missense_Mutation_p.R717Q|SEC14L1_uc010wth.1_3'UTR|SEC14L1_uc002jtm.2_3'UTR|SEC14L1_uc010wti.1_3'UTR	NM_003003	NP_002994			SEC14 (S. cerevisiae)-like 1 isoform a						transport	Golgi apparatus|integral to membrane	binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	76487517	76487517	+	IGR	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76487517C>A								DNAH17 (18661 upstream) : CYTH1 (182614 downstream)																																			---	---	---	---
DNAH17	8632	broad.mit.edu	37	17	76506595	76506595	+	5'UTR	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76506595G>A	uc010wtu.1	-	1										full-length cDNA clone CS0DJ002YI14 of T cells (Jurkat cell line) Cot 10-normalized of Homo sapiens (human).											ovary(6)|breast(2)|skin(1)	9			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)															---	---	---	---
ENGASE	64772	broad.mit.edu	37	17	77082376	77082376	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77082376G>T	uc002jwv.2	+	14	2185	c.2177G>T	c.(2176-2178)CGG>CTG	p.R726L	ENGASE_uc002jww.2_Missense_Mutation_p.R431L	NM_001042573	NP_001036038	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase	726						cytosol	mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity			skin(1)	1																		---	---	---	---
CARD14	79092	broad.mit.edu	37	17	78176086	78176086	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78176086C>T	uc002jxw.1	+	15	2281	c.2086C>T	c.(2086-2088)CAG>TAG	p.Q696*	CARD14_uc002jxt.1_RNA|CARD14_uc002jxv.2_Nonsense_Mutation_p.Q696*|CARD14_uc010wud.1_RNA	NM_024110	NP_077015	Q9BXL6	CAR14_HUMAN	caspase recruitment domain protein 14 isoform 1	696					activation of NF-kappaB-inducing kinase activity|positive regulation of protein phosphorylation|regulation of apoptosis	aggresome|cytoplasm|plasma membrane	CARD domain binding			ovary(4)|skin(1)	5	all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.017)|BRCA - Breast invasive adenocarcinoma(99;0.0908)															---	---	---	---
RNF213	57674	broad.mit.edu	37	17	78354648	78354648	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78354648C>T	uc002jyh.1	+	31	8100	c.7877C>T	c.(7876-7878)ACG>ATG	p.T2626M	uc002jyi.1_Intron|RNF213_uc010dhw.1_Missense_Mutation_p.T1008M	NM_020914	NP_065965	Q9HCF4	ALO17_HUMAN	ring finger protein 213	Error:Variant_position_missing_in_Q9HCF4_after_alignment										ovary(8)|lung(6)|breast(3)|large_intestine(2)|central_nervous_system(1)|pancreas(1)	21	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)															---	---	---	---
RPTOR	57521	broad.mit.edu	37	17	78599546	78599546	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78599546C>A	uc002jyt.1	+	2	1023	c.218C>A	c.(217-219)CCC>CAC	p.P73H	RPTOR_uc002jys.2_Missense_Mutation_p.P73H|RPTOR_uc010wuf.1_5'UTR|RPTOR_uc010wug.1_Missense_Mutation_p.P73H	NM_020761	NP_065812	Q8N122	RPTOR_HUMAN	raptor isoform 1	73					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	78820269	78820269	+	Intron	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78820269G>A	uc002jyt.1	+						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																		---	---	---	---
GPS1	2873	broad.mit.edu	37	17	80011774	80011774	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80011774G>A	uc002kdl.1	+	3	202	c.157G>A	c.(157-159)GGC>AGC	p.G53S	RFNG_uc002kdj.2_5'Flank|GPS1_uc002kdk.1_Missense_Mutation_p.G93S|GPS1_uc010dij.1_Missense_Mutation_p.G93S|GPS1_uc002kdm.1_Missense_Mutation_p.G37S|GPS1_uc002kdn.1_Missense_Mutation_p.G53S|GPS1_uc002kdo.1_Missense_Mutation_p.G53S|GPS1_uc010wvh.1_Missense_Mutation_p.G45S	NM_004127	NP_004118	Q13098	CSN1_HUMAN	G protein pathway suppressor 1 isoform 2	53					cell cycle|cullin deneddylation|inactivation of MAPK activity|JNK cascade	cytoplasm|signalosome	GTPase inhibitor activity|protein binding			central_nervous_system(1)	1	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0211)															---	---	---	---
DUS1L	64118	broad.mit.edu	37	17	80019841	80019841	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80019841G>A	uc002kdq.2	-	5	948	c.529C>T	c.(529-531)CGC>TGC	p.R177C	DUS1L_uc002kdp.2_Missense_Mutation_p.R46C|DUS1L_uc002kdr.2_Missense_Mutation_p.R177C|DUS1L_uc002kds.2_RNA|DUS1L_uc002kdt.2_RNA|DUS1L_uc010wvi.1_Missense_Mutation_p.R160C	NM_022156	NP_071439	Q6P1R4	DUS1L_HUMAN	PP3111 protein	177					tRNA processing		flavin adenine dinucleotide binding|tRNA dihydrouridine synthase activity			skin(1)	1	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0211)															---	---	---	---
FASN	2194	broad.mit.edu	37	17	80037221	80037221	+	Intron	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80037221C>A	uc002kdu.2	-						FASN_uc002kdv.1_Intron	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)													---	---	---	---
ZNF750	79755	broad.mit.edu	37	17	80788993	80788993	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80788993G>A	uc002kga.2	-	2	1649	c.1338C>T	c.(1336-1338)TAC>TAT	p.Y446Y	TBCD_uc002kfx.1_Intron|TBCD_uc002kfy.1_Intron|TBCD_uc002kfz.2_Intron	NM_024702	NP_078978	Q32MQ0	ZN750_HUMAN	zinc finger protein 750	446						intracellular	zinc ion binding			central_nervous_system(1)	1	Breast(20;0.000523)|all_neural(118;0.0779)	all_cancers(8;0.0514)|all_epithelial(8;0.0748)	OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.149)															---	---	---	---
LAMA1	284217	broad.mit.edu	37	18	7008483	7008483	+	Intron	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:7008483G>A	uc002knm.2	-						LAMA1_uc010wzj.1_Intron	NM_005559	NP_005550			laminin, alpha 1 precursor						axon guidance|cell adhesion|cell surface receptor linked signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	extracellular space|laminin-1 complex|laminin-3 complex	extracellular matrix structural constituent|receptor binding			ovary(8)|large_intestine(4)|upper_aerodigestive_tract(2)|breast(2)|skin(2)|pancreas(2)|central_nervous_system(1)	21		Colorectal(10;0.172)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
RAB31	11031	broad.mit.edu	37	18	9774872	9774872	+	Intron	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9774872C>T	uc002kog.2	+							NM_006868	NP_006859			RAB31, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding|GTPase activity			skin(1)	1																		---	---	---	---
C18orf1	753	broad.mit.edu	37	18	13621228	13621228	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13621228C>T	uc002ksa.2	+	5	962	c.294C>T	c.(292-294)AAC>AAT	p.N98N	C18orf1_uc002ksb.2_Silent_p.N98N|C18orf1_uc002kse.2_Silent_p.N61N|C18orf1_uc002ksf.2_Silent_p.N61N|C18orf1_uc002ksg.1_Silent_p.N21N|C18orf1_uc002ksh.1_Silent_p.N40N|C18orf1_uc002ksi.1_Silent_p.N40N	NM_181481	NP_852146	O15165	CR001_HUMAN	hypothetical protein LOC753 isoform alpha 1	98	Cytoplasmic (Potential).					integral to membrane|plasma membrane				ovary(2)|skin(1)	3				READ - Rectum adenocarcinoma(73;0.0642)														---	---	---	---
LAMA3	3909	broad.mit.edu	37	18	21495282	21495282	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21495282C>T	uc002kuq.2	+	59	7760	c.7674C>T	c.(7672-7674)TAC>TAT	p.Y2558Y	LAMA3_uc002kur.2_Silent_p.Y2502Y|LAMA3_uc002kus.3_Silent_p.Y949Y|LAMA3_uc002kut.3_Silent_p.Y893Y	NM_198129	NP_937762	Q16787	LAMA3_HUMAN	laminin alpha 3 subunit isoform 1	2558	Laminin G-like 1.				cell adhesion|epidermis development|hemidesmosome assembly|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|skin(2)|central_nervous_system(1)	11	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)				Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
DSG3	1830	broad.mit.edu	37	18	29038474	29038474	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29038474C>T	uc002kws.2	+	4	392	c.283C>T	c.(283-285)CCG>TCG	p.P95S		NM_001944	NP_001935	P32926	DSG3_HUMAN	desmoglein 3 preproprotein	95	Extracellular (Potential).|Cadherin 1.				cellular component disassembly involved in apoptosis|homophilic cell adhesion	cytosol|desmosome|integral to membrane	calcium ion binding			skin(4)|ovary(3)|lung(1)|central_nervous_system(1)	9			OV - Ovarian serous cystadenocarcinoma(10;0.00504)															---	---	---	---
ASXL3	80816	broad.mit.edu	37	18	31323494	31323494	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:31323494C>T	uc010dmg.1	+	12	3737	c.3682C>T	c.(3682-3684)CCC>TCC	p.P1228S	ASXL3_uc002kxq.2_Missense_Mutation_p.P935S	NM_030632	NP_085135	Q9C0F0	ASXL3_HUMAN	additional sex combs like 3	1228	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	31325001	31325001	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:31325001T>A	uc010dmg.1	+	12	5244	c.5189T>A	c.(5188-5190)GTC>GAC	p.V1730D	ASXL3_uc002kxq.2_Missense_Mutation_p.V1437D	NM_030632	NP_085135	Q9C0F0	ASXL3_HUMAN	additional sex combs like 3	1730					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding			ovary(2)|pancreas(1)	3																		---	---	---	---
ASXL3	80816	broad.mit.edu	37	18	31326157	31326157	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:31326157C>T	uc010dmg.1	+	12	6400	c.6345C>T	c.(6343-6345)TTC>TTT	p.F2115F	ASXL3_uc002kxq.2_Silent_p.F1822F	NM_030632	NP_085135	Q9C0F0	ASXL3_HUMAN	additional sex combs like 3	2115					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding			ovary(2)|pancreas(1)	3																		---	---	---	---
FHOD3	80206	broad.mit.edu	37	18	34261513	34261513	+	Silent	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34261513G>T	uc002kzt.1	+	12	1522	c.1425G>T	c.(1423-1425)CGG>CGT	p.R475R	FHOD3_uc002kzr.1_Silent_p.R475R|FHOD3_uc002kzs.1_Silent_p.R475R|FHOD3_uc010dmz.1_Silent_p.R190R	NM_025135	NP_079411	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3	475	Potential.				actin cytoskeleton organization	cytoplasm|cytoskeleton	actin binding			skin(3)|large_intestine(2)|breast(2)|ovary(1)	8		all_epithelial(2;0.0181)|Colorectal(2;0.0195)																---	---	---	---
CELF4	56853	broad.mit.edu	37	18	34855071	34855071	+	Intron	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34855071C>T	uc002lae.2	-						CELF4_uc010dnd.1_Intron|CELF4_uc002lag.2_Intron|CELF4_uc002laf.2_Intron|CELF4_uc002lai.2_Intron|CELF4_uc002lah.1_5'Flank|CELF4_uc002laj.1_5'Flank	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																		---	---	---	---
BCL2	596	broad.mit.edu	37	18	60985789	60985789	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:60985789G>A	uc002lit.1	-	2	604	c.111C>T	c.(109-111)GCC>GCT	p.A37A	BCL2_uc002liu.1_Silent_p.A37A|BCL2_uc002liv.1_Silent_p.A37A	NM_000633	NP_000624	P10415	BCL2_HUMAN	B-cell lymphoma protein 2 alpha isoform	37					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								---	---	---	---
RTTN	25914	broad.mit.edu	37	18	67776813	67776813	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:67776813G>A	uc002lkp.2	-	28	3892	c.3824C>T	c.(3823-3825)GCG>GTG	p.A1275V	RTTN_uc002lko.2_RNA|RTTN_uc010xfb.1_Missense_Mutation_p.A363V	NM_173630	NP_775901	Q86VV8	RTTN_HUMAN	rotatin	1275							binding			ovary(3)|pancreas(2)|skin(1)|breast(1)|central_nervous_system(1)	8		Esophageal squamous(42;0.129)																---	---	---	---
ZNF407	55628	broad.mit.edu	37	18	72343485	72343485	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:72343485G>A	uc002llw.2	+	1	567	c.510G>A	c.(508-510)CCG>CCA	p.P170P	ZNF407_uc010xfc.1_Silent_p.P170P|ZNF407_uc010dqu.1_Silent_p.P170P|ZNF407_uc002llu.2_Silent_p.P169P	NM_017757	NP_060227	Q9C0G0	ZN407_HUMAN	zinc finger protein 407 isoform 1	170					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)														---	---	---	---
ZNF236	7776	broad.mit.edu	37	18	74583706	74583706	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74583706A>G	uc002lmi.2	+	5	784	c.586A>G	c.(586-588)ACG>GCG	p.T196A	ZNF236_uc002lmj.2_RNA|ZNF236_uc002lmk.1_Missense_Mutation_p.T196A	NM_007345	NP_031371	Q9UL36	ZN236_HUMAN	zinc finger protein 236	196					cellular response to glucose stimulus	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)	4		Prostate(75;0.0405)|Esophageal squamous(42;0.129)|Melanoma(33;0.132)		OV - Ovarian serous cystadenocarcinoma(15;4.36e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0686)														---	---	---	---
GALR1	2587	broad.mit.edu	37	18	74980856	74980856	+	Nonstop_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74980856T>C	uc002lms.3	+	3	1545	c.1048T>C	c.(1048-1050)TGA>CGA	p.*350R		NM_001480	NP_001471	P47211	GALR1_HUMAN	galanin receptor 1	350					digestion|negative regulation of adenylate cyclase activity	integral to membrane|plasma membrane	galanin receptor activity			lung(1)	1		Prostate(75;0.0865)|Esophageal squamous(42;0.129)|Melanoma(33;0.211)		OV - Ovarian serous cystadenocarcinoma(15;1.03e-06)|BRCA - Breast invasive adenocarcinoma(31;0.104)														---	---	---	---
POLRMT	5442	broad.mit.edu	37	19	621855	621855	+	Intron	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:621855C>T	uc002lpf.1	-							NM_005035	NP_005026			mitochondrial DNA-directed RNA polymerase						transcription initiation from mitochondrial promoter	mitochondrial nucleoid	DNA binding|DNA-directed RNA polymerase activity|protein binding			ovary(1)|pancreas(1)	2		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	810550	810550	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:810550G>A	uc002lpr.2	+	13	1499	c.1393G>A	c.(1393-1395)GTC>ATC	p.V465I	PTBP1_uc002lpp.2_Missense_Mutation_p.V491I|PTBP1_uc002lpq.2_Missense_Mutation_p.V484I|PTBP1_uc002lps.2_Missense_Mutation_p.V131I|PTBP1_uc002lpt.2_RNA|PTBP1_uc002lpu.1_Missense_Mutation_p.V461I	NM_031991	NP_114368	P26599	PTBP1_HUMAN	polypyrimidine tract-binding protein 1 isoform	465	RRM 4.				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)														---	---	---	---
PRTN3	5657	broad.mit.edu	37	19	847857	847857	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:847857T>C	uc002lqa.1	+	5	683	c.659T>C	c.(658-660)GTG>GCG	p.V220A		NM_002777	NP_002768	P24158	PRTN3_HUMAN	myeloblastin	220	Peptidase S1.				collagen catabolic process|positive regulation of cell proliferation|proteolysis		protein binding|serine-type endopeptidase activity			ovary(1)	1		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)														---	---	---	---
AP3D1	8943	broad.mit.edu	37	19	2102224	2102224	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2102224G>A	uc002luz.2	-	30	3633	c.3410C>T	c.(3409-3411)ACG>ATG	p.T1137M	AP3D1_uc010dsv.2_Missense_Mutation_p.T227M|AP3D1_uc002luy.2_Missense_Mutation_p.T1096M|AP3D1_uc002lva.2_Missense_Mutation_p.T1199M	NM_003938	NP_003929	O14617	AP3D1_HUMAN	adaptor-related protein complex 3, delta 1	1137					eye pigment biosynthetic process|intracellular protein transport|regulation of sequestering of zinc ion|vesicle-mediated transport	endosome membrane|Golgi membrane|membrane coat	binding|protein transporter activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
AP3D1	8943	broad.mit.edu	37	19	2138638	2138638	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2138638C>T	uc002luz.2	-	2	395	c.172G>A	c.(172-174)GCG>ACG	p.A58T	AP3D1_uc002luy.2_Missense_Mutation_p.A58T|AP3D1_uc002lva.2_Missense_Mutation_p.A58T	NM_003938	NP_003929	O14617	AP3D1_HUMAN	adaptor-related protein complex 3, delta 1	58	HEAT 1.				eye pigment biosynthetic process|intracellular protein transport|regulation of sequestering of zinc ion|vesicle-mediated transport	endosome membrane|Golgi membrane|membrane coat	binding|protein transporter activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
C19orf29	58509	broad.mit.edu	37	19	3612416	3612416	+	Intron	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3612416G>A	uc002lyh.2	-						C19orf29_uc010xho.1_Intron|C19orf29_uc010dtn.2_Intron|C19orf29_uc002lyi.3_Intron|C19orf29_uc010dto.2_Intron	NM_001080543	NP_001074012			chromosome 19 open reading frame 29							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)														---	---	---	---
CHAF1A	10036	broad.mit.edu	37	19	4433328	4433328	+	Missense_Mutation	SNP	C	A	A	rs150699024		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4433328C>A	uc002mal.2	+	13	2565	c.2465C>A	c.(2464-2466)CCG>CAG	p.P822Q		NM_005483	NP_005474	Q13111	CAF1A_HUMAN	chromatin assembly factor 1, subunit A (p150)	822	Binds to p60.				cell cycle|DNA repair|DNA replication|DNA replication-dependent nucleosome assembly|protein complex assembly|regulation of transcription, DNA-dependent|transcription, DNA-dependent	CAF-1 complex|WINAC complex	chromatin binding|chromo shadow domain binding|unfolded protein binding			ovary(1)|skin(1)	2		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0148)|STAD - Stomach adenocarcinoma(1328;0.18)									Chromatin_Structure					---	---	---	---
UBXN6	80700	broad.mit.edu	37	19	4453928	4453928	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4453928C>A	uc002man.1	-	2	342	c.246G>T	c.(244-246)CAG>CAT	p.Q82H	UBXN6_uc010dty.1_Missense_Mutation_p.Q29H|UBXN6_uc002mam.1_Missense_Mutation_p.Q29H	NM_025241	NP_079517	Q9BZV1	UBXN6_HUMAN	UBX domain protein 6	82						microtubule organizing center|nucleus	protein binding				0																		---	---	---	---
KDM4B	23030	broad.mit.edu	37	19	5040028	5040028	+	Intron	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5040028C>T	uc002mbq.3	+						KDM4B_uc010xil.1_Intron|KDM4B_uc010xim.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	5047625	5047625	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5047625G>A	uc002mbq.3	+	6	797	c.571G>A	c.(571-573)GAG>AAG	p.E191K	KDM4B_uc010xil.1_Missense_Mutation_p.E191K|KDM4B_uc010xim.1_Missense_Mutation_p.E191K	NM_015015	NP_055830	O94953	KDM4B_HUMAN	jumonji domain containing 2B	191	JmjC.	Iron; catalytic (By similarity).			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	5219994	5219994	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5219994G>A	uc002mbv.2	-	22	3955	c.3721C>T	c.(3721-3723)CGC>TGC	p.R1241C	PTPRS_uc002mbu.1_Missense_Mutation_p.R810C|PTPRS_uc010xin.1_Missense_Mutation_p.R810C|PTPRS_uc002mbw.2_Missense_Mutation_p.R1219C|PTPRS_uc002mbx.2_Missense_Mutation_p.R814C|PTPRS_uc002mby.2_Missense_Mutation_p.R810C	NM_002850	NP_002841	Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type,	1241	Extracellular (Potential).				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)														---	---	---	---
ACSBG2	81616	broad.mit.edu	37	19	6183243	6183243	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6183243C>T	uc002mef.1	+	10	1509	c.1282C>T	c.(1282-1284)CCC>TCC	p.P428S	ACSBG2_uc002mee.1_Missense_Mutation_p.P241S|ACSBG2_uc002meg.1_Missense_Mutation_p.P428S|ACSBG2_uc002meh.1_Missense_Mutation_p.P428S|ACSBG2_uc002mei.1_Missense_Mutation_p.P378S|ACSBG2_uc010xiz.1_Missense_Mutation_p.P428S	NM_030924	NP_112186	Q5FVE4	ACBG2_HUMAN	bubblegum-related acyl-CoA synthetase 2	428					cell differentiation|fatty acid metabolic process|multicellular organismal development|spermatogenesis	membrane|microsome|mitochondrion	acyl-CoA thioesterase activity|ATP binding|long-chain fatty acid-CoA ligase activity			ovary(1)	1																		---	---	---	---
GPR108	56927	broad.mit.edu	37	19	6732509	6732509	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6732509C>T	uc002mfp.2	-	11	1031	c.985G>A	c.(985-987)GTC>ATC	p.V329I	GPR108_uc010duv.2_5'Flank|GPR108_uc002mfn.2_5'UTR|GPR108_uc002mfo.3_Missense_Mutation_p.V87I|GPR108_uc010duw.2_RNA	NM_001080452	NP_001073921	Q9NPR9	GP108_HUMAN	G protein-coupled receptor 108 isoform 1	329						integral to membrane					0																		---	---	---	---
VAV1	7409	broad.mit.edu	37	19	6821674	6821674	+	Silent	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6821674C>A	uc002mfu.1	+	3	460	c.363C>A	c.(361-363)GCC>GCA	p.A121A	VAV1_uc010xjh.1_Silent_p.A121A|VAV1_uc010dva.1_Silent_p.A121A|VAV1_uc002mfv.1_Silent_p.A66A	NM_005428	NP_005419	P15498	VAV_HUMAN	vav 1 guanine nucleotide exchange factor	121					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																		---	---	---	---
MUC16	94025	broad.mit.edu	37	19	9011368	9011368	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9011368T>G	uc002mkp.2	-	36	39069	c.38865A>C	c.(38863-38865)AAA>AAC	p.K12955N	MUC16_uc010xki.1_Intron	NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	12957	SEA 6.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57																		---	---	---	---
MUC16	94025	broad.mit.edu	37	19	9087335	9087335	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9087335T>C	uc002mkp.2	-	1	4684	c.4480A>G	c.(4480-4482)ACA>GCA	p.T1494A		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	1494	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																		---	---	---	---
OR7D2	162998	broad.mit.edu	37	19	9296531	9296531	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9296531C>T	uc002mkz.1	+	1	262	c.74C>T	c.(73-75)CCG>CTG	p.P25L		NM_175883	NP_787079	Q96RA2	OR7D2_HUMAN	olfactory receptor, family 7, subfamily D,	25	Extracellular (Potential).				regulation of transcription, DNA-dependent|sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|upper_aerodigestive_tract(1)	3																		---	---	---	---
ZNF699	374879	broad.mit.edu	37	19	9415798	9415798	+	5'Flank	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9415798C>T	uc002mlc.1	-							NM_198535	NP_940937			zinc finger protein 699						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
OLFM2	93145	broad.mit.edu	37	19	9965414	9965414	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9965414G>A	uc002mmp.2	-	6	841	c.813C>T	c.(811-813)CAC>CAT	p.H271H	OLFM2_uc002mmo.2_Silent_p.H193H	NM_058164	NP_477512	O95897	NOE2_HUMAN	olfactomedin 2 precursor	271	Olfactomedin-like.					extracellular region				large_intestine(1)|skin(1)	2																		---	---	---	---
DNMT1	1786	broad.mit.edu	37	19	10250433	10250433	+	Silent	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10250433G>T	uc002mng.2	-	33	3999	c.3819C>A	c.(3817-3819)TCC>TCA	p.S1273S	DNMT1_uc002mne.2_RNA|DNMT1_uc002mnf.2_Silent_p.S197S|DNMT1_uc010xlc.1_Silent_p.S1289S|DNMT1_uc002mnh.2_Silent_p.S1168S|DNMT1_uc010xld.1_Silent_p.S1273S	NM_001379	NP_001370	P26358	DNMT1_HUMAN	DNA (cytosine-5-)-methyltransferase 1 isoform b	1273	Catalytic.|Interaction with the PRC2/EED-EZH2 complex (By similarity).				chromatin modification|maintenance of DNA methylation|negative regulation of histone H3-K9 methylation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of gene expression|positive regulation of histone H3-K4 methylation|transcription, DNA-dependent	nucleus	DNA (cytosine-5-)-methyltransferase activity|DNA binding|transcription factor binding			ovary(2)|prostate(1)|lung(1)|breast(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(20;1.59e-09)|Epithelial(33;2.86e-06)|all cancers(31;6.68e-06)		Azacitidine(DB00928)|Decitabine(DB01262)|Flucytosine(DB01099)|Ifosfamide(DB01181)|Procainamide(DB01035)													---	---	---	---
ICAM1	3383	broad.mit.edu	37	19	10394931	10394931	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10394931G>A	uc002mnq.2	+	4	1179	c.860G>A	c.(859-861)CGG>CAG	p.R287Q	ICAM1_uc010xle.1_Missense_Mutation_p.R65Q|ICAM4_uc002mnr.1_5'Flank|ICAM4_uc002mns.1_5'Flank|ICAM4_uc002mnt.1_5'Flank	NM_000201	NP_000192	P05362	ICAM1_HUMAN	intercellular adhesion molecule 1 precursor	287	Ig-like C2-type 3.|Extracellular (Potential).				adhesion to symbiont|heterophilic cell-cell adhesion|interferon-gamma-mediated signaling pathway|leukocyte cell-cell adhesion|leukocyte migration|membrane to membrane docking|positive regulation of cellular extravasation|regulation of immune response|regulation of leukocyte mediated cytotoxicity|T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell|virion attachment, binding of host cell surface receptor	extracellular space|integral to plasma membrane	integrin binding|transmembrane receptor activity			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(20;1.39e-09)|Epithelial(33;2.81e-06)|all cancers(31;6.56e-06)		Natalizumab(DB00108)|Simvastatin(DB00641)													---	---	---	---
PDE4A	5141	broad.mit.edu	37	19	10568738	10568738	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10568738G>A	uc002moj.2	+	8	1169	c.1061G>A	c.(1060-1062)CGA>CAA	p.R354Q	PDE4A_uc002mok.2_Missense_Mutation_p.R328Q|PDE4A_uc002mol.2_Missense_Mutation_p.R293Q|PDE4A_uc002mom.2_Missense_Mutation_p.R115Q|PDE4A_uc002mon.2_Intron|PDE4A_uc002moo.2_5'Flank	NM_001111307	NP_001104777	P27815	PDE4A_HUMAN	phosphodiesterase 4A isoform 1	354	Catalytic.				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)													---	---	---	---
SMARCA4	6597	broad.mit.edu	37	19	11143999	11143999	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11143999G>A	uc002mqf.3	+	26	3864	c.3580G>A	c.(3580-3582)GGG>AGG	p.G1194R	SMARCA4_uc010dxp.2_Missense_Mutation_p.G1194R|SMARCA4_uc010dxo.2_Missense_Mutation_p.G1194R|SMARCA4_uc010dxq.2_Missense_Mutation_p.G1194R|SMARCA4_uc010dxr.2_Missense_Mutation_p.G1194R|SMARCA4_uc002mqj.3_Missense_Mutation_p.G1194R|SMARCA4_uc010dxs.2_Missense_Mutation_p.G1194R|SMARCA4_uc010dxt.1_Missense_Mutation_p.G414R|SMARCA4_uc002mqh.3_Missense_Mutation_p.G317R|SMARCA4_uc002mqi.1_Missense_Mutation_p.G397R	NM_003072	NP_003063	P51532	SMCA4_HUMAN	SWI/SNF-related matrix-associated	1194	Helicase C-terminal.				chromatin remodeling|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nBAF complex|npBAF complex|nuclear chromatin|SWI/SNF complex|WINAC complex	androgen receptor binding|ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|histone acetyl-lysine binding|identical protein binding|p53 binding|protein N-terminus binding|transcription corepressor activity			lung(29)|ovary(8)|pancreas(7)|large_intestine(5)|central_nervous_system(5)|skin(3)|prostate(3)|breast(2)|adrenal_gland(1)|stomach(1)|liver(1)|autonomic_ganglia(1)|kidney(1)	67		all_lung(6;0.0512)|Lung NSC(9;0.0568)						F|N|Mis		NSCLC				Rhabdoid_Predisposition_syndrome				---	---	---	---
DOCK6	57572	broad.mit.edu	37	19	11312679	11312679	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11312679C>T	uc002mqs.3	-	44	5615	c.5574G>A	c.(5572-5574)CCG>CCA	p.P1858P	DOCK6_uc002mqr.3_Silent_p.P258P|DOCK6_uc010xlq.1_Silent_p.P1197P	NM_020812	NP_065863	Q96HP0	DOCK6_HUMAN	dedicator of cytokinesis 6	1858	DHR-2.				blood coagulation	cytosol	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(2)|skin(1)	3																		---	---	---	---
DOCK6	57572	broad.mit.edu	37	19	11312758	11312758	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11312758T>C	uc002mqs.3	-	44	5536	c.5495A>G	c.(5494-5496)TAC>TGC	p.Y1832C	DOCK6_uc002mqr.3_Missense_Mutation_p.Y232C|DOCK6_uc010xlq.1_Missense_Mutation_p.Y1171C	NM_020812	NP_065863	Q96HP0	DOCK6_HUMAN	dedicator of cytokinesis 6	1832	DHR-2.				blood coagulation	cytosol	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(2)|skin(1)	3																		---	---	---	---
ZNF799	90576	broad.mit.edu	37	19	12501739	12501739	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12501739A>G	uc010dyt.2	-	4	1623	c.1473T>C	c.(1471-1473)CTT>CTC	p.L491L	ZNF799_uc002mts.3_Intron	NM_001080821	NP_001074290	Q96GE5	ZN799_HUMAN	zinc finger protein 799	491	C2H2-type 13.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(3)|ovary(2)|skin(1)	6																		---	---	---	---
MAST1	22983	broad.mit.edu	37	19	12984811	12984811	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12984811C>T	uc002mvm.2	+	26	3968	c.3840C>T	c.(3838-3840)GGC>GGT	p.G1280G		NM_014975	NP_055790	Q9Y2H9	MAST1_HUMAN	microtubule associated serine/threonine kinase	1280					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																		---	---	---	---
RFX1	5989	broad.mit.edu	37	19	14077273	14077273	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14077273A>G	uc002mxv.2	-	14	2193	c.1921T>C	c.(1921-1923)TAC>CAC	p.Y641H		NM_002918	NP_002909	P22670	RFX1_HUMAN	regulatory factor X1	641					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)															---	---	---	---
PKN1	5585	broad.mit.edu	37	19	14561127	14561127	+	Intron	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14561127C>T	uc002myp.2	+						PKN1_uc002myq.2_Intron	NM_002741	NP_002732			protein kinase N1 isoform 2						activation of JUN kinase activity|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription, DNA-dependent	endosome|nucleus|plasma membrane	androgen receptor binding|ATP binding|chromatin binding|GTP-Rho binding|histone binding|histone deacetylase binding|histone kinase activity (H3-T11 specific)|ligand-dependent nuclear receptor transcription coactivator activity|protein kinase C activity|protein kinase C binding|Rac GTPase binding			ovary(2)|breast(2)|skin(2)|large_intestine(1)|central_nervous_system(1)	8																		---	---	---	---
CCDC105	126402	broad.mit.edu	37	19	15132473	15132473	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15132473C>T	uc002nae.2	+	5	1186	c.1087C>T	c.(1087-1089)CGG>TGG	p.R363W		NM_173482	NP_775753	Q8IYK2	CC105_HUMAN	coiled-coil domain containing 105	363					microtubule cytoskeleton organization	microtubule				ovary(1)	1																		---	---	---	---
EPHX3	79852	broad.mit.edu	37	19	15342161	15342161	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15342161C>T	uc002nap.2	-	3	585	c.376G>A	c.(376-378)GTT>ATT	p.V126I	EPHX3_uc002naq.2_Missense_Mutation_p.V126I	NM_024794	NP_079070	Q9H6B9	EPHX3_HUMAN	abhydrolase domain containing 9 precursor	126						extracellular region	hydrolase activity				0																		---	---	---	---
BRD4	23476	broad.mit.edu	37	19	15364508	15364508	+	Intron	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15364508G>A	uc002nar.2	-						BRD4_uc002nas.2_Intron|BRD4_uc002nat.3_Missense_Mutation_p.R749C	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								---	---	---	---
WIZ	58525	broad.mit.edu	37	19	15538021	15538021	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15538021G>A	uc002nbc.2	-	4	1398	c.1375C>T	c.(1375-1377)CCA>TCA	p.P459S	WIZ_uc002nba.3_Missense_Mutation_p.P326S|WIZ_uc002nbb.3_Missense_Mutation_p.P285S	NM_021241	NP_067064	O95785	WIZ_HUMAN	widely-interspaced zinc finger motifs	1142	Pro-rich.					nucleus	zinc ion binding				0																		---	---	---	---
C19orf44	84167	broad.mit.edu	37	19	16612314	16612314	+	Silent	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16612314C>A	uc002neh.1	+	2	784	c.711C>A	c.(709-711)GGC>GGA	p.G237G	MED26_uc002nee.2_Intron|C19orf44_uc002nef.1_Silent_p.G237G|C19orf44_uc002neg.2_Silent_p.G237G|C19orf44_uc010eai.1_RNA	NM_032207	NP_115583	Q9H6X5	CS044_HUMAN	hypothetical protein LOC84167	237											0																		---	---	---	---
SLC35E1	79939	broad.mit.edu	37	19	16677452	16677452	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16677452C>T	uc010xph.1	-	4	665	c.647G>A	c.(646-648)CGG>CAG	p.R216Q	MED26_uc002nee.2_RNA|SLC35E1_uc002nem.1_Missense_Mutation_p.R216Q	NM_024881	NP_079157	Q96K37	S35E1_HUMAN	solute carrier family 35, member E1	216					transport	integral to membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
JAK3	3718	broad.mit.edu	37	19	17943458	17943458	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17943458G>A	uc002nhn.3	-	19	2650	c.2550C>T	c.(2548-2550)GCC>GCT	p.A850A	JAK3_uc010ebh.2_Intron|JAK3_uc002nho.2_Silent_p.A850A	NM_000215	NP_000206	P52333	JAK3_HUMAN	Janus kinase 3	850	Protein kinase 2.				B cell differentiation|cytokine-mediated signaling pathway|enzyme linked receptor protein signaling pathway|intracellular protein kinase cascade|negative regulation of dendritic cell cytokine production|negative regulation of FasL biosynthetic process|negative regulation of interleukin-10 production|negative regulation of interleukin-12 production|negative regulation of T-helper 1 cell differentiation|negative regulation of thymocyte apoptosis|peptidyl-tyrosine phosphorylation|positive regulation of anti-apoptosis|response to interleukin-15|response to interleukin-2|response to interleukin-4|response to interleukin-9|T cell homeostasis	cytoskeleton|cytosol|endomembrane system|membrane	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding			haematopoietic_and_lymphoid_tissue(40)|lung(5)|breast(5)|ovary(3)|stomach(2)|upper_aerodigestive_tract(1)	56							2	Mis		acute megakaryocytic leukemia|								---	---	---	---
KLHL26	55295	broad.mit.edu	37	19	18779089	18779089	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18779089G>A	uc002njz.1	+	3	909	c.882G>A	c.(880-882)CAG>CAA	p.Q294Q		NM_018316	NP_060786	Q53HC5	KLH26_HUMAN	kelch-like 26	294										ovary(1)	1																		---	---	---	---
ARMC6	93436	broad.mit.edu	37	19	19165124	19165124	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19165124C>T	uc002nld.2	+	6	1365	c.1017C>T	c.(1015-1017)GGC>GGT	p.G339G	ARMC6_uc002nlc.2_Silent_p.G314G|ARMC6_uc010xql.1_Silent_p.G246G|ARMC6_uc002nle.2_Silent_p.G314G|ARMC6_uc010xqm.1_Silent_p.G339G	NM_033415	NP_219483	Q6NXE6	ARMC6_HUMAN	armadillo repeat containing 6	339	ARM 3.						protein binding				0			OV - Ovarian serous cystadenocarcinoma(5;5.66e-06)|Epithelial(12;0.000391)													OREG0025376	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
GMIP	51291	broad.mit.edu	37	19	19747568	19747568	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19747568G>A	uc002nnd.2	-	13	1392	c.1275C>T	c.(1273-1275)AGC>AGT	p.S425S	GMIP_uc010xrb.1_Silent_p.S425S|GMIP_uc010xrc.1_Silent_p.S422S	NM_016573	NP_057657	Q9P107	GMIP_HUMAN	GEM interacting protein	425					negative regulation of Rho GTPase activity|small GTPase mediated signal transduction	cytosol	metal ion binding|protein binding|Rho GTPase activator activity			ovary(1)	1																		---	---	---	---
ZNF536	9745	broad.mit.edu	37	19	31039431	31039431	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31039431G>A	uc002nsu.1	+	4	3043	c.2905G>A	c.(2905-2907)GAG>AAG	p.E969K	ZNF536_uc010edd.1_Missense_Mutation_p.E969K	NM_014717	NP_055532	O15090	ZN536_HUMAN	zinc finger protein 536	969					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(7)|large_intestine(2)|skin(2)	11	Esophageal squamous(110;0.0834)																	---	---	---	---
TSHZ3	57616	broad.mit.edu	37	19	31769889	31769889	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31769889G>A	uc002nsy.3	-	2	875	c.810C>T	c.(808-810)GAC>GAT	p.D270D		NM_020856	NP_065907	Q63HK5	TSH3_HUMAN	zinc finger protein 537	270					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)																	---	---	---	---
GPATCH1	55094	broad.mit.edu	37	19	33621034	33621034	+	Splice_Site	SNP	A	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33621034A>C	uc002nug.1	+	20	3080	c.2766_splice	c.e20-2	p.R922_splice	GPATCH1_uc002nuh.1_Splice_Site_p.R299_splice|WDR88_uc002nui.2_5'Flank	NM_018025	NP_060495			G patch domain containing 1							catalytic step 2 spliceosome	nucleic acid binding			skin(1)	1	Esophageal squamous(110;0.137)																	---	---	---	---
LRP3	4037	broad.mit.edu	37	19	33697607	33697607	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33697607G>A	uc010edh.2	+	6	1786	c.1693G>A	c.(1693-1695)GTG>ATG	p.V565M	LRP3_uc010xrp.1_3'UTR|LRP3_uc002nuk.3_Missense_Mutation_p.V439M	NM_002333	NP_002324	O75074	LRP3_HUMAN	low density lipoprotein receptor-related protein	565	Cytoplasmic (Potential).				receptor-mediated endocytosis	coated pit|integral to membrane	receptor activity			pancreas(2)|ovary(1)	3	Esophageal squamous(110;0.137)																	---	---	---	---
GRAMD1A	57655	broad.mit.edu	37	19	35514416	35514416	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35514416C>T	uc010xse.1	+	19	2184	c.2047C>T	c.(2047-2049)CAG>TAG	p.Q683*	GRAMD1A_uc002nxk.2_Nonsense_Mutation_p.Q672*|GRAMD1A_uc002nxl.2_Nonsense_Mutation_p.Q445*|GRAMD1A_uc010xsf.1_Nonsense_Mutation_p.Q684*|GRAMD1A_uc002nxm.1_RNA|GRAMD1A_uc002nxn.1_Nonsense_Mutation_p.Q294*	NM_020895	NP_065946	Q96CP6	GRM1A_HUMAN	GRAM domain containing 1A isoform 1	683						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)															---	---	---	---
KRTDAP	388533	broad.mit.edu	37	19	35981334	35981334	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35981334G>A	uc002nzh.2	-	1	23	c.11C>T	c.(10-12)CCG>CTG	p.P4L		NM_207392	NP_997275	P60985	KTDAP_HUMAN	keratinocyte differentiation-associated protein	4					cell differentiation	extracellular region					0	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)															---	---	---	---
PRODH2	58510	broad.mit.edu	37	19	36290978	36290978	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36290978G>A	uc002obx.1	-	11	1591	c.1573C>T	c.(1573-1575)CGG>TGG	p.R525W	uc002obw.1_5'Flank	NM_021232	NP_067055	Q9UF12	PROD2_HUMAN	kidney and liver proline oxidase 1	525					glutamate biosynthetic process|proline catabolic process		proline dehydrogenase activity	p.R525W(1)		ovary(2)	2	all_lung(56;2.87e-07)|Lung NSC(56;4.32e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)															---	---	---	---
ZNF527	84503	broad.mit.edu	37	19	37879513	37879513	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37879513C>T	uc010efk.1	+	5	673	c.562C>T	c.(562-564)CAG>TAG	p.Q188*	ZNF527_uc002ogf.3_Nonsense_Mutation_p.Q156*|ZNF527_uc010xtq.1_RNA	NM_032453	NP_115829	Q8NB42	ZN527_HUMAN	zinc finger protein 527	188					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)															---	---	---	---
SIPA1L3	23094	broad.mit.edu	37	19	38673271	38673271	+	Missense_Mutation	SNP	G	A	A	rs139858184	byFrequency	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38673271G>A	uc002ohk.2	+	16	4830	c.4321G>A	c.(4321-4323)GTC>ATC	p.V1441I		NM_015073	NP_055888	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like	1441					regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity			ovary(1)|central_nervous_system(1)	2			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)															---	---	---	---
RYR1	6261	broad.mit.edu	37	19	38959976	38959976	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38959976C>T	uc002oit.2	+	27	3718	c.3588C>T	c.(3586-3588)GGC>GGT	p.G1196G	RYR1_uc002oiu.2_Silent_p.G1196G	NM_000540	NP_000531	P21817	RYR1_HUMAN	skeletal muscle ryanodine receptor isoform 1	1196	6 X approximate repeats.|Cytoplasmic.|B30.2/SPRY 2.				muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia	cell cortex|cytosol|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna	calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(7)|pancreas(2)|breast(1)|central_nervous_system(1)|skin(1)	12	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Dantrolene(DB01219)													---	---	---	---
RYR1	6261	broad.mit.edu	37	19	38976392	38976392	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38976392C>T	uc002oit.2	+	34	5227	c.5097C>T	c.(5095-5097)GAC>GAT	p.D1699D	RYR1_uc002oiu.2_Silent_p.D1699D	NM_000540	NP_000531	P21817	RYR1_HUMAN	skeletal muscle ryanodine receptor isoform 1	1699	Cytoplasmic.|6 X approximate repeats.				muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia	cell cortex|cytosol|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna	calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(7)|pancreas(2)|breast(1)|central_nervous_system(1)|skin(1)	12	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Dantrolene(DB01219)													---	---	---	---
RYR1	6261	broad.mit.edu	37	19	38993326	38993326	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38993326G>A	uc002oit.2	+	48	7924	c.7794G>A	c.(7792-7794)GCG>GCA	p.A2598A	RYR1_uc002oiu.2_Silent_p.A2598A|RYR1_uc002oiv.1_5'UTR	NM_000540	NP_000531	P21817	RYR1_HUMAN	skeletal muscle ryanodine receptor isoform 1	2598	Cytoplasmic.|6 X approximate repeats.				muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia	cell cortex|cytosol|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna	calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(7)|pancreas(2)|breast(1)|central_nervous_system(1)|skin(1)	12	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Dantrolene(DB01219)													---	---	---	---
FCGBP	8857	broad.mit.edu	37	19	40368650	40368650	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40368650C>T	uc002omp.3	-	28	12706	c.12698G>A	c.(12697-12699)GGC>GAC	p.G4233D		NM_003890	NP_003881	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein precursor	4233	VWFD 10.					extracellular region	protein binding			ovary(4)|skin(4)|central_nervous_system(1)	9	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)															---	---	---	---
SPTBN4	57731	broad.mit.edu	37	19	40996007	40996007	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40996007G>A	uc002ony.2	+	4	433	c.347G>A	c.(346-348)CGG>CAG	p.R116Q	SPTBN4_uc002onx.2_Missense_Mutation_p.R116Q|SPTBN4_uc002onz.2_Missense_Mutation_p.R116Q	NM_020971	NP_066022	Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4 isoform	116	CH 1.|Actin-binding.				actin filament capping|axon guidance|cytoskeletal anchoring at plasma membrane|vesicle-mediated transport	cytosol|nuclear matrix|PML body|spectrin	actin binding|ankyrin binding|structural constituent of cytoskeleton			ovary(3)|central_nervous_system(1)|skin(1)	5			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)															---	---	---	---
CEACAM7	1087	broad.mit.edu	37	19	42190985	42190985	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42190985G>A	uc002ori.1	-	2	234	c.232C>T	c.(232-234)CGA>TGA	p.R78*	CEACAM7_uc010ehx.2_Nonsense_Mutation_p.R78*|CEACAM7_uc010ehy.1_Nonsense_Mutation_p.R78*	NM_006890	NP_008821	Q14002	CEAM7_HUMAN	carcinoembryonic antigen-related cell adhesion	78	Ig-like V-type.					anchored to membrane|integral to membrane|plasma membrane				ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(3;0.0027)|all cancers(3;0.00979)|Epithelial(262;0.0366)														---	---	---	---
CIC	23152	broad.mit.edu	37	19	42797150	42797150	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42797150G>A	uc002otf.1	+	15	3552	c.3512G>A	c.(3511-3513)CGG>CAG	p.R1171Q		NM_015125	NP_055940	Q96RK0	CIC_HUMAN	capicua homolog	1171	Pro-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding			ovary(4)|breast(4)|lung(1)|central_nervous_system(1)|skin(1)	11		Prostate(69;0.00682)						T	DUX4	soft tissue sarcoma								---	---	---	---
LIPE	3991	broad.mit.edu	37	19	42909697	42909697	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42909697G>A	uc002otr.2	-	8	2659	c.2382C>T	c.(2380-2382)GAC>GAT	p.D794D	uc010eif.1_Intron	NM_005357	NP_005348	Q05469	LIPS_HUMAN	hormone-sensitive lipase	794					cholesterol metabolic process|protein phosphorylation|triglyceride catabolic process	caveola|cytosol	hormone-sensitive lipase activity|protein binding			ovary(1)|breast(1)	2		Prostate(69;0.00682)																---	---	---	---
PSG1	5669	broad.mit.edu	37	19	43375950	43375950	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43375950G>A	uc002ovb.2	-	3	816	c.678C>T	c.(676-678)AGC>AGT	p.S226S	PSG3_uc002ouf.2_Intron|PSG1_uc002oug.1_Silent_p.S226S|PSG11_uc002ouw.2_Intron|PSG7_uc002ous.1_Intron|PSG7_uc002out.1_Intron|PSG10_uc002ouv.1_Intron|PSG1_uc002oun.2_RNA|PSG1_uc002our.1_Silent_p.S226S|PSG1_uc010eio.1_Silent_p.S226S|PSG1_uc002oux.1_Silent_p.S155S|PSG1_uc002ouy.1_Silent_p.S226S|PSG1_uc002ouz.1_Silent_p.S226S|PSG1_uc002ova.1_Intron|PSG1_uc002ovc.2_Intron|PSG1_uc002ovd.1_Silent_p.S226S	NM_006905	NP_008836	P11464	PSG1_HUMAN	pregnancy specific beta-1-glycoprotein 1	226	Ig-like C2-type 1.				female pregnancy	extracellular region				ovary(2)	2		Prostate(69;0.00682)																---	---	---	---
PVR	5817	broad.mit.edu	37	19	45150854	45150854	+	Intron	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45150854G>T	uc002ozm.2	+						PVR_uc010ejs.2_Intron|PVR_uc010xxb.1_Intron|PVR_uc010xxc.1_Intron|PVR_uc002ozn.2_Intron	NM_006505	NP_006496			poliovirus receptor isoform alpha						adherens junction organization|cell adhesion|cell junction assembly|interspecies interaction between organisms|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target|susceptibility to natural killer cell mediated cytotoxicity|susceptibility to T cell mediated cytotoxicity	cell junction|cell surface|cytoplasm|extracellular space|integral to membrane|nucleus	cell adhesion molecule binding|receptor activity				0	Lung NSC(12;0.00608)|all_lung(12;0.0148)	Medulloblastoma(540;0.0425)|Ovarian(192;0.0728)|Prostate(69;0.081)|all_neural(266;0.112)		Epithelial(262;0.000601)														---	---	---	---
BCAM	4059	broad.mit.edu	37	19	45315631	45315631	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45315631C>T	uc002ozu.2	+	3	460	c.416C>T	c.(415-417)GCG>GTG	p.A139V	BCAM_uc002ozt.1_Missense_Mutation_p.A139V	NM_005581	NP_005572	P50895	BCAM_HUMAN	basal cell adhesion molecule isoform 1	139	Extracellular (Potential).|Ig-like V-type 1.				cell-matrix adhesion	integral to plasma membrane	laminin binding|laminin receptor activity			skin(1)	1	Lung NSC(12;0.000789)|all_lung(12;0.00218)	Ovarian(192;0.0728)|all_neural(266;0.112)																---	---	---	---
BCAM	4059	broad.mit.edu	37	19	45321843	45321843	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45321843C>T	uc002ozu.2	+	9	1187	c.1143C>T	c.(1141-1143)GTC>GTT	p.V381V	BCAM_uc002ozt.1_Silent_p.V381V	NM_005581	NP_005572	P50895	BCAM_HUMAN	basal cell adhesion molecule isoform 1	381	Extracellular (Potential).|Ig-like C2-type 2.				cell-matrix adhesion	integral to plasma membrane	laminin binding|laminin receptor activity			skin(1)	1	Lung NSC(12;0.000789)|all_lung(12;0.00218)	Ovarian(192;0.0728)|all_neural(266;0.112)																---	---	---	---
ERCC2	2068	broad.mit.edu	37	19	45868424	45868424	+	Intron	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45868424T>C	uc002pbj.2	-						ERCC2_uc010ejz.2_Intron|ERCC2_uc002pbk.2_Intron|ERCC2_uc002pbl.3_Intron|ERCC2_uc010xxj.1_Intron	NM_000400	NP_000391			excision repair cross-complementing rodent						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				---	---	---	---
PNMAL1	55228	broad.mit.edu	37	19	46974273	46974273	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46974273A>G	uc002peq.3	-	2	326	c.20T>C	c.(19-21)ATG>ACG	p.M7T	PNMAL1_uc002per.3_Missense_Mutation_p.M7T	NM_018215	NP_060685	Q86V59	PNML1_HUMAN	PNMA-like 1 isoform a	7											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)														---	---	---	---
PRR12	57479	broad.mit.edu	37	19	50118249	50118249	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50118249G>A	uc002poo.3	+	8	5007	c.5007G>A	c.(5005-5007)CGG>CGA	p.R1669R		NM_020719	NP_065770	Q9ULL5	PRR12_HUMAN	proline rich 12	848	Pro-rich.						DNA binding			central_nervous_system(1)|pancreas(1)	2		all_lung(116;2.45e-07)|Lung NSC(112;1.24e-06)|Ovarian(192;0.0728)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00319)|GBM - Glioblastoma multiforme(134;0.0132)														---	---	---	---
PRR12	57479	broad.mit.edu	37	19	50123625	50123625	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50123625G>A	uc002poo.3	+	10	5514	c.5514G>A	c.(5512-5514)GGG>GGA	p.G1838G		NM_020719	NP_065770	Q9ULL5	PRR12_HUMAN	proline rich 12	1017							DNA binding			central_nervous_system(1)|pancreas(1)	2		all_lung(116;2.45e-07)|Lung NSC(112;1.24e-06)|Ovarian(192;0.0728)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00319)|GBM - Glioblastoma multiforme(134;0.0132)														---	---	---	---
PRR12	57479	broad.mit.edu	37	19	50124783	50124783	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50124783C>T	uc002poo.3	+	11	5625	c.5625C>T	c.(5623-5625)GAC>GAT	p.D1875D		NM_020719	NP_065770	Q9ULL5	PRR12_HUMAN	proline rich 12	1054							DNA binding			central_nervous_system(1)|pancreas(1)	2		all_lung(116;2.45e-07)|Lung NSC(112;1.24e-06)|Ovarian(192;0.0728)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00319)|GBM - Glioblastoma multiforme(134;0.0132)														---	---	---	---
VRK3	51231	broad.mit.edu	37	19	50482461	50482461	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50482461T>C	uc002prg.2	-	14	1413	c.1315A>G	c.(1315-1317)ACG>GCG	p.T439A	VRK3_uc002prh.1_Missense_Mutation_p.T439A|VRK3_uc002pri.1_Missense_Mutation_p.T389A|VRK3_uc010ens.2_Missense_Mutation_p.T439A|VRK3_uc010ybl.1_Missense_Mutation_p.T389A|VRK3_uc010ybm.1_Missense_Mutation_p.T208A	NM_016440	NP_057524	Q8IV63	VRK3_HUMAN	vaccinia related kinase 3 isoform 1	439	Protein kinase.					nucleus	ATP binding|protein kinase activity			stomach(1)|skin(1)	2		all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00166)|OV - Ovarian serous cystadenocarcinoma(262;0.00652)														---	---	---	---
MYH14	79784	broad.mit.edu	37	19	50726368	50726368	+	Splice_Site	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50726368G>A	uc002prr.1	+	4	637	c.590_splice	c.e4+1	p.T197_splice	MYH14_uc010enu.1_Splice_Site_p.T197_splice|MYH14_uc002prq.1_Splice_Site_p.T197_splice	NM_024729	NP_079005			myosin, heavy chain 14 isoform 2						axon guidance|regulation of cell shape	myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			central_nervous_system(1)	1		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)														---	---	---	---
NAPSA	9476	broad.mit.edu	37	19	50864954	50864954	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50864954C>T	uc002prx.2	-	4	487	c.434G>A	c.(433-435)CGG>CAG	p.R145Q	NR1H2_uc002prv.3_Intron	NM_004851	NP_004842	O96009	NAPSA_HUMAN	napsin A preproprotein	145					proteolysis	extracellular region	aspartic-type endopeptidase activity				0		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00743)|GBM - Glioblastoma multiforme(134;0.0183)														---	---	---	---
SPIB	6689	broad.mit.edu	37	19	50926203	50926203	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50926203A>G	uc002psd.2	+	4	273	c.248A>G	c.(247-249)TAC>TGC	p.Y83C	SPIB_uc002pse.2_Missense_Mutation_p.Y83C|SPIB_uc010ycc.1_Intron	NM_003121	NP_003112	Q01892	SPIB_HUMAN	Spi-B transcription factor (Spi-1/PU.1 related)	83					regulation of transcription from RNA polymerase II promoter	cytoplasm|microtubule cytoskeleton|nucleus	sequence-specific DNA binding			lung(1)|kidney(1)	2		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00757)|GBM - Glioblastoma multiforme(134;0.0186)														---	---	---	---
LIM2	3982	broad.mit.edu	37	19	51883795	51883795	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51883795G>T	uc002pwm.2	-	4	468	c.424C>A	c.(424-426)CTG>ATG	p.L142M	LIM2_uc002pwl.2_Missense_Mutation_p.L184M	NM_001161748	NP_001155220	P55344	LMIP_HUMAN	lens intrinsic membrane protein 2, 19kDa isoform	142	Helical; (Potential).				cell-cell junction assembly	cell junction|integral to membrane	structural constituent of eye lens				0		all_neural(266;0.0529)		GBM - Glioblastoma multiforme(134;0.000214)|OV - Ovarian serous cystadenocarcinoma(262;0.00985)														---	---	---	---
FPR3	2359	broad.mit.edu	37	19	52328045	52328045	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52328045G>A	uc002pxt.1	+	2	1228	c.1044G>A	c.(1042-1044)ACG>ACA	p.T348T		NM_002030	NP_002021	P25089	FPR3_HUMAN	formyl peptide receptor-like 2	348	Cytoplasmic (Potential).				cellular component movement|chemotaxis	integral to membrane|plasma membrane	N-formyl peptide receptor activity	p.T348M(1)		lung(4)|breast(1)|skin(1)	6																		---	---	---	---
ZNF350	59348	broad.mit.edu	37	19	52471832	52471832	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52471832T>C	uc002pyd.2	-	4	465	c.237A>G	c.(235-237)TCA>TCG	p.S79S	uc002pyb.2_Intron|uc002pyc.2_Intron	NM_021632	NP_067645	Q9GZX5	ZN350_HUMAN	zinc finger protein 350	79	KRAB.				negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear matrix|transcriptional repressor complex	DNA binding|protein binding|zinc ion binding			breast(1)	1		all_neural(266;0.0505)		GBM - Glioblastoma multiforme(134;0.00124)|OV - Ovarian serous cystadenocarcinoma(262;0.0179)														---	---	---	---
PPP2R1A	5518	broad.mit.edu	37	19	52719049	52719049	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52719049G>A	uc002pyp.2	+	7	984	c.825G>A	c.(823-825)GGG>GGA	p.G275G	PPP2R1A_uc010ydk.1_Silent_p.G220G|PPP2R1A_uc010epm.1_Silent_p.G315G|PPP2R1A_uc002pyq.2_Silent_p.G96G	NM_014225	NP_055040	P30153	2AAA_HUMAN	alpha isoform of regulatory subunit A, protein	275	HEAT 7.|PP2A subunit B binding.|Polyoma small and medium T antigens Binding.				ceramide metabolic process|chromosome segregation|G2/M transition of mitotic cell cycle|inactivation of MAPK activity|induction of apoptosis|negative regulation of cell growth|negative regulation of tyrosine phosphorylation of Stat3 protein|protein complex assembly|protein dephosphorylation|regulation of cell adhesion|regulation of cell differentiation|regulation of DNA replication|regulation of transcription, DNA-dependent|regulation of Wnt receptor signaling pathway|response to organic substance|RNA splicing|second-messenger-mediated signaling	chromosome, centromeric region|cytosol|membrane|microtubule cytoskeleton|mitochondrion|nucleus|protein phosphatase type 2A complex|soluble fraction	antigen binding|protein heterodimerization activity|protein phosphatase type 2A regulator activity			endometrium(31)|ovary(28)|lung(2)|breast(2)|skin(1)|kidney(1)|pancreas(1)	66				GBM - Glioblastoma multiforme(134;0.00456)|OV - Ovarian serous cystadenocarcinoma(262;0.015)				Mis		clear cell ovarian carcinoma								---	---	---	---
ZNF528	84436	broad.mit.edu	37	19	52919216	52919216	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52919216C>A	uc002pzh.2	+	7	1537	c.1111C>A	c.(1111-1113)CAT>AAT	p.H371N	ZNF528_uc002pzi.2_Missense_Mutation_p.H138N	NM_032423	NP_115799	Q3MIS6	ZN528_HUMAN	zinc finger protein 528	371	C2H2-type 6.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|skin(1)	2				GBM - Glioblastoma multiforme(134;0.00249)|OV - Ovarian serous cystadenocarcinoma(262;0.00817)														---	---	---	---
ZNF331	55422	broad.mit.edu	37	19	54080491	54080491	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54080491G>A	uc002qbx.1	+	7	2111	c.677G>A	c.(676-678)CGT>CAT	p.R226H	ZNF331_uc002qby.1_Missense_Mutation_p.R226H|ZNF331_uc002qbz.1_Missense_Mutation_p.R226H|ZNF331_uc002qca.1_Missense_Mutation_p.R226H|ZNF331_uc010eqr.1_Missense_Mutation_p.R226H|ZNF331_uc002qcb.1_Missense_Mutation_p.R226H|ZNF331_uc002qcc.1_Missense_Mutation_p.R226H|ZNF331_uc002qcd.1_Missense_Mutation_p.R226H	NM_018555	NP_061025	Q9NQX6	ZN331_HUMAN	zinc finger protein 331	226	C2H2-type 4.				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								---	---	---	---
MIR371	442916	broad.mit.edu	37	19	54290948	54290948	+	RNA	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54290948G>T	hsa-mir-371|MI0000779	+			c.20G>T			uc010yec.1_RNA|uc010yed.1_5'Flank|MIR372_hsa-mir-372|MI0000780_5'Flank|uc010yee.1_5'Flank|MIR373_hsa-mir-373|MI0000781_5'Flank																	0																		---	---	---	---
VSTM1	284415	broad.mit.edu	37	19	54567029	54567029	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54567029C>T	uc002qcw.3	-	1	179	c.3G>A	c.(1-3)ATG>ATA	p.M1I	VSTM1_uc010erb.2_RNA|VSTM1_uc002qcx.3_Missense_Mutation_p.M1I	NM_198481	NP_940883	Q6UX27	VSTM1_HUMAN	V-set and transmembrane domain containing 1	1						integral to membrane					0	all_cancers(19;0.0128)|all_epithelial(19;0.00564)|all_lung(19;0.031)|Lung NSC(19;0.0358)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.165)														---	---	---	---
LILRB4	11006	broad.mit.edu	37	19	55177749	55177749	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55177749C>T	uc002qgp.2	+	8	1295	c.933C>T	c.(931-933)GAC>GAT	p.D311D	LILRB4_uc002qgq.2_Silent_p.D311D|LILRB4_uc002qgr.2_Silent_p.D352D|LILRB4_uc010ert.2_Silent_p.D352D|LILRB4_uc010eru.2_Silent_p.D340D	NM_006847	NP_006838	Q8NHJ6	LIRB4_HUMAN	leukocyte immunoglobulin-like receptor,	311	Cytoplasmic (Potential).					integral to membrane|plasma membrane	antigen binding|receptor activity			ovary(3)	3				GBM - Glioblastoma multiforme(193;0.035)														---	---	---	---
NLRP2	55655	broad.mit.edu	37	19	55481397	55481397	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55481397C>T	uc002qij.2	+	2	100	c.14C>T	c.(13-15)GCG>GTG	p.A5V	NLRP2_uc010yfp.1_Missense_Mutation_p.A5V|NLRP2_uc010esn.2_Missense_Mutation_p.A5V|NLRP2_uc010eso.2_Missense_Mutation_p.A5V|NLRP2_uc010esp.2_Missense_Mutation_p.A5V	NM_017852	NP_060322	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2	5	DAPIN.				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)														---	---	---	---
ZNF835	90485	broad.mit.edu	37	19	57176390	57176390	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57176390T>C	uc010ygo.1	-	2	243	c.243A>G	c.(241-243)CGA>CGG	p.R81R	ZNF835_uc010ygn.1_Silent_p.R59R	NM_001005850	NP_001005850			zinc finger protein 835											pancreas(3)|skin(1)	4																		---	---	---	---
ZIM2	23619	broad.mit.edu	37	19	57286130	57286130	+	Missense_Mutation	SNP	C	T	T	rs138640675		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57286130C>T	uc002qnr.2	-	11	1892	c.1510G>A	c.(1510-1512)GGC>AGC	p.G504S	uc010ygp.1_Intron|uc002qnp.1_Intron|ZIM2_uc010ygq.1_Missense_Mutation_p.G300S|ZIM2_uc010ygr.1_Missense_Mutation_p.G300S|ZIM2_uc002qnq.2_Missense_Mutation_p.G504S|ZIM2_uc010etp.2_Missense_Mutation_p.G504S|ZIM2_uc010ygs.1_Missense_Mutation_p.G504S	NM_015363	NP_056178	Q9NZV7	ZIM2_HUMAN	zinc finger, imprinted 2	504	C2H2-type 5.				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)														---	---	---	---
ZNF543	125919	broad.mit.edu	37	19	57839233	57839233	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57839233T>C	uc002qoi.1	+	4	748	c.403T>C	c.(403-405)TTG>CTG	p.L135L		NM_213598	NP_998763	Q08ER8	ZN543_HUMAN	zinc finger protein 543	135					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)														---	---	---	---
ZNF749	388567	broad.mit.edu	37	19	57956447	57956447	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57956447A>G	uc002qoq.2	+	3	2185	c.1931A>G	c.(1930-1932)GAA>GGA	p.E644G	ZNF547_uc002qpm.3_Intron	NM_001023561	NP_001018855	O43361	ZN749_HUMAN	zinc finger protein 749	644	C2H2-type 16.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0264)|Lung(386;0.177)														---	---	---	---
ZNF772	400720	broad.mit.edu	37	19	57985255	57985255	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57985255C>A	uc002qot.2	-	5	1118	c.857G>T	c.(856-858)AGA>ATA	p.R286I	ZNF547_uc002qpm.3_Intron|ZNF772_uc010ygy.1_Missense_Mutation_p.R245I|ZNF772_uc010ygz.1_Missense_Mutation_p.R174I|ZNF772_uc010yha.1_Missense_Mutation_p.R232I|ZNF772_uc002qou.2_Missense_Mutation_p.R174I	NM_001024596	NP_001019767	Q68DY9	ZN772_HUMAN	zinc finger protein 772 isoform 1	286	C2H2-type 3.				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)														---	---	---	---
ZNF552	79818	broad.mit.edu	37	19	58319993	58319993	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58319993G>T	uc002qqg.2	-	3	809	c.639C>A	c.(637-639)AGC>AGA	p.S213R	ZNF587_uc002qqb.2_Intron|ZNF552_uc010yhg.1_Missense_Mutation_p.S209R	NM_024762	NP_079038	Q9H707	ZN552_HUMAN	zinc finger protein 552	213	C2H2-type 3; degenerate.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0259)														---	---	---	---
ZNF606	80095	broad.mit.edu	37	19	58490096	58490096	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58490096G>A	uc002qqw.2	-	7	2570	c.1952C>T	c.(1951-1953)CCC>CTC	p.P651L	ZNF606_uc010yhp.1_Missense_Mutation_p.P561L	NM_025027	NP_079303	Q8WXB4	ZN606_HUMAN	zinc finger protein 606	651					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)	2		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)														---	---	---	---
ZSCAN1	284312	broad.mit.edu	37	19	58564966	58564966	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58564966C>T	uc002qrc.1	+	6	1021	c.774C>T	c.(772-774)AGC>AGT	p.S258S		NM_182572	NP_872378	Q8NBB4	ZSCA1_HUMAN	zinc finger and SCAN domain containing 1	258					viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0152)														---	---	---	---
ZNF274	10782	broad.mit.edu	37	19	58724502	58724502	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58724502C>T	uc002qrq.1	+	10	2414	c.1955C>T	c.(1954-1956)ACC>ATC	p.T652I	ZNF274_uc002qrr.1_Missense_Mutation_p.T620I|ZNF274_uc002qrs.1_Missense_Mutation_p.T547I|ZNF274_uc010eum.1_Missense_Mutation_p.T411I	NM_133502	NP_598009	Q96GC6	ZN274_HUMAN	zinc finger protein 274 isoform c	652					viral reproduction	centrosome|nucleolus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			ovary(1)	1		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Ovarian(87;0.0443)|Breast(46;0.0889)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)|Lung(386;0.215)														---	---	---	---
ZBTB45	84878	broad.mit.edu	37	19	59028801	59028801	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:59028801C>T	uc002qtd.2	-	2	532	c.240G>A	c.(238-240)GTG>GTA	p.V80V	ZBTB45_uc002qte.2_Silent_p.V80V|ZBTB45_uc002qtf.2_Silent_p.V80V	NM_032792	NP_116181	Q96K62	ZBT45_HUMAN	zinc finger and BTB domain containing 45	80	BTB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(17;1.81e-17)|all_epithelial(17;1.21e-12)|Lung NSC(17;2.8e-05)|all_lung(17;0.000139)|Colorectal(82;0.000147)|Renal(17;0.00528)|all_neural(62;0.0133)|Ovarian(87;0.156)|Medulloblastoma(540;0.232)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0165)|Lung(386;0.18)												OREG0025700	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
TGM3	7053	broad.mit.edu	37	20	2308989	2308989	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2308989G>A	uc002wfx.3	+	9	1408	c.1311G>A	c.(1309-1311)ACG>ACA	p.T437T		NM_003245	NP_003236	Q08188	TGM3_HUMAN	transglutaminase 3 precursor	437					cell envelope organization|hair follicle morphogenesis|keratinization|peptide cross-linking|protein tetramerization	cytoplasm|extrinsic to internal side of plasma membrane	acyltransferase activity|calcium ion binding|GDP binding|GTP binding|GTPase activity|magnesium ion binding|protein-glutamine gamma-glutamyltransferase activity			large_intestine(4)|ovary(3)|breast(1)|skin(1)	9					L-Glutamine(DB00130)													---	---	---	---
FAM113A	64773	broad.mit.edu	37	20	2820491	2820491	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2820491G>A	uc002wgz.1	-	2	565	c.68C>T	c.(67-69)GCC>GTC	p.A23V	FAM113A_uc002whb.1_5'UTR|FAM113A_uc002wha.1_5'UTR|FAM113A_uc010zqa.1_5'UTR|FAM113A_uc002whc.1_Missense_Mutation_p.A23V|VPS16_uc002whe.2_5'Flank|VPS16_uc002whf.2_5'Flank|VPS16_uc002whd.2_5'Flank	NM_022760	NP_073597	Q9H1Q7	F113A_HUMAN	hypothetical protein LOC64773	23							hydrolase activity|protein binding			ovary(2)	2																		---	---	---	---
SMOX	54498	broad.mit.edu	37	20	4155753	4155753	+	Silent	SNP	C	T	T	rs141854482		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4155753C>T	uc002wkm.1	+	2	252	c.51C>T	c.(49-51)CGC>CGT	p.R17R	SMOX_uc002wkk.1_Silent_p.R17R|SMOX_uc002wkl.1_Silent_p.R17R|SMOX_uc002wkn.1_Silent_p.R17R|SMOX_uc002wkp.2_Silent_p.R17R|SMOX_uc010zqo.1_Silent_p.R17R|SMOX_uc002wko.1_Silent_p.R17R	NM_175839	NP_787033	Q9NWM0	SMOX_HUMAN	spermine oxidase isoform 1	17					polyamine biosynthetic process|xenobiotic metabolic process	cytosol|nucleus	polyamine oxidase activity			breast(1)	1					Spermine(DB00127)													---	---	---	---
SMOX	54498	broad.mit.edu	37	20	4167954	4167954	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4167954G>A	uc002wkm.1	+	7	1769	c.1568G>A	c.(1567-1569)CGC>CAC	p.R523H	SMOX_uc002wkk.1_Missense_Mutation_p.R500H|SMOX_uc002wkl.1_Missense_Mutation_p.R470H|SMOX_uc002wkn.1_Missense_Mutation_p.R158H|SMOX_uc002wkp.2_Missense_Mutation_p.R553H|SMOX_uc010zqo.1_Missense_Mutation_p.R447H|SMOX_uc002wko.1_Missense_Mutation_p.R523H	NM_175839	NP_787033	Q9NWM0	SMOX_HUMAN	spermine oxidase isoform 1	523					polyamine biosynthetic process|xenobiotic metabolic process	cytosol|nucleus	polyamine oxidase activity			breast(1)	1					Spermine(DB00127)													---	---	---	---
PROKR2	128674	broad.mit.edu	37	20	5282888	5282888	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5282888A>G	uc010zqw.1	-	2	953	c.953T>C	c.(952-954)GTC>GCC	p.V318A	PROKR2_uc010zqx.1_Missense_Mutation_p.V318A|PROKR2_uc010zqy.1_Missense_Mutation_p.V318A	NM_144773	NP_658986	Q8NFJ6	PKR2_HUMAN	prokineticin receptor 2	318	Helical; Name=7; (Potential).					integral to membrane|plasma membrane	neuropeptide Y receptor activity			ovary(3)|central_nervous_system(1)|pancreas(1)	5															HNSCC(71;0.22)			---	---	---	---
PLCB4	5332	broad.mit.edu	37	20	9404516	9404516	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9404516G>A	uc002wnf.2	+	26	2541	c.2405G>A	c.(2404-2406)CGA>CAA	p.R802Q	PLCB4_uc010gbw.1_Missense_Mutation_p.R802Q|PLCB4_uc010gbx.2_Missense_Mutation_p.R814Q|PLCB4_uc002wne.2_Missense_Mutation_p.R802Q|PLCB4_uc002wnh.2_Missense_Mutation_p.R649Q	NM_182797	NP_877949	Q15147	PLCB4_HUMAN	phospholipase C beta 4 isoform b	802					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																		---	---	---	---
ZNF133	7692	broad.mit.edu	37	20	18295755	18295755	+	Missense_Mutation	SNP	C	T	T	rs151186857	byFrequency;by1000genomes	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18295755C>T	uc010gcq.2	+	5	565	c.260C>T	c.(259-261)CCG>CTG	p.P87L	ZNF133_uc010zrv.1_Missense_Mutation_p.P90L|ZNF133_uc010zrw.1_Missense_Mutation_p.P24L|ZNF133_uc010gcr.2_Missense_Mutation_p.P87L|ZNF133_uc010zrx.1_5'UTR|ZNF133_uc002wql.3_Missense_Mutation_p.P86L|ZNF133_uc010gcs.2_Missense_Mutation_p.P86L|ZNF133_uc010zry.1_5'UTR|ZNF133_uc002wqm.2_Missense_Mutation_p.P87L	NM_003434	NP_003425	P52736	ZN133_HUMAN	zinc finger protein 133	87						nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|pancreas(1)	2																		---	---	---	---
CRNKL1	51340	broad.mit.edu	37	20	20016922	20016922	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20016922C>T	uc002wrs.2	-	15	2496	c.2464G>A	c.(2464-2466)GCC>ACC	p.A822T		NM_016652	NP_057736	Q9BZJ0	CRNL1_HUMAN	crooked neck-like 1 protein	822	HAT 17.				spliceosome assembly	catalytic step 2 spliceosome|cytoplasm|nuclear speck	RNA binding			ovary(2)|large_intestine(1)	3																		---	---	---	---
PAX1	5075	broad.mit.edu	37	20	21687619	21687619	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21687619C>T	uc002wsj.2	+	2	884	c.830C>T	c.(829-831)GCG>GTG	p.A277V	PAX1_uc010zsl.1_Missense_Mutation_p.A277V|PAX1_uc010zsm.1_Missense_Mutation_p.A253V	NM_006192	NP_006183	P15863	PAX1_HUMAN	paired box 1	277					regulation of transcription, DNA-dependent|skeletal system development|transcription from RNA polymerase II promoter	nucleus	DNA binding			upper_aerodigestive_tract(1)|kidney(1)	2																		---	---	---	---
GGTLC1	92086	broad.mit.edu	37	20	23967095	23967095	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23967095C>T	uc002wts.2	-	2	287	c.154G>A	c.(154-156)GCC>ACC	p.A52T	GGTLC1_uc002wtu.2_Missense_Mutation_p.A52T	NM_178312	NP_842564	Q9BX51	GGTL1_HUMAN	gamma-glutamyltransferase light chain 1	52							gamma-glutamyltransferase activity			ovary(1)	1																		---	---	---	---
PYGB	5834	broad.mit.edu	37	20	25239910	25239910	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25239910G>A	uc002wup.2	+	2	390	c.281G>A	c.(280-282)CGC>CAC	p.R94H		NM_002862	NP_002853	P11216	PYGB_HUMAN	brain glycogen phosphorylase	94					glucose metabolic process|glycogen catabolic process	cytoplasm	glycogen phosphorylase activity|pyridoxal phosphate binding			central_nervous_system(1)|skin(1)	2					Pyridoxal Phosphate(DB00114)													---	---	---	---
SUN5	140732	broad.mit.edu	37	20	31590444	31590444	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31590444G>A	uc002wyi.2	-	3	253	c.160C>T	c.(160-162)CGC>TGC	p.R54C		NM_080675	NP_542406	Q8TC36	SUN5_HUMAN	sperm associated antigen 4-like	54					spermatogenesis					skin(1)	1																		---	---	---	---
NCOA6	23054	broad.mit.edu	37	20	33356268	33356268	+	Silent	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33356268T>C	uc002xav.2	-	6	3084	c.513A>G	c.(511-513)CCA>CCG	p.P171P	NCOA6_uc002xaw.2_Silent_p.P171P|NCOA6_uc010gew.1_Silent_p.P171P	NM_014071	NP_054790	Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	171	TBP/GTF2A-binding region.|NCOA1-binding region.|CREBBP-binding region.				brain development|cellular lipid metabolic process|DNA recombination|DNA repair|DNA replication|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|heart development|myeloid cell differentiation|positive regulation of transcription from RNA polymerase II promoter|response to hormone stimulus|transcription initiation from RNA polymerase II promoter	transcription factor complex	chromatin binding|enzyme binding|estrogen receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|retinoid X receptor binding|thyroid hormone receptor binding			ovary(3)|breast(3)|central_nervous_system(1)	7																		---	---	---	---
RBM39	9584	broad.mit.edu	37	20	34295045	34295045	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34295045T>C	uc002xeb.2	-	14	1648	c.1304A>G	c.(1303-1305)CAA>CGA	p.Q435R	RBM39_uc002xdz.2_Missense_Mutation_p.Q411R|RBM39_uc002xea.2_Missense_Mutation_p.Q278R|RBM39_uc010gfn.2_Missense_Mutation_p.Q278R|RBM39_uc010zvm.1_Missense_Mutation_p.Q407R|RBM39_uc002xeg.2_Missense_Mutation_p.Q413R|RBM39_uc002xec.2_Missense_Mutation_p.Q429R|RBM39_uc002xed.2_Missense_Mutation_p.Q153R|RBM39_uc002xee.2_Missense_Mutation_p.Q278R|RBM39_uc002xef.2_Missense_Mutation_p.Q272R|RBM39_uc010zvn.1_Missense_Mutation_p.Q278R	NM_184234	NP_909122	Q14498	RBM39_HUMAN	RNA binding motif protein 39 isoform a	435	Interaction with NCOA6 (By similarity).				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)																	---	---	---	---
TGM2	7052	broad.mit.edu	37	20	36770552	36770552	+	Silent	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36770552C>A	uc002xhr.2	-	7	1009	c.909G>T	c.(907-909)TCG>TCT	p.S303S	TGM2_uc010zvx.1_Silent_p.S222S|TGM2_uc010zvy.1_Silent_p.S243S|TGM2_uc002xhs.1_Silent_p.S279S|TGM2_uc002xht.2_Silent_p.S303S	NM_004613	NP_004604	P21980	TGM2_HUMAN	transglutaminase 2 isoform a	303					apoptotic cell clearance|peptide cross-linking|positive regulation of cell adhesion		acyltransferase activity|metal ion binding|protein binding|protein-glutamine gamma-glutamyltransferase activity			large_intestine(1)|lung(1)|ovary(1)	3		Myeloproliferative disorder(115;0.00878)			L-Glutamine(DB00130)													---	---	---	---
SLC32A1	140679	broad.mit.edu	37	20	37357184	37357184	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									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)													---	---	---	---
CHD6	84181	broad.mit.edu	37	20	40081539	40081539	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40081539T>G	uc002xka.1	-	21	3342	c.3164A>C	c.(3163-3165)AAA>ACA	p.K1055T		NM_032221	NP_115597	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	1055					chromatin remodeling|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding			ovary(6)|skin(5)|lung(2)|central_nervous_system(1)	14		Myeloproliferative disorder(115;0.00425)																---	---	---	---
SFRS6	6431	broad.mit.edu	37	20	42088547	42088547	+	Intron	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42088547A>G	uc010zwg.1	+						SFRS6_uc002xki.2_Intron|SFRS6_uc002xkk.2_Intron	NM_006275	NP_006266			arginine/serine-rich splicing factor 6						mRNA 3'-end processing|mRNA export from nucleus|mRNA splice site selection|termination of RNA polymerase II transcription	nucleoplasm	nucleotide binding|protein binding|RNA binding				0		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)															---	---	---	---
SFRS6	6431	broad.mit.edu	37	20	42089154	42089154	+	Splice_Site	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42089154G>T	uc010zwg.1	+	5	761	c.591_splice	c.e5-1	p.R197_splice	SFRS6_uc002xki.2_Splice_Site_p.R68_splice|SFRS6_uc002xkk.2_Splice_Site_p.R197_splice	NM_006275	NP_006266			arginine/serine-rich splicing factor 6						mRNA 3'-end processing|mRNA export from nucleus|mRNA splice site selection|termination of RNA polymerase II transcription	nucleoplasm	nucleotide binding|protein binding|RNA binding				0		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)															---	---	---	---
MATN4	8785	broad.mit.edu	37	20	43933295	43933295	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43933295G>A	uc002xnn.2	-	3	403	c.216C>T	c.(214-216)CGC>CGT	p.R72R	MATN4_uc002xno.2_Silent_p.R72R|MATN4_uc002xnp.2_Silent_p.R72R|MATN4_uc010zwr.1_Silent_p.R20R|MATN4_uc002xnr.1_Silent_p.R72R|RBPJL_uc002xns.2_5'Flank|RBPJL_uc002xnt.2_5'Flank	NM_003833	NP_003824	O95460	MATN4_HUMAN	matrilin 4 isoform 1 precursor	72	VWFA 1.					extracellular region	protein binding				0		Myeloproliferative disorder(115;0.0122)																---	---	---	---
RBPJL	11317	broad.mit.edu	37	20	43941018	43941018	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43941018C>T	uc002xns.2	+	6	674	c.602C>T	c.(601-603)TCG>TTG	p.S201L	RBPJL_uc002xnt.2_Missense_Mutation_p.S201L	NM_014276	NP_055091	Q9UBG7	RBPJL_HUMAN	recombining binding protein L	201					signal transduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Myeloproliferative disorder(115;0.0122)																---	---	---	---
SYS1-DBNDD2	767557	broad.mit.edu	37	20	44037177	44037177	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44037177G>A	uc002xnx.2	+	4	566	c.70G>A	c.(70-72)GAG>AAG	p.E24K	DBNDD2_uc002xnz.2_Missense_Mutation_p.E24K|DBNDD2_uc002xoa.2_Missense_Mutation_p.E24K|DBNDD2_uc002xob.2_Missense_Mutation_p.E24K|DBNDD2_uc002xoc.2_Missense_Mutation_p.E24K|DBNDD2_uc002xod.2_Missense_Mutation_p.E24K|DBNDD2_uc002xoe.2_Missense_Mutation_p.E24K|DBNDD2_uc002xof.2_Missense_Mutation_p.E24K|DBNDD2_uc002xog.2_Missense_Mutation_p.E24K	NM_001048225	NP_001041690			SCF apoptosis response protein 1 isoform a												0																		---	---	---	---
SPINLW1	57119	broad.mit.edu	37	20	44166631	44166631	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44166631C>T	uc010zxc.1	-	4	526	c.494G>A	c.(493-495)CGT>CAT	p.R165H	WFDC6_uc002xos.1_Missense_Mutation_p.R65H	NM_020398	NP_065131	O95925	EPPI_HUMAN	serine peptidase inhibitor-like, with Kunitz and	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment						extracellular region	serine-type endopeptidase inhibitor activity			pancreas(1)	1		Myeloproliferative disorder(115;0.0122)																---	---	---	---
CTSA	5476	broad.mit.edu	37	20	44521441	44521441	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44521441G>A	uc002xqj.3	+	6	996	c.522G>A	c.(520-522)CTG>CTA	p.L174L	NEURL2_uc002xqg.1_5'Flank|CTSA_uc002xqh.2_Silent_p.L192L|CTSA_uc002xqi.2_RNA|CTSA_uc010zxi.1_Silent_p.L175L|CTSA_uc002xqk.3_Silent_p.L174L	NM_001127695	NP_001121167	P10619	PPGB_HUMAN	cathepsin A isoform b precursor	174					intracellular protein transport|proteolysis	endoplasmic reticulum|lysosome|nucleus	enzyme activator activity|protein binding|serine-type carboxypeptidase activity			ovary(1)	1		Myeloproliferative disorder(115;0.0122)																---	---	---	---
CTCFL	140690	broad.mit.edu	37	20	56098737	56098737	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56098737T>A	uc010gix.1	-	1	1187	c.525A>T	c.(523-525)GAA>GAT	p.E175D	CTCFL_uc010giw.1_Missense_Mutation_p.E175D|CTCFL_uc002xym.2_Missense_Mutation_p.E175D|CTCFL_uc010giz.1_Intron|CTCFL_uc010giy.1_Intron|CTCFL_uc010gja.1_Missense_Mutation_p.E175D|CTCFL_uc010gjb.1_Missense_Mutation_p.E175D|CTCFL_uc010gjc.1_Missense_Mutation_p.E175D|CTCFL_uc010gjd.1_Missense_Mutation_p.E175D|CTCFL_uc010gje.2_Missense_Mutation_p.E175D|CTCFL_uc010gjf.2_Intron|CTCFL_uc010gjg.2_Intron|CTCFL_uc010gjh.1_Missense_Mutation_p.E175D|CTCFL_uc010gji.1_Intron|CTCFL_uc010gjj.1_Missense_Mutation_p.E175D|CTCFL_uc010gjk.1_Missense_Mutation_p.E175D|CTCFL_uc010gjl.1_Missense_Mutation_p.E175D	NM_080618	NP_542185	Q8NI51	CTCFL_HUMAN	CCCTC-binding factor-like protein	175					cell cycle|DNA methylation involved in gamete generation|histone methylation|positive regulation of transcription, DNA-dependent|regulation of gene expression by genetic imprinting|regulation of histone H3-K4 methylation|transcription, DNA-dependent	cytoplasm|nucleus	histone binding|sequence-specific DNA binding|transcription regulatory region DNA binding|zinc ion binding			ovary(2)|large_intestine(1)|skin(1)	4	Lung NSC(12;0.00132)|all_lung(29;0.00433)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;3.95e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.09e-07)															---	---	---	---
GNAS	2778	broad.mit.edu	37	20	57415375	57415375	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57415375G>A	uc002xzt.2	+	1	581	c.214G>A	c.(214-216)GGC>AGC	p.G72S	GNASAS_uc002xzs.1_Intron|GNAS_uc002xzu.3_5'Flank|GNAS_uc010gjq.2_5'Flank	NM_016592	NP_057676	P63092	GNAS2_HUMAN	GNAS complex locus NESP55	72				Missing (in Ref. 8; AAH66923).	activation of adenylate cyclase activity|cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|intracellular transport|platelet activation|regulation of insulin secretion|sensory perception of smell|transmembrane transport|water transport	heterotrimeric G-protein complex|intrinsic to membrane|trans-Golgi network membrane	adenylate cyclase activity|GTP binding|GTPase activity|guanyl-nucleotide exchange factor activity|identical protein binding|signal transducer activity			pituitary(201)|thyroid(35)|ovary(15)|adrenal_gland(9)|liver(7)|large_intestine(5)|parathyroid(5)|kidney(5)|haematopoietic_and_lymphoid_tissue(3)|lung(2)|testis(1)|stomach(1)|small_intestine(1)|autonomic_ganglia(1)|pancreas(1)	292	all_lung(29;0.0104)		BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109)					Mis		pituitary adenoma		McCune-Albright syndrome; pseudohypoparathyroidism|type IA		3-Methylglutaconic_Aciduria_and_Myelodysplasia|McCune-Albright_syndrome|Mazabraud_syndrome	TSP Lung(22;0.16)			---	---	---	---
TH1L	51497	broad.mit.edu	37	20	57564992	57564992	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57564992G>A	uc002yag.2	+	7	791	c.764G>A	c.(763-765)GGC>GAC	p.G255D	TH1L_uc002yaf.1_RNA|TH1L_uc002yah.2_Missense_Mutation_p.G255D	NM_198976	NP_945327	Q8IXH7	NELFD_HUMAN	TH1-like protein	255					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)															---	---	---	---
C20orf197	284756	broad.mit.edu	37	20	58645855	58645855	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58645855G>A	uc002ybj.1	+	4	579	c.273G>A	c.(271-273)ATG>ATA	p.M91I		NM_173644	NP_775915	Q8N268	CT197_HUMAN	hypothetical protein LOC284756	91										upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3			BRCA - Breast invasive adenocarcinoma(7;2.33e-09)															---	---	---	---
PSMA7	5688	broad.mit.edu	37	20	60714901	60714901	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60714901C>T	uc002ybx.1	-	3	399	c.284G>A	c.(283-285)CGG>CAG	p.R95Q	PSMA7_uc002yby.1_RNA	NM_002792	NP_002783	O14818	PSA7_HUMAN	proteasome alpha 7 subunit	95					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|interspecies interaction between organisms|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|proteasome core complex, alpha-subunit complex	identical protein binding|threonine-type endopeptidase activity				0	Breast(26;3.97e-09)		BRCA - Breast invasive adenocarcinoma(19;1.28e-07)															---	---	---	---
OSBPL2	9885	broad.mit.edu	37	20	60854271	60854271	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60854271G>A	uc002yck.1	+	7	752	c.550G>A	c.(550-552)GCG>ACG	p.A184T	OSBPL2_uc002ycl.1_Missense_Mutation_p.A172T|OSBPL2_uc011aah.1_Missense_Mutation_p.A92T|OSBPL2_uc002ycm.1_5'UTR	NM_144498	NP_653081	Q9H1P3	OSBL2_HUMAN	oxysterol-binding protein-like protein 2 isoform	184					lipid transport		lipid binding			ovary(1)|central_nervous_system(1)	2	Breast(26;7.76e-09)		BRCA - Breast invasive adenocarcinoma(19;1.33e-06)															---	---	---	---
DIDO1	11083	broad.mit.edu	37	20	61525803	61525803	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61525803C>T	uc002ydr.1	-	11	2798	c.2534G>A	c.(2533-2535)CGC>CAC	p.R845H	DIDO1_uc002yds.1_Missense_Mutation_p.R845H|DIDO1_uc002ydt.1_Missense_Mutation_p.R845H|DIDO1_uc002ydu.1_Missense_Mutation_p.R845H	NM_033081	NP_149072	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1 isoform c	845					apoptosis|transcription, DNA-dependent	cytoplasm|nucleus	zinc ion binding			ovary(3)|skin(3)	6	Breast(26;5.68e-08)																	---	---	---	---
YTHDF1	54915	broad.mit.edu	37	20	61835152	61835152	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61835152C>T	uc002yeh.2	-	4	434	c.140G>A	c.(139-141)AGT>AAT	p.S47N	YTHDF1_uc011aaq.1_5'UTR	NM_017798	NP_060268	Q9BYJ9	YTHD1_HUMAN	YTH domain family, member 1	47										ovary(2)	2																		---	---	---	---
PRIC285	85441	broad.mit.edu	37	20	62196162	62196162	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62196162C>T	uc002yfm.2	-	9	4905	c.4013G>A	c.(4012-4014)CGC>CAC	p.R1338H	PRIC285_uc002yfl.1_Missense_Mutation_p.R769H	NM_001037335	NP_001032412	Q9BYK8	PR285_HUMAN	PPAR-alpha interacting complex protein 285	1338					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)															---	---	---	---
TNFRSF6B	8771	broad.mit.edu	37	20	62329757	62329757	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62329757G>A	uc002yfy.2	+	7	1178	c.744G>A	c.(742-744)GCG>GCA	p.A248A	RTEL1_uc002yfw.2_RNA|TNFRSF6B_uc002yfz.2_Silent_p.A248A	NM_032945	NP_116563	O95407	TNF6B_HUMAN	tumor necrosis factor receptor superfamily,	248					anti-apoptosis|apoptosis	extracellular region|soluble fraction	protein binding|receptor activity			central_nervous_system(1)|skin(1)	2	all_cancers(38;4.66e-12)|all_epithelial(29;2.56e-13)|Lung NSC(23;1.06e-08)|all_lung(23;3.34e-08)		Epithelial(9;1.78e-08)|all cancers(9;7.89e-08)|OV - Ovarian serous cystadenocarcinoma(5;0.00504)															---	---	---	---
TCEA2	6919	broad.mit.edu	37	20	62697836	62697836	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62697836C>T	uc011abs.1	+	2	736	c.80C>T	c.(79-81)GCC>GTC	p.A27V	TCEA2_uc011abr.1_5'UTR|TCEA2_uc010gkq.2_5'UTR|TCEA2_uc010gks.2_Missense_Mutation_p.A27V|TCEA2_uc010gkt.2_5'UTR|TCEA2_uc010gku.1_5'UTR	NM_003195	NP_003186	Q15560	TCEA2_HUMAN	transcription elongation factor A protein 2	27	TFIIS N-terminal.				regulation of transcription elongation, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription elongation, DNA-dependent	transcription elongation factor complex	DNA binding|protein binding|translation elongation factor activity|zinc ion binding				0	all_cancers(38;3.45e-11)|all_epithelial(29;9.12e-13)|Lung NSC(23;2e-09)|all_lung(23;6.77e-09)																	---	---	---	---
NPBWR2	2832	broad.mit.edu	37	20	62737901	62737901	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62737901G>A	uc011abt.1	-	1	284	c.284C>T	c.(283-285)ACG>ATG	p.T95M		NM_005286	NP_005277	P48146	NPBW2_HUMAN	neuropeptides B/W receptor 2	95	Helical; Name=2; (Potential).					plasma membrane	opioid receptor activity|protein binding			large_intestine(1)	1	all_cancers(38;2.58e-11)|all_epithelial(29;6.4e-13)|Lung NSC(23;1.25e-09)|all_lung(23;4.21e-09)																	---	---	---	---
NRIP1	8204	broad.mit.edu	37	21	16340294	16340294	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:16340294G>T	uc002yjx.2	-	4	818	c.220C>A	c.(220-222)CAG>AAG	p.Q74K		NM_003489	NP_003480	P48552	NRIP1_HUMAN	nuclear receptor interacting protein 1	74					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)														---	---	---	---
USP25	29761	broad.mit.edu	37	21	17250724	17250724	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:17250724C>T	uc002yjy.1	+	24	3315	c.3098C>T	c.(3097-3099)ACG>ATG	p.T1033M	USP25_uc011aby.1_Missense_Mutation_p.T1103M|USP25_uc002yjz.1_Missense_Mutation_p.T1065M|USP25_uc010gla.1_Missense_Mutation_p.T428M	NM_013396	NP_037528	Q9UHP3	UBP25_HUMAN	ubiquitin specific peptidase 25	1033					protein modification process|ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(3)|liver(2)	5				Epithelial(23;7.55e-05)|all cancers(11;0.000429)|COAD - Colon adenocarcinoma(22;0.00543)|OV - Ovarian serous cystadenocarcinoma(11;0.00743)|Colorectal(24;0.0116)|Lung(58;0.0853)|LUSC - Lung squamous cell carcinoma(23;0.0889)														---	---	---	---
C21orf34	388815	broad.mit.edu	37	21	17443426	17443426	+	Intron	SNP	T	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:17443426T>C	uc002ykb.2	+						C21orf34_uc010glc.2_5'Flank	NR_027790				Homo sapiens C21ORF34 (C21orf34) mRNA, partial cds, alternatively spliced.												0		Breast(209;0.152)		Epithelial(23;8.3e-05)|all cancers(11;0.000383)|Colorectal(24;0.00387)|COAD - Colon adenocarcinoma(22;0.0113)|OV - Ovarian serous cystadenocarcinoma(11;0.0127)|LUSC - Lung squamous cell carcinoma(23;0.153)														---	---	---	---
ADAMTS1	9510	broad.mit.edu	37	21	28212641	28212641	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:28212641C>T	uc002ymf.2	-	5	2074	c.1619G>A	c.(1618-1620)TGT>TAT	p.C540Y		NM_006988	NP_008919	Q9UHI8	ATS1_HUMAN	ADAM metallopeptidase with thrombospondin type 1	540	Disintegrin.				integrin-mediated signaling pathway|negative regulation of cell proliferation|proteolysis		heparin binding|zinc ion binding			lung(3)|large_intestine(2)|central_nervous_system(1)	6		Breast(209;0.000962)		Lung(58;0.215)														---	---	---	---
KRTAP27-1	643812	broad.mit.edu	37	21	31709741	31709741	+	Silent	SNP	G	T	T	rs139729864		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31709741G>T	uc002ynx.1	-	1	272	c.246C>A	c.(244-246)CCC>CCA	p.P82P		NM_001077711	NP_001071179	Q3LI81	KR271_HUMAN	keratin associated protein 27-1	82						intermediate filament				ovary(2)	2																		---	---	---	---
C21orf59	56683	broad.mit.edu	37	21	33954519	33954519	+	Silent	SNP	C	T	T	rs145187250		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33954519C>T	uc002ypy.1	-	7	1082	c.969G>A	c.(967-969)TCG>TCA	p.S323S	TCP10L_uc002ypw.3_Silent_p.S117S|C21orf59_uc002ypx.1_Silent_p.S140S|C21orf59_uc002ypz.1_Silent_p.S291S	NM_021254	NP_067077	P57076	CU059_HUMAN	hypothetical protein LOC56683	Error:Variant_position_missing_in_P57076_after_alignment						cytosol|nucleus					0																		---	---	---	---
SON	6651	broad.mit.edu	37	21	34923905	34923905	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34923905A>T	uc002yse.1	+	3	2417	c.2368A>T	c.(2368-2370)ACT>TCT	p.T790S	SON_uc002ysb.1_Missense_Mutation_p.T790S|SON_uc002ysc.2_Missense_Mutation_p.T790S|SON_uc002ysd.2_Intron|SON_uc002ysf.1_Intron|SON_uc002ysg.2_5'Flank	NM_138927	NP_620305	P18583	SON_HUMAN	SON DNA-binding protein isoform F	790	17 X 10 AA tandem repeats of L-A-[ST]- [NSG]-[TS]-MDSQM.				anti-apoptosis|cytokinesis|mRNA processing|regulation of cell cycle|regulation of RNA splicing|RNA splicing|spindle pole body separation	nuclear speck	DNA binding|double-stranded RNA binding			ovary(4)|skin(2)	6																		---	---	---	---
KCNJ15	3772	broad.mit.edu	37	21	39672159	39672159	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39672159G>A	uc002ywv.2	+	4	1278	c.976G>A	c.(976-978)GAT>AAT	p.D326N	KCNJ15_uc002yww.2_Missense_Mutation_p.D326N|KCNJ15_uc002ywx.2_Missense_Mutation_p.D326N	NM_002243	NP_002234	Q99712	IRK15_HUMAN	potassium inwardly-rectifying channel J15	326	Cytoplasmic (By similarity).				synaptic transmission	integral to plasma membrane	inward rectifier potassium channel activity			ovary(2)|skin(2)|breast(1)|central_nervous_system(1)	6																		---	---	---	---
UMODL1	89766	broad.mit.edu	37	21	43533673	43533673	+	Intron	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43533673C>A	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																		---	---	---	---
TRAPPC10	7109	broad.mit.edu	37	21	45511891	45511891	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45511891C>T	uc002zea.2	+	19	3127	c.2958C>T	c.(2956-2958)ACC>ACT	p.T986T	TRAPPC10_uc010gpo.2_Silent_p.T697T|TRAPPC10_uc011afa.1_Silent_p.T364T|TRAPPC10_uc011afb.1_Silent_p.T91T	NM_003274	NP_003265	P48553	TPC10_HUMAN	trafficking protein particle complex 10	986					vesicle-mediated transport	Golgi apparatus|integral to membrane	binding|sodium ion transmembrane transporter activity			ovary(1)|skin(1)	2																		---	---	---	---
ADARB1	104	broad.mit.edu	37	21	46640907	46640907	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46640907G>A	uc002zgy.2	+	11	2459	c.2024G>A	c.(2023-2025)CGC>CAC	p.R675H	ADARB1_uc002zgr.2_Missense_Mutation_p.R675H|ADARB1_uc002zgs.2_RNA|ADARB1_uc002zgw.2_Missense_Mutation_p.R635H|ADARB1_uc002zgv.2_RNA|ADARB1_uc002zgt.2_Missense_Mutation_p.R635H|ADARB1_uc010gpx.2_RNA|ADARB1_uc002zgq.2_RNA|ADARB1_uc002zgu.2_RNA	NM_015833	NP_056648	P78563	RED1_HUMAN	RNA-specific adenosine deaminase B1 isoform 2	675	A to I editase.				adenosine to inosine editing|mRNA modification|mRNA processing|RNA processing	nucleoplasm|nucleus	double-stranded RNA adenosine deaminase activity|double-stranded RNA adenosine deaminase activity|double-stranded RNA binding|double-stranded RNA binding|metal ion binding|mRNA binding|RNA binding			skin(1)	1				Colorectal(79;0.115)														---	---	---	---
PCNT	5116	broad.mit.edu	37	21	47808672	47808672	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47808672C>T	uc002zji.3	+	18	3587	c.3480C>T	c.(3478-3480)GAC>GAT	p.D1160D	PCNT_uc002zjj.2_Silent_p.D1042D	NM_006031	NP_006022	O95613	PCNT_HUMAN	pericentrin	1160					cilium assembly|G2/M transition of mitotic cell cycle	cytosol|microtubule	calmodulin binding			ovary(4)|breast(2)|pancreas(2)	8	Breast(49;0.112)																	---	---	---	---
C22orf29	79680	broad.mit.edu	37	22	19839076	19839076	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19839076C>T	uc002zqg.2	-	2	1308	c.709G>A	c.(709-711)GCC>ACC	p.A237T	GNB1L_uc002zqd.1_Intron|GNB1L_uc002zqe.1_Intron|GNB1L_uc002zqf.1_Intron|C22orf29_uc002zqh.2_Missense_Mutation_p.A237T|C22orf29_uc002zqi.2_Missense_Mutation_p.A237T|C22orf29_uc010grt.1_Intron	NM_024627	NP_078903	Q7L3V2	CV029_HUMAN	hypothetical protein LOC79680	237											0	Colorectal(54;0.0993)																	---	---	---	---
C22orf29	79680	broad.mit.edu	37	22	19839620	19839620	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19839620G>A	uc002zqg.2	-	2	764	c.165C>T	c.(163-165)ACC>ACT	p.T55T	GNB1L_uc002zqd.1_Intron|GNB1L_uc002zqe.1_Intron|GNB1L_uc002zqf.1_Intron|C22orf29_uc002zqh.2_Silent_p.T55T|C22orf29_uc002zqi.2_Silent_p.T55T|C22orf29_uc010grt.1_Intron	NM_024627	NP_078903	Q7L3V2	CV029_HUMAN	hypothetical protein LOC79680	55											0	Colorectal(54;0.0993)																	---	---	---	---
ZDHHC8	29801	broad.mit.edu	37	22	20128528	20128528	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20128528G>A	uc002zrq.2	+	7	993	c.887G>A	c.(886-888)CGT>CAT	p.R296H	ZDHHC8_uc002zrr.1_Missense_Mutation_p.R296H|ZDHHC8_uc010gsa.2_Missense_Mutation_p.R102H	NM_013373	NP_037505	Q9ULC8	ZDHC8_HUMAN	zinc finger, DHHC domain containing 8	296	Cytoplasmic (Potential).					cytoplasmic vesicle membrane|integral to membrane	acyltransferase activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2	Colorectal(54;0.0993)																	---	---	---	---
RTN4R	65078	broad.mit.edu	37	22	20229616	20229616	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20229616A>G	uc002zrv.2	-	2	1241	c.1040T>C	c.(1039-1041)CTG>CCG	p.L347P	RTN4R_uc002zru.2_Missense_Mutation_p.L119P	NM_023004	NP_075380	Q9BZR6	RTN4R_HUMAN	reticulon 4 receptor precursor	347					axonogenesis|negative regulation of axonogenesis|nerve growth factor receptor signaling pathway	anchored to membrane|cell surface|endoplasmic reticulum|plasma membrane	protein binding|receptor activity				0	Colorectal(54;0.0993)																	---	---	---	---
ZNF74	7625	broad.mit.edu	37	22	20760748	20760748	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20760748C>T	uc010gsm.2	+	6	1637	c.1425C>T	c.(1423-1425)AAC>AAT	p.N475N	ZNF74_uc002zsg.2_Silent_p.N404N|ZNF74_uc002zsh.2_Silent_p.N475N|ZNF74_uc002zsi.2_Silent_p.N404N|ZNF74_uc010gsn.2_Silent_p.N404N	NM_003426	NP_003417	Q16587	ZNF74_HUMAN	zinc finger protein 74	475	C2H2-type 9.				multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	actin cytoskeleton|nucleus	DNA binding|RNA binding|zinc ion binding			ovary(1)	1	Melanoma(16;0.000465)|Ovarian(15;0.0025)|Colorectal(54;0.0221)|all_neural(72;0.219)	Lung SC(17;0.0262)|all_lung(157;0.248)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)															---	---	---	---
KLHL22	84861	broad.mit.edu	37	22	20796481	20796481	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20796481C>T	uc002zsl.1	-	7	1893	c.1784G>A	c.(1783-1785)CGC>CAC	p.R595H	KLHL22_uc011ahr.1_Missense_Mutation_p.R452H	NM_032775	NP_116164	Q53GT1	KLH22_HUMAN	kelch-like	595					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)															---	---	---	---
MED15	51586	broad.mit.edu	37	22	20929406	20929406	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20929406A>G	uc002zsp.2	+	9	1239	c.1159A>G	c.(1159-1161)ACG>GCG	p.T387A	MED15_uc002zsq.2_Intron|MED15_uc010gso.2_Intron|MED15_uc002zsr.2_Intron|MED15_uc011ahs.1_Intron|MED15_uc002zss.2_Intron|MED15_uc011ahu.1_Missense_Mutation_p.T113A|MED15_uc002zst.2_Missense_Mutation_p.T3A	NM_001003891	NP_001003891	Q96RN5	MED15_HUMAN	mediator complex subunit 15 isoform a	387	Pro-rich.				regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	Golgi apparatus|mediator complex	protein binding			skin(1)	1	all_cancers(11;2.07e-24)|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)|Epithelial(17;0.209)															---	---	---	---
SLC7A4	6545	broad.mit.edu	37	22	21385960	21385960	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21385960C>A	uc002zud.2	-	2	210	c.142G>T	c.(142-144)GGT>TGT	p.G48C	SLC7A4_uc002zue.2_Missense_Mutation_p.G48C	NM_004173	NP_004164	O43246	CTR4_HUMAN	solute carrier family 7 (cationic amino acid	48	Helical; (Potential).				cellular amino acid metabolic process	integral to membrane	basic amino acid transmembrane transporter activity			ovary(1)|lung(1)	2	all_cancers(11;2.85e-22)|Lung NSC(8;4.21e-14)|all_lung(8;6.08e-13)|Melanoma(16;0.000465)|Ovarian(15;0.0028)|Colorectal(54;0.0968)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.195)		L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129)													---	---	---	---
MAPK1	5594	broad.mit.edu	37	22	22162145	22162145	+	Intron	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22162145G>A	uc002zvn.2	-						MAPK1_uc002zvo.2_Intron|MAPK1_uc010gtk.1_Intron	NM_002745	NP_002736			mitogen-activated protein kinase 1						activation of MAPK activity|activation of MAPKK activity|axon guidance|cell cycle|epidermal growth factor receptor signaling pathway|ERK1 and ERK2 cascade|induction of apoptosis|innate immune response|insulin receptor signaling pathway|interspecies interaction between organisms|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|platelet activation|Ras protein signal transduction|regulation of sequence-specific DNA binding transcription factor activity|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|transcription, DNA-dependent	cytosol|nucleoplasm	ATP binding|DNA binding|MAP kinase activity|phosphatase binding|RNA polymerase II carboxy-terminal domain kinase activity			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3	Colorectal(54;0.105)	all_lung(157;3.89e-05)		READ - Rectum adenocarcinoma(21;0.0689)	Arsenic trioxide(DB01169)													---	---	---	---
TOP3B	8940	broad.mit.edu	37	22	22316806	22316806	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22316806C>A	uc002zvs.2	-	13	1955	c.1520G>T	c.(1519-1521)GGC>GTC	p.G507V	TOP3B_uc010gtm.1_Missense_Mutation_p.G52V|TOP3B_uc002zvr.2_Missense_Mutation_p.G232V|TOP3B_uc010gtl.2_Missense_Mutation_p.G507V|TOP3B_uc002zvt.3_Missense_Mutation_p.G507V	NM_003935	NP_003926	O95985	TOP3B_HUMAN	topoisomerase (DNA) III beta	507					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)														---	---	---	---
ZNF280A	129025	broad.mit.edu	37	22	22869868	22869868	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22869868A>T	uc002zwe.2	-	2	340	c.87T>A	c.(85-87)GAT>GAA	p.D29E	LOC96610_uc011aim.1_Intron	NM_080740	NP_542778	P59817	Z280A_HUMAN	zinc finger protein 280A	29					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)		READ - Rectum adenocarcinoma(21;0.145)														---	---	---	---
CABIN1	23523	broad.mit.edu	37	22	24573539	24573539	+	Silent	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24573539C>A	uc002zzi.1	+	36	6400	c.6273C>A	c.(6271-6273)CCC>CCA	p.P2091P	CABIN1_uc002zzj.1_Silent_p.P2012P|CABIN1_uc002zzl.1_Silent_p.P2091P|CABIN1_uc010gul.1_Silent_p.P29P	NM_012295	NP_036427	Q9Y6J0	CABIN_HUMAN	calcineurin binding protein 1	2091					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																		---	---	---	---
C22orf13	83606	broad.mit.edu	37	22	24939903	24939903	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24939903G>A	uc003aah.2	-	5	851	c.535C>T	c.(535-537)CGC>TGC	p.R179C	C22orf13_uc003aal.2_Missense_Mutation_p.R235C|C22orf13_uc003aai.3_Missense_Mutation_p.R136C|C22orf13_uc003aaj.3_Missense_Mutation_p.R179C|C22orf13_uc003aak.3_Missense_Mutation_p.R235C	NM_031444	NP_113632	Q96NT3	CV013_HUMAN	chromosome 22 open reading frame 13	179											0																		---	---	---	---
SGSM1	129049	broad.mit.edu	37	22	25246318	25246318	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25246318C>T	uc003abg.2	+	5	531	c.374C>T	c.(373-375)GCC>GTC	p.A125V	SGSM1_uc003abh.2_Missense_Mutation_p.A125V|SGSM1_uc010guu.1_Missense_Mutation_p.A125V|SGSM1_uc003abj.2_Missense_Mutation_p.A125V|SGSM1_uc003abi.1_Missense_Mutation_p.A100V|SGSM1_uc003abf.2_Missense_Mutation_p.A125V	NM_001039948	NP_001035037	Q2NKQ1	SGSM1_HUMAN	RUN and TBC1 domain containing 2 isoform 1	125	RUN.					Golgi apparatus	Rab GTPase activator activity			ovary(2)|central_nervous_system(2)|pancreas(1)	5																OREG0026418	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
SGSM1	129049	broad.mit.edu	37	22	25264717	25264717	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25264717C>T	uc003abg.2	+	12	1343	c.1186C>T	c.(1186-1188)CGA>TGA	p.R396*	SGSM1_uc003abh.2_Nonsense_Mutation_p.R396*|SGSM1_uc010guu.1_Nonsense_Mutation_p.R396*|SGSM1_uc003abj.2_Nonsense_Mutation_p.R396*|SGSM1_uc003abi.1_Nonsense_Mutation_p.R371*	NM_001039948	NP_001035037	Q2NKQ1	SGSM1_HUMAN	RUN and TBC1 domain containing 2 isoform 1	396						Golgi apparatus	Rab GTPase activator activity			ovary(2)|central_nervous_system(2)|pancreas(1)	5																		---	---	---	---
ADRBK2	157	broad.mit.edu	37	22	26091137	26091137	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26091137C>T	uc003abx.3	+	13	1263	c.1116C>T	c.(1114-1116)GCC>GCT	p.A372A	ADRBK2_uc010gux.2_Silent_p.A372A|ADRBK2_uc003abw.2_Silent_p.A259A|ADRBK2_uc003aby.3_RNA	NM_005160	NP_005151	P35626	ARBK2_HUMAN	beta-adrenergic receptor kinase 2	372	Protein kinase.						ATP binding|beta-adrenergic receptor kinase activity|signal transducer activity			lung(3)|ovary(2)|stomach(1)|central_nervous_system(1)	7					Adenosine triphosphate(DB00171)													---	---	---	---
MYO18B	84700	broad.mit.edu	37	22	26422615	26422615	+	Silent	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26422615C>A	uc003abz.1	+	43	6925	c.6675C>A	c.(6673-6675)TCC>TCA	p.S2225S	MYO18B_uc003aca.1_Silent_p.S2106S|MYO18B_uc010guy.1_Silent_p.S2107S|MYO18B_uc010guz.1_Silent_p.S2105S|MYO18B_uc011aka.1_Silent_p.S1379S|MYO18B_uc011akb.1_Silent_p.S1738S|MYO18B_uc010gva.1_Silent_p.S208S|MYO18B_uc010gvb.1_RNA	NM_032608	NP_115997	Q8IUG5	MY18B_HUMAN	myosin XVIIIB	2225						nucleus|sarcomere|unconventional myosin complex	actin binding|ATP binding|motor activity			ovary(5)|central_nervous_system(3)|large_intestine(2)|breast(2)	12																		---	---	---	---
EIF4ENIF1	56478	broad.mit.edu	37	22	31850237	31850237	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31850237C>T	uc003akz.1	-	10	1569	c.1405G>A	c.(1405-1407)GTA>ATA	p.V469I	EIF4ENIF1_uc003akx.1_Missense_Mutation_p.V148I|EIF4ENIF1_uc003aky.1_Missense_Mutation_p.V148I|EIF4ENIF1_uc003ala.1_Missense_Mutation_p.V469I|EIF4ENIF1_uc003alb.1_Missense_Mutation_p.V306I|EIF4ENIF1_uc003akw.1_5'Flank	NM_019843	NP_062817	Q9NRA8	4ET_HUMAN	eukaryotic translation initiation factor 4E	469						nucleus	protein binding|protein transporter activity			ovary(1)	1																		---	---	---	---
FBXO7	25793	broad.mit.edu	37	22	32887072	32887072	+	Splice_Site	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32887072G>T	uc003amq.2	+	6	1155	c.872_splice	c.e6-1	p.G291_splice	FBXO7_uc003amp.1_3'UTR|FBXO7_uc003amr.2_Splice_Site_p.G177_splice|FBXO7_uc003ams.2_Splice_Site_p.G135_splice|FBXO7_uc003amt.2_Splice_Site_p.G212_splice|FBXO7_uc003amu.2_Splice_Site_p.G177_splice|FBXO7_uc003amv.2_5'Flank	NM_012179	NP_036311			F-box only protein 7 isoform 1						cell death|regulation of protein stability|ubiquitin-dependent protein catabolic process	ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity			ovary(1)	1																		---	---	---	---
MYH9	4627	broad.mit.edu	37	22	36696961	36696961	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36696961T>A	uc003apg.2	-	22	3005	c.2774A>T	c.(2773-2775)GAG>GTG	p.E925V	MYH9_uc003aph.1_Missense_Mutation_p.E789V	NM_002473	NP_002464	P35579	MYH9_HUMAN	myosin, heavy polypeptide 9, non-muscle	925	Potential.				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				---	---	---	---
GGA1	26088	broad.mit.edu	37	22	38026101	38026101	+	Missense_Mutation	SNP	G	A	A	rs150957887		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38026101G>A	uc003atc.2	+	13	1620	c.1255G>A	c.(1255-1257)GGT>AGT	p.G419S	GGA1_uc003atd.2_Missense_Mutation_p.G332S|GGA1_uc003ate.2_Missense_Mutation_p.G419S|GGA1_uc003atf.2_Missense_Mutation_p.G346S	NM_013365	NP_037497	Q9UJY5	GGA1_HUMAN	golgi associated, gamma adaptin ear containing,	419	Unstructured hinge.				intracellular protein transport|vesicle-mediated transport	clathrin adaptor complex|endosome membrane|Golgi apparatus part	protein binding			breast(2)|ovary(1)	3	Melanoma(58;0.0574)																	---	---	---	---
SH3BP1	23616	broad.mit.edu	37	22	38039705	38039705	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38039705G>A	uc003ati.2	+	7	639	c.528G>A	c.(526-528)CCG>CCA	p.P176P	SH3BP1_uc003atg.1_RNA|SH3BP1_uc011anl.1_Silent_p.P176P|SH3BP1_uc003ath.1_Silent_p.P176P|SH3BP1_uc003atj.1_Silent_p.P112P|SH3BP1_uc003atk.1_Silent_p.P90P|uc003atl.1_RNA	NM_018957	NP_061830	Q9Y3L3	3BP1_HUMAN	SH3-domain binding protein 1	176	BAR.				signal transduction	cytoplasm	GTPase activator activity|SH3 domain binding			central_nervous_system(1)	1	Melanoma(58;0.0574)															OREG0026546	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
SMCR7L	54471	broad.mit.edu	37	22	39910152	39910152	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39910152G>A	uc003axx.2	+	6	1714	c.1216G>A	c.(1216-1218)GAC>AAC	p.D406N	SMCR7L_uc003axw.2_Missense_Mutation_p.D406N|SMCR7L_uc010gxz.1_Missense_Mutation_p.D228N|SMCR7L_uc003axy.2_Missense_Mutation_p.D228N	NM_019008	NP_061881	Q9NQG6	SMC7L_HUMAN	hypothetical protein LOC54471	406						integral to membrane|mitochondrion				central_nervous_system(1)	1	Melanoma(58;0.04)															OREG0026577	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
MKL1	57591	broad.mit.edu	37	22	40807697	40807697	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40807697A>G	uc003ayv.1	-	12	2700	c.2493T>C	c.(2491-2493)CAT>CAC	p.H831H	MKL1_uc003ayw.1_Silent_p.H831H|MKL1_uc010gye.1_3'UTR|MKL1_uc010gyf.1_Silent_p.H781H	NM_020831	NP_065882	Q969V6	MKL1_HUMAN	megakaryoblastic leukemia 1 protein	831					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								---	---	---	---
EP300	2033	broad.mit.edu	37	22	41513716	41513716	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41513716A>G	uc003azl.3	+	2	1015	c.620A>G	c.(619-621)TAC>TGC	p.Y207C		NM_001429	NP_001420	Q09472	EP300_HUMAN	E1A binding protein p300	207					apoptosis|cell cycle|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|histone H4 acetylation|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of androgen receptor signaling pathway|response to estrogen stimulus|response to hypoxia	centrosome|histone acetyltransferase complex	androgen receptor binding|beta-catenin binding|DNA binding|histone acetyltransferase activity|RNA polymerase II activating transcription factor binding|transcription coactivator activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(22)|large_intestine(13)|breast(9)|central_nervous_system(5)|upper_aerodigestive_tract(4)|pancreas(4)|lung(3)|ovary(2)|stomach(1)|skin(1)	64								T| N|F|Mis|O	MLL|RUNXBP2	colorectal|breast|pancreatic|AML|ALL|DLBCL				Rubinstein-Taybi_syndrome				---	---	---	---
EP300	2033	broad.mit.edu	37	22	41523693	41523693	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41523693G>A	uc003azl.3	+	4	1504	c.1109G>A	c.(1108-1110)CGC>CAC	p.R370H		NM_001429	NP_001420	Q09472	EP300_HUMAN	E1A binding protein p300	370	TAZ-type 1.				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				---	---	---	---
TCF20	6942	broad.mit.edu	37	22	42607837	42607837	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42607837C>A	uc003bcj.1	-	1	3609	c.3475G>T	c.(3475-3477)GAG>TAG	p.E1159*	TCF20_uc003bck.1_Nonsense_Mutation_p.E1159*|TCF20_uc003bnt.2_Nonsense_Mutation_p.E1159*	NM_005650	NP_005641	Q9UGU0	TCF20_HUMAN	transcription factor 20 isoform 1	1159					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|transcription coactivator activity|zinc ion binding			ovary(4)|skin(1)	5																		---	---	---	---
PARVB	29780	broad.mit.edu	37	22	44536011	44536011	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44536011A>G	uc003ben.2	+	8	752	c.700A>G	c.(700-702)ATG>GTG	p.M234V	PARVB_uc003bem.2_Missense_Mutation_p.M267V|PARVB_uc010gzn.2_Missense_Mutation_p.M182V|PARVB_uc003beo.2_Missense_Mutation_p.M197V	NM_013327	NP_037459	Q9HBI1	PARVB_HUMAN	parvin, beta isoform b	234					cell adhesion|cell junction assembly	cytoskeleton|cytosol|focal adhesion	actin binding				0		Ovarian(80;0.0246)|all_neural(38;0.0423)																---	---	---	---
KIAA1644	85352	broad.mit.edu	37	22	44681393	44681393	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44681393G>A	uc003bet.2	-	4	647	c.514C>T	c.(514-516)CTG>TTG	p.L172L		NM_001099294	NP_001092764	Q3SXP7	K1644_HUMAN	hypothetical protein LOC85352 precursor	172	Cytoplasmic (Potential).					integral to membrane				ovary(1)	1		all_neural(38;0.0762)|Ovarian(80;0.105)|Glioma(61;0.222)																---	---	---	---
BRD1	23774	broad.mit.edu	37	22	50217191	50217191	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50217191G>A	uc003biv.2	-	1	1262	c.775C>T	c.(775-777)CGC>TGC	p.R259C	BRD1_uc011arf.1_5'UTR|BRD1_uc011arg.1_Missense_Mutation_p.R259C|BRD1_uc011arh.1_Missense_Mutation_p.R259C|BRD1_uc003biu.3_Missense_Mutation_p.R259C	NM_014577	NP_055392	O95696	BRD1_HUMAN	bromodomain containing protein 1	259	PHD-type.				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)														---	---	---	---
ZBED4	9889	broad.mit.edu	37	22	50278153	50278153	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50278153C>T	uc003bix.2	+	2	1313	c.843C>T	c.(841-843)ACC>ACT	p.T281T		NM_014838	NP_055653	O75132	ZBED4_HUMAN	zinc finger, BED-type containing 4	281						cytoplasm|nucleus	DNA binding|metal ion binding|protein dimerization activity			ovary(2)	2		all_cancers(38;8.58e-10)|all_epithelial(38;1.15e-08)|all_lung(38;0.000109)|Lung NSC(38;0.0018)|Breast(42;0.00191)|Ovarian(80;0.0164)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.168)|BRCA - Breast invasive adenocarcinoma(115;0.2)|LUAD - Lung adenocarcinoma(64;0.247)														---	---	---	---
TTLL8	164714	broad.mit.edu	37	22	50487735	50487735	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50487735T>G	uc011ark.1	-	3	207	c.207A>C	c.(205-207)AAA>AAC	p.K69N		NM_001080447	NP_001073916			tubulin tyrosine ligase-like family, member 8											ovary(2)	2		all_cancers(38;3.44e-07)|all_epithelial(38;2.44e-06)|all_lung(38;0.00141)|Breast(42;0.00519)|Lung NSC(38;0.0199)|Ovarian(80;0.142)|Lung SC(80;0.162)		READ - Rectum adenocarcinoma(2;0.000882)|Colorectal(2;0.00311)|BRCA - Breast invasive adenocarcinoma(115;0.226)														---	---	---	---
TUBGCP6	85378	broad.mit.edu	37	22	50671772	50671772	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50671772G>A	uc003bkb.1	-	3	1601	c.1089C>T	c.(1087-1089)GTC>GTT	p.V363V	TUBGCP6_uc010har.1_Silent_p.V363V|TUBGCP6_uc010has.1_RNA	NM_020461	NP_065194	Q96RT7	GCP6_HUMAN	tubulin, gamma complex associated protein 6	363					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)														---	---	---	---
PPP2R3B	28227	broad.mit.edu	37	X	306335	306335	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:306335C>T	uc004cpg.2	-	7	1153	c.952G>A	c.(952-954)GTC>ATC	p.V318I	PPP2R3B_uc011mha.1_Missense_Mutation_p.V157I	NM_013239	NP_037371	Q9Y5P8	P2R3B_HUMAN	protein phosphatase 2, regulatory subunit B'',	318					cell cycle arrest|protein dephosphorylation	nucleus|protein phosphatase type 2A complex	calcium ion binding|protein phosphatase type 2A regulator activity|protein serine/threonine phosphatase activity				0		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)																---	---	---	---
ZBED1	9189	broad.mit.edu	37	X	2407303	2407303	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2407303G>A	uc004cqg.2	-	2	1659	c.1458C>T	c.(1456-1458)TCC>TCT	p.S486S	DHRSX_uc004cqf.3_Intron|ZBED1_uc004cqh.1_Silent_p.S486S	NM_004729	NP_004720	O96006	ZBED1_HUMAN	zinc finger, BED-type containing 1	486						nuclear chromosome	DNA binding|metal ion binding|protein dimerization activity|transposase activity				0		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)																---	---	---	---
TBL1X	6907	broad.mit.edu	37	X	9679824	9679824	+	Intron	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:9679824C>T	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)																---	---	---	---
TLR8	51311	broad.mit.edu	37	X	12939516	12939516	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:12939516G>T	uc004cve.2	+	2	2425	c.2357G>T	c.(2356-2358)TGG>TTG	p.W786L	TLR8_uc004cvd.2_Missense_Mutation_p.W804L	NM_138636	NP_619542	Q9NR97	TLR8_HUMAN	toll-like receptor 8 precursor	786	Extracellular (Potential).|LRRCT.				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																		---	---	---	---
BMX	660	broad.mit.edu	37	X	15543416	15543416	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:15543416G>A	uc004cww.2	+	8	946	c.758G>A	c.(757-759)AGC>AAC	p.S253N	BMX_uc004cwx.3_Missense_Mutation_p.S253N|BMX_uc004cwy.3_Missense_Mutation_p.S253N	NM_203281	NP_975010	P51813	BMX_HUMAN	BMX non-receptor tyrosine kinase	253	Poly-Ser.				cellular component disassembly involved in apoptosis|intracellular signal transduction|mesoderm development	cytosol	ATP binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding|signal transducer activity			lung(3)|ovary(2)	5	Hepatocellular(33;0.183)																	---	---	---	---
ACE2	59272	broad.mit.edu	37	X	15585915	15585915	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:15585915C>T	uc004cxa.1	-	15	2099	c.1931G>A	c.(1930-1932)CGA>CAA	p.R644Q	ACE2_uc004cxb.2_Missense_Mutation_p.R644Q	NM_021804	NP_068576	Q9BYF1	ACE2_HUMAN	angiotensin I converting enzyme 2 precursor	644	Extracellular (Potential).				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)													---	---	---	---
NHS	4810	broad.mit.edu	37	X	17705908	17705908	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:17705908C>T	uc004cxx.2	+	2	950	c.612C>T	c.(610-612)CGC>CGT	p.R204R	NHS_uc011mix.1_Silent_p.R204R|NHS_uc004cxy.2_Silent_p.R27R|NHS_uc004cxz.2_Silent_p.R27R|NHS_uc004cya.2_5'UTR	NM_198270	NP_938011	Q6T4R5	NHS_HUMAN	Nance-Horan syndrome protein isoform 1	204						nucleus				skin(3)|ovary(2)|breast(1)|central_nervous_system(1)	7	Hepatocellular(33;0.183)																	---	---	---	---
PHEX	5251	broad.mit.edu	37	X	22117151	22117151	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:22117151G>A	uc004dah.2	+	9	1164	c.961G>A	c.(961-963)GTC>ATC	p.V321I	PHEX_uc011mjr.1_Missense_Mutation_p.V321I|PHEX_uc011mjs.1_Missense_Mutation_p.V224I	NM_000444	NP_000435	P78562	PHEX_HUMAN	phosphate-regulating neutral endopeptidase	321	Extracellular (Potential).				biomineral tissue development|cell-cell signaling|protein modification process|proteolysis|skeletal system development	integral to plasma membrane	aminopeptidase activity|metalloendopeptidase activity|zinc ion binding			ovary(2)|lung(1)	3																		---	---	---	---
DCAF8L1	139425	broad.mit.edu	37	X	27997798	27997798	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:27997798C>T	uc004dbx.1	-	1	1769	c.1654G>A	c.(1654-1656)GTG>ATG	p.V552M		NM_001017930	NP_001017930	A6NGE4	DC8L1_HUMAN	DDB1 and CUL4 associated factor 8-like 1	552										ovary(3)|skin(1)	4																		---	---	---	---
CXorf21	80231	broad.mit.edu	37	X	30577555	30577555	+	3'UTR	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:30577555G>A	uc004dcg.1	-	3						NM_025159	NP_079435			hypothetical protein LOC80231											ovary(1)	1																		---	---	---	---
DMD	1756	broad.mit.edu	37	X	31676228	31676228	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:31676228T>G	uc004dda.1	-	54	8150	c.7906A>C	c.(7906-7908)AAT>CAT	p.N2636H	DMD_uc004dcr.1_Missense_Mutation_p.N176H|DMD_uc004dcs.1_Missense_Mutation_p.N176H|DMD_uc004dct.1_Missense_Mutation_p.N176H|DMD_uc004dcu.1_Missense_Mutation_p.N176H|DMD_uc004dcv.1_Missense_Mutation_p.N176H|DMD_uc004dcw.2_Missense_Mutation_p.N1292H|DMD_uc004dcx.2_Missense_Mutation_p.N1295H|DMD_uc004dcz.2_Missense_Mutation_p.N2513H|DMD_uc004dcy.1_Missense_Mutation_p.N2632H|DMD_uc004ddb.1_Missense_Mutation_p.N2628H	NM_004006	NP_003997	P11532	DMD_HUMAN	dystrophin Dp427m isoform	2636	Spectrin 18.				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	31792185	31792185	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:31792185A>G	uc004dda.1	-	51	7678	c.7434T>C	c.(7432-7434)GCT>GCC	p.A2478A	DMD_uc004dcr.1_Silent_p.A18A|DMD_uc004dcs.1_Silent_p.A18A|DMD_uc004dct.1_Silent_p.A18A|DMD_uc004dcu.1_Silent_p.A18A|DMD_uc004dcv.1_Silent_p.A18A|DMD_uc004dcw.2_Silent_p.A1134A|DMD_uc004dcx.2_Silent_p.A1137A|DMD_uc004dcz.2_Silent_p.A2355A|DMD_uc004dcy.1_Silent_p.A2474A|DMD_uc004ddb.1_Silent_p.A2470A|DMD_uc004ddd.1_Silent_p.A18A	NM_004006	NP_003997	P11532	DMD_HUMAN	dystrophin Dp427m isoform	2478	Spectrin 17.				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)																---	---	---	---
USP11	8237	broad.mit.edu	37	X	47098875	47098875	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47098875C>T	uc004dhp.2	+	3	541	c.541C>T	c.(541-543)CGC>TGC	p.R181C	USP11_uc004dhq.2_Translation_Start_Site	NM_004651	NP_004642	P51784	UBP11_HUMAN	ubiquitin specific peptidase 11	181	DUSP.				protein deubiquitination|ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(1)|lung(1)|central_nervous_system(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	47663981	47663981	+	IGR	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47663981G>A								LOC100133957 (144205 upstream) : ZNF81 (32320 downstream)																																			---	---	---	---
SSX6	280657	broad.mit.edu	37	X	47970652	47970652	+	Missense_Mutation	SNP	G	A	A	rs149866259	byFrequency	TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47970652G>A	uc004dix.1	+	4	315	c.193G>A	c.(193-195)GTC>ATC	p.V65I	SSX6_uc011mlv.1_Missense_Mutation_p.V65I	NM_173357	NP_775493			SubName: Full=Putative uncharacterized protein SSX1;												0																		---	---	---	---
PAGE1	8712	broad.mit.edu	37	X	49459349	49459349	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:49459349A>G	uc004dom.2	-	2	158	c.25T>C	c.(25-27)TAT>CAT	p.Y9H		NM_003785	NP_003776	O75459	GAGB1_HUMAN	P antigen family, member 1	9					cellular defense response					skin(1)	1	Ovarian(276;0.236)																	---	---	---	---
KDM5C	8242	broad.mit.edu	37	X	53228052	53228052	+	Silent	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53228052A>G	uc004drz.2	-	16	2795	c.2262T>C	c.(2260-2262)GAT>GAC	p.D754D	KDM5C_uc011moc.1_RNA|KDM5C_uc011mod.1_Silent_p.D687D|KDM5C_uc004dsa.2_Silent_p.D753D	NM_004187	NP_004178	P41229	KDM5C_HUMAN	jumonji, AT rich interactive domain 1C isoform	754					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|zinc ion binding			kidney(9)|ovary(5)|salivary_gland(1)|autonomic_ganglia(1)|haematopoietic_and_lymphoid_tissue(1)|oesophagus(1)	18								N|F|S		clear cell renal carcinoma								---	---	---	---
XKRX	402415	broad.mit.edu	37	X	100169759	100169759	+	Silent	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100169759G>A	uc004egn.2	-	3	1523	c.918C>T	c.(916-918)GTC>GTT	p.V306V	XKRX_uc011mre.1_Silent_p.V102V	NM_212559	NP_997724	Q6PP77	XKR2_HUMAN	XK, Kell blood group complex subunit-related,	306	Helical; (Potential).					integral to membrane|plasma membrane				breast(1)	1																		---	---	---	---
AMOT	154796	broad.mit.edu	37	X	112035060	112035060	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:112035060C>A	uc004epr.2	-	6	1926	c.1926G>T	c.(1924-1926)CAG>CAT	p.Q642H	AMOT_uc004eps.2_Missense_Mutation_p.Q233H	NM_001113490	NP_001106962	Q4VCS5	AMOT_HUMAN	angiomotin isoform 1	642	Potential.				actin cytoskeleton organization|cell-cell junction assembly|negative regulation of angiogenesis|negative regulation of vascular permeability|positive regulation of blood vessel endothelial cell migration|positive regulation of cell size|positive regulation of stress fiber assembly|regulation of cell migration	actin filament|cell surface|cytoplasm|endocytic vesicle|external side of plasma membrane|integral to membrane|lamellipodium|ruffle|stress fiber|tight junction|tight junction	angiostatin binding|protein binding|receptor activity			ovary(1)	1																		---	---	---	---
DOCK11	139818	broad.mit.edu	37	X	117722266	117722266	+	Silent	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:117722266C>T	uc004eqp.2	+	17	2025	c.1962C>T	c.(1960-1962)AGC>AGT	p.S654S	DOCK11_uc004eqq.2_Silent_p.S420S	NM_144658	NP_653259	Q5JSL3	DOC11_HUMAN	dedicator of cytokinesis 11	654	DHR-1.				blood coagulation	cytosol	GTP binding			ovary(3)	3																		---	---	---	---
THOC2	57187	broad.mit.edu	37	X	122805587	122805587	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:122805587G>C	uc004etu.2	-	9	826	c.794C>G	c.(793-795)TCT>TGT	p.S265C	THOC2_uc011muh.1_Missense_Mutation_p.S186C|THOC2_uc011mui.1_Missense_Mutation_p.S150C	NM_001081550	NP_001075019	Q8NI27	THOC2_HUMAN	THO complex 2	265					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																		---	---	---	---
ZIC3	7547	broad.mit.edu	37	X	136651232	136651232	+	Intron	SNP	C	T	T			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:136651232C>T	uc004fak.2	+							NM_003413	NP_003404			zinc finger protein of the cerebellum 3						cell differentiation|positive regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|breast(1)	3	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
MAMLD1	10046	broad.mit.edu	37	X	149639052	149639052	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:149639052A>G	uc004fee.1	+	3	1283	c.1207A>G	c.(1207-1209)ATG>GTG	p.M403V	MAMLD1_uc011mxt.1_Missense_Mutation_p.M365V|MAMLD1_uc011mxu.1_Missense_Mutation_p.M378V|MAMLD1_uc011mxv.1_Missense_Mutation_p.M378V|MAMLD1_uc011mxw.1_Missense_Mutation_p.M330V	NM_005491	NP_005482	Q13495	MAMD1_HUMAN	mastermind-like domain containing 1	403					male gonad development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
SRPK3	26576	broad.mit.edu	37	X	153050422	153050422	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153050422G>A	uc004fil.2	+	13	1422	c.1390G>A	c.(1390-1392)GAG>AAG	p.E464K	SRPK3_uc004fik.2_Missense_Mutation_p.E530K|SRPK3_uc010nul.2_Missense_Mutation_p.E388K|SRPK3_uc004fin.2_Missense_Mutation_p.E463K|SRPK3_uc004fim.2_Missense_Mutation_p.E430K	NM_014370	NP_055185	Q9UPE1	SRPK3_HUMAN	serine arginine rich protein-specific kinase 3	464	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)																	---	---	---	---
MECP2	4204	broad.mit.edu	37	X	153296471	153296471	+	Nonsense_Mutation	SNP	G	A	A	rs62931162		TCGA-BR-4201-01A-01D-1126-08	TCGA-BR-4201-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153296471G>A	uc004fjv.2	-	4	1034	c.808C>T	c.(808-810)CGA>TGA	p.R270*	MECP2_uc004fjw.2_Nonsense_Mutation_p.R282*	NM_004992	NP_004983	P51608	MECP2_HUMAN	methyl CpG binding protein 2 isoform 1	270	A.T hook 2.				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)																	---	---	---	---
